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PubMed1988

Quantitative and rapid estimation of h fluxes in membrane vesicles : software for analysis of fluorescence quenching and relaxation.

Proton transport is often visualized in membrane vesicles by use of fluorescent monoamines which accumulate in acidic intravesicular compartments and undergo concentration-dependent fluorescence quenching. Software for an IBM microcomputer is described which permits logging and editing of changes in fluorescence monitored by a Perkin-Elmer LS-5 luminescence spectrometer. An accurate estimate of the instantaneous rate of fluorescence quenching or recovery is then facilitated by least squares fitting of fluorescence data to a nonlinear function. The software is tested with tonoplast vesicles from Beta vulgaris. Quenching of acridine orange fluorescence by ATP-driven (primary) transport and relaxation of quenching by Na(+)/H(+) antiport can both be fitted with single exponential functions. Initial rates of ATP- and Na(+) -dependent fluorescence changes are derived and can be used for K(m) determinations. The method constitutes a simple and efficient alternative to manual analysis of analog fluorescence traces and results in a reliable quantitative measurement of the relative rate of proton transport in membrane vesicle preparations.

Journal Article↗
PubMed2002

Symmetry-general ab initio computation of physical properties using quantum software integrated with crystal structure databases: results and perspectives.

The timely integration of crystal structure databases, such as CRYSTMET, ICSD etc., with quantum software, like VASP, OresteS, ElectrA etc., allows ab initio cell and structure optimization on existing pure-phase compounds to be performed seamlessly with just a few mouse clicks. Application to the optimization of rough structure models, and possibly new atomic arrangements, is detailed. The ability to reproduce observed cell data can lead to an assessment of the intrinsic plausibility of a structure model, even without a competing model. The accuracy of optimized atom positions is analogous to that from routine powder studies. Recently, the ab initio symmetry-general least-squares extraction of the coefficients of the elastic tensor for pure-phase materials using data from corresponding entries in crystal structure databases was automated. A selection of highly encouraging results is presented, stressing the complementarity of simulation and experiment. Additional physical properties also appear to be computable using existing quantum software under the guidance of an automation scheme designed following the above automation for the elastic tensor. This possibility creates the exciting perspective of mining crystal structure databases for new materials with combinations of physical properties that were never measured before. Crystal structure databases can accordingly be expected to become the cornerstone of materials science research within a very few years, adding immense practical value to the archived structure data.

Journal Article↗
PubMed1993

Programs for phasing by entropy maximization as implemented in Xtal3.2: a crystallographic software system.

Xtal3.2, a crystallographic software package, is an international development project involving about 40 researchers over a full spectrum of crystallographic interests. This development has been supported by many national and international agencies and commercial institutions since the first version in 1983. The 1992 release, Xtal3.2, contains software for 95 different calculations. These range from the processing of raw diffraction data to interactive molecular graphics, atomic charge estimation, electronic publication preparation, and the structure solution and refinement of small and large molecules. Tests of the Xtal programs for phase determination and phase refinement by the application of 'maximum entropy' are presented.

Journal Article↗
PubMed1998

SEDEM, a software package for EXAFS data extraction and modelling.

A software package for extended X-ray absorption fine structure (EXAFS) data extraction and modelling, running on DOS- or Windows-operated PCs, is described. This package is written with the aim of giving the user a tool to undertake all steps of data processing and modelling, rather than making use of the most recent programming facilities. However, it remains easy to use, and self-explanatory to those who have already worked with EXAFS. It is divided into two main executable pieces of software. The first one is used to extract the EXAFS k(n)chi(k) function from the data and isolate the shell contributions by Fourier filtering. A tool to sum the spectra before EXAFS extraction is provided. The second one is designed to model the EXAFS spectra or the shell contributions, using amplitude and phase data either from McKale's tables, computed from the FEFF program or extracted from experimental reference spectra. This modelling program allows either an optimization of the simulation by a least-mean-square gradient algorithm, with a statistical evaluation of the result of optimization, or, in the case of a single shell, a direct determination of the four main parameters (neighbour distance and number, energy shift and Debye-Waller factor) by decorrelation of the phase and amplitude. In the presence of anharmonicity, the cumulant expansion of the radial distribution of distances is obtained from the phase and amplