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PubMed2001

MXAN: a new software procedure to perform geometrical fitting of experimental XANES spectra.

A new software procedure, MXAN, to fit experimental XANES spectra is presented here. The method is based on the comparison between the experimental spectrum and several theoretical calculations generated by changing the relevant geometrical parameter of the site around the absorbing atom. The x-ray photoabsorption cross section is calculated using the general multiple-scattering scheme, utilizing a complex Hedin-Lunqvist energy-dependent potential to describe the exchange correlation interaction. Our method has been applied to the study of geometrical environment of the tetrahedral zinc site of the protein superoxide dismutase (SOD). The experimental Zn K-edge XANES spectrum has been fitted in the space of the first shell coordination parameters (ligand distances and angles) following the behavior of the chi-square as a function of the local distortion from the starting crystallographic structure. The recovered structure is found to be independent on the starting conditions, showing the theoretical uniqueness of the structural solution. Strengths and limitations of the application to real systems are also discussed.

Animals↗

PubMed2002

Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines.

The Blu-Ice and Distributed Control System (DCS) software packages were developed to provide unified control over the disparate hardware resources available at a macromolecular crystallography beamline. Blu-Ice is a user interface that provides scientific experimenters and beamline support staff with intuitive graphical tools for collecting diffraction data and configuring beamlines for experiments. Blu-Ice communicates with the hardware at a beamline via DCS, an instrument-control and data-acquisition package designed to integrate hardware resources in a highly heterogeneous networked computing environment. Together, Blu-Ice and DCS provide a flexible platform for increasing the ease of use, the level of automation and the remote accessibility of beamlines. Blu-Ice and DCS are currently installed on four Stanford Synchrotron Radiation Laboratory crystallographic beamlines and are being implemented at sister light sources.

Crystallography, X-Ray↗

PubMed2003

Recent developments in the PHENIX software for automated crystallographic structure determination.

A new software system called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is being developed for the automation of crystallographic structure solution. This will provide the necessary algorithms to proceed from reduced intensity data to a refined molecular model, and facilitate structure solution for both the novice and expert crystallographer. Here, the features of PHENIXare reviewed and the recent advances in infrastructure and algorithms are briefly described.

Algorithms↗

PubMed1994

Optimal discrimination and classification of neuronal action potential waveforms from multiunit, multichannel recordings using software-based linear filters.

We describe advanced protocols for the discrimination and classification of neuronal spike waveforms within multichannel electrophysiological recordings. The programs are capable of detecting and classifying the spikes from multiple, simultaneously active neurons, even in situations where there is a high degree of spike waveform superposition on the recording channels. The protocols are based on the derivation of an optimal linear filter for each individual neuron. Each filter is tuned to selectively respond to the spike waveform generated by the corresponding neuron, and to attenuate noise and the spike waveforms from all other neurons. The protocol is essentially an extension of earlier work [1], [13], [18]. However, the protocols extend the power and utility of the original implementations in two significant respects. First, a general single-pass automatic template estimation algorithm was derived and implemented. Second, the filters were implemented within a software environment providing a greatly enhanced functional organization and user interface. The utility of the analysis approach was demonstrated on samples of multiunit electrophysiological recordings from the cricket abdominal nerve cord.

Action Potentials↗

PubMed1989

Algorithms, hardware, and software for a digital signal processor microcomputer-based speech processor in a multielectrode cochlear implant system.

Software and hardware have been developed to create a powerful, inexpensive, compact digital signal processing system which in real-time extracts a low-bit rate linear predictive coding (LPC) speech system model. The model parameters derived include accurate spectral envelope, formant, pitch, and amplitude information. The system is based on the Texas Instruments TMS320 family, and the most compact realization requires only three chips (TMS320E17, A/D-D/A, op-amp), consuming a total of less than 0.5 W. The processor is part of programmable cochlear implant system under development by a multiuniversity Canadian team, but also has other applications in aids to the hearing handicapped.

Algorithms↗

PubMed2000

A software data generator for radiographic imaging investigations.

A software data generation tool, intended to be used in radiographic applications, has been developed. The application integrates a phantom design module and an imaging simulator. Phantoms can be described as a set of either geometrical objects or voxels, or contours drawn on multiple tomographic slices. Radiographic projections of the phantoms are formed on the basis of a simulated irradiation process, with selectable imaging parameters. Comparison between actual projection images from a physical and a simulated phantom shows good correspondence. The application was used for digital tomosynthesis (DTS) investigations and has proven to be a useful tool in the study of tomographic noise. Further development is expected to expand the use of the application to more areas of radiological imaging research.

Algorithms↗

PubMed2004

Efficient migration of complex off-line computer vision software to real-time system implementation on generic computer hardware.

This paper addresses the problem of migrating large and complex computer vision code bases that have been developed off-line, into efficient real-time implementations avoiding the need for rewriting the software, and the associated costs. Creative linking strategies based on Linux loadable kernel modules are presented to create a simultaneous realization of real-time and off-line frame rate computer vision systems from a single code base. In this approach, systemic predictability is achieved by inserting time-critical components of a user-level executable directly into the kernel as a virtual device driver. This effectively emulates a single process space model that is nonpreemptable, nonpageable, and that has direct access to a powerful set of system-level services. This overall approach is shown to provide the basis for building a predictable frame-rate vision system using commercial off-the-shelf hardware and a standard uniprocessor Linux operating system. Experiments on a frame-rate vision system designed for computer-assisted laser retinal surgery show that this method reduces the variance of observed per-frame central processing unit cycle counts by two orders of magnitude. The conclusion is that when predictable application algorithms are used, it is possible to efficiently migrate to a predictable frame-rate computer vision system.

Algorithms↗

PubMed2006

BCI meeting 2005--workshop on technology: hardware and software.

This paper describes the outcome of discussions held during the Third International BCI Meeting at a workshop to review and evaluate the current state of BCI-related hardware and software. Technical requirements and current technologies, standardization procedures and future trends are covered. The main conclusion was recognition of the need to focus technical requirements on the users' needs and the need for consistent standards in BCI research.

Algorithms↗

PubMed2026

Combining Annotation Software to Identify Orthologous Genes (CASIO) Provides a New Dataset of Orthologous Genes for Swallowtail Butterflies.

With the massive increase in genomic resources, it is becoming increasingly popular to analyse thousands of loci across many species. However, many of the available genomes are not annotated, which hinders an efficient search for orthologous protein-coding genes. Here, we aim to develop a semi-automated pipeline and compare four genomic annotation methods (BRAKER2, BUSCO, Miniprot and Scipio). Our results highlight the importance of integrating multiple annotation tools to optimise ortholog detection and improve genomic studies. Each annotation method showed different strengths. BRAKER2 annotated a substantial number of genes. BUSCO, despite limitations inherent to its reference database, identified a higher number of orthologs. Miniprot exhibited notable flexibility in accommodating diverse protein datasets, whereas Scipio successfully recovered a considerable set of genes that were not detected by the other tools. The combination of these tools allowed for more comprehensive ortholog detection. Taking advantage of this pipeline, we developed a comprehensive dataset of orthologous genes for swallowtail butterflies (Lepidoptera: Papilionidae), called Papilionidae_odb, which will facilitate future studies, especially for a non-model group with abundant genomic data and few transcriptomic resources. We tested Papilionidae_odb by inferring a robust phylogenetic framework for Leptocircini using 142 complete genomes, which improved branch support for some phylogenetic relationships, although challenges remained in resolving relationships within certain species groups, likely due to rapid radiations. Our results highlight the complementary nature of the annotation methods and suggest that combining these tools can yield more accurate results in genomic research. This approach was implemented in a Snakemake workflow called CASIO (Combining Annotation Software to Identify Orthologous genes) and can easily be applied to other non-model groups to improve genomic datasets in diverse taxa where transcriptomic resources are still limited.

Animals↗

PubMed2000

Fitting nonlinear and constrained generalized estimating equations with optimization software.

In this article, we present an estimation approach for solving nonlinear constrained generalized estimating equations that can be implemented using object-oriented software for nonlinear programming, such as nlminb in Splus or fmincon and lsqnonlin in Matlab. We show how standard estimating equation theory includes this method as a special case so that our estimates, when unconstrained, will remain consistent and asymptotically normal. To illustrate this method, we fit a nonlinear dose-response model with nonnegative mixed bound constraints to clustered binary data from a developmental toxicity study. Satisfactory confidence intervals are found using a nonparametric bootstrap method when a common correlation coefficient is assumed for all the dose groups and for some of the dose-specific groups.

Animals↗

PubMed2004

Comparison of gentamicin dose estimates derived from manual calculations, the Australian 'Therapeutic Guidelines: Antibiotic' nomogram and the SeBA-GEN and DoseCalc software programs.

AIM: To compare gentamicin dose estimates from four predictive methods. METHODS: A retrospective study was conducted, comprising patients at Fremantle Hospital who received gentamicin therapy and had at least one gentamicin serum concentration reported. A manual calculation method, the Australian 'Therapeutic Guidelines: Antibiotic' (TGA) nomogram and the SeBA-GEN and DoseCalc software packages were compared. SeBA-GEN dose estimates were regarded as the reference standard. RESULTS: There were 64 males and 30 females with mean age of 58 +/- 16 years. In patients with moderate renal impairment (CL(Cr) = 30-60 ml min(-1); n = 21), mean dose estimates using DoseCalc and the manual calculation method were comparable to SeBA-GEN but the mean TGA nomogram dose (230 mg; 95% confidence interval 179, 281) was significantly lower than SeBA-GEN (286 mg; 261, 311; P = 0.002; one-way RM anova). In patients with mild renal impairment (CL(Cr) = 60-90 ml min(-1); n = 48), DoseCalc (392 mg; 367, 427) was comparable to SeBA-GEN (377 mg; 362, 392). Although the manual method (341 mg; 306, 376; P = 0.007) and the TGA nomogram (335 mg; 302, 368; P < 0.001) estimates were significantly lower than SeBA-GEN, the practical difference was modest. CONCLUSIONS: SeBA-GEN and DoseCalc are generally comparable for estimation of gentamicin doses in patients with renal impairment. The 'Therapeutic Guidelines: Antibiotic' nomogram is a valid approach to dosage estimation, but only when used in patients with normal renal function. Simple manual calculations are a suitable alternative in patients with renal impairment.

Anti-Bacterial Agents↗

PubMed1993

Precise area determination of skin-prick tests: validation of a scanning device and software for a personal computer.

When skin-prick tests (SPTs) are used quantitatively, the circumference of the weal and/or the flare is outlined using a felt tip pen, and transferred to paper by adhesive tape. The aim of the study was to develop and validate a procedure, objectively and precisely determining these areas after transfer to paper. A system was developed enabling the drawing of the area of weal or flare to be read by a hand-held scanner and calculated on a personal computer. Areas in the 5-500 mm2 range could be determined with day-to-day and interoperator coefficients of variation (CVs) of 3.1% and 1.8%, respectively. Accuracy was determined in two ways: by correlation to cutting/weighing of four times enlarged SPT areas (r2 = 0.999, P < 0.001) and by measuring standardized areas (deviations less than intra-assay CV, i.e. 1-2%). For comparison, CV of alternative methods were also determined: eight different areas (9-76 mm2) were evaluated in quadruplicate using the SPT-scanner (CV = 1.4%), by cutting/weighing of paper (CV = 2.3%), by digitizing (CV = 4.4%) or by measuring longest and orthogonal diameters (CV = 13.6%). In conclusion, the scanning device and software provides an objective and reproducible procedure for rapid determination of SPT areas. When areas are determined by scanning, digitizing or cutting/weighing the variations in area determination becomes negligible compared to the variations of the entire skin test procedure.

Diagnosis, Computer-Assisted↗

PubMed2005

Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study.

The identification of genetically homogeneous groups of individuals is a long standing issue in population genetics. A recent Bayesian algorithm implemented in the software STRUCTURE allows the identification of such groups. However, the ability of this algorithm to detect the true number of clusters (K) in a sample of individuals when patterns of dispersal among populations are not homogeneous has not been tested. The goal of this study is to carry out such tests, using various dispersal scenarios from data generated with an individual-based model. We found that in most cases the estimated 'log probability of data' does not provide a correct estimation of the number of clusters, K. However, using an ad hoc statistic DeltaK based on the rate of change in the log probability of data between successive K values, we found that STRUCTURE accurately detects the uppermost hierarchical level of structure for the scenarios we tested. As might be expected, the results are sensitive to the type of genetic marker used (AFLP vs. microsatellite), the number of loci scored, the number of populations sampled, and the number of individuals typed in each sample.

Bayes Theorem↗

PubMed1991

IBM-PC compatible software for establishing metacarpophalangeal pattern profiles.

We briefly present software for performing metacarpophalangeal pattern (MCPP) profile analysis, which runs on generally available low-cost IBM (PC, XT, AT) and compatible PCs. The program is easy for the medical geneticist to handle and apply. We compared the mean MCPP of our own patients with Ullrich-Turner syndrome with the mean MCPP for Ullrich-Turner patients originally published by Poznanski.

Adult↗

PubMed2004

Assign 2.0: software for the analysis of Phred quality values for quality control of HLA sequencing-based typing.

As improvements to DNA sequencing technology have resulted in increasing the throughput of DNA sequencing, the bottleneck for high throughput DNA sequencing-based typing (SBT) has shifted to sequence analysis, genotyping and quality control (QC). Consistent high-quality DNA sequence is required in order to reduce manual verification and editing of sequence electropherograms. However, identifying systematic changes in quality is difficult to achieve without the aid of sophisticated sequence analysis programs dedicated to this purpose. We describe a computer software program called Assign 2.0, which integrates sequence QC analysis and genotyping in order to facilitate high-throughput SBT. Assign 2.0 performs an analysis of Phred quality values in order to produce quality scores for a sample and a sequencing run. This enables sample-to-sample and run-to-run QC monitoring and provides a mechanism for the comparison of sequence quality between various genes, various reagents and various protocols with the aim of improving the overall quality of DNA sequence data. This, in turn, will result in reducing sequence analysis as a bottleneck for high-throughput SBT.

Alleles↗

PubMed2004

Digital quantification of fibrosis in liver biopsy sections: description of a new method by Photoshop software.

BACKGROUND: The precise quantification of fibrous tissue in liver biopsy sections is extremely important in the classification, diagnosis and grading of chronic liver disease, as well as in evaluating the response to antifibrotic therapy. Because the recently described methods of digital image analysis of fibrosis in liver biopsy sections have major flaws, including the use of out-dated techniques in image processing, inadequate precision and inability to detect and quantify perisinusoidal fibrosis, we developed a new technique in computerized image analysis of liver biopsy sections based on Adobe Photoshop software. METHODS: We prepared an experimental model of liver fibrosis involving treatment of rats with oral CCl4 for 6 weeks. After staining liver sections with Masson's trichrome, a series of computer operations were performed including (i) reconstitution of seamless widefield images from a number of acquired fields of liver sections; (ii) image size and solution adjustment; (iii) color correction; (iv) digital selection of a specified color range representing all fibrous tissue in the image and; (v) extraction and calculation. RESULTS: This technique is fully computerized with no manual interference at any step, and thus could be very reliable for objectively quantifying any pattern of fibrosis in liver biopsy sections and in assessing the response to antifibrotic therapy. It could also be a valuable tool in the precise assessment of antifibrotic therapy to other tissue regardless of the pattern of tissue or fibrosis.

Animals↗

PubMed1993

Computer hardware and software to assist the visually impaired and blind.

Modern developments in computer hardware and software for the business world have been adapted to allow the partially sighted and blind to participate successfully in computer usage in education, employment and recreation. Adaptations such as the enlargement of the whole screen display, production of enlarged print and voice output of screen contents can assist the partially sighted. Conversion of computer screen information into speech or braille can be used in conjunction with sound boards and touch pads to allow the totally blind access to the exact spatial layout of screen contents. Optical character recognition devices whereby the printed page can be accessed by computer, and recent voice recognition techniques which allow a computer to interpret voiced commands, can also be used to assist the totally blind. Developments in these areas are discussed together with specific examples of equipment now available which make use of the various methods described.

Blindness↗

PubMed2000

First trimester ultrasound with nuchal translucency measurement for Down syndrome risk estimation using software developed by the Fetal Medicine Foundation, United Kingdom--the first 2000 examinations in Newcastle, New South Wales, Australia.

In September 1997 screening for Down syndrome using first trimester ultrasound to measure nuchal translucency, with risk estimation by the software program developed in the United Kingdom by the Fetal Medicine Foundation, was introduced in Newcastle, New South Wales. In the first 2,000 such risk estimations 134 women (6.7 %) were screen positive (with a risk of greater than 1 in 300 at that gestation for Trisomy 21). In the first 1,000 of these 2,000 fetuses delivered thus far there were 8 cases of Trisomy 21, 2 of Trisomy 18 and 1 of 47 XXX. Nine of these 11 were screen positive, the only false negative results being for 2 cases of Trisomy 21. The detection rate for Trisomy 21 was 6 out of 8 (75%) and for every case of Trisomy 21 (Down Syndrome) detected by this process, 11.3 invasive tests would have been needed to make that diagnosis in a screen positive woman.

Down Syndrome↗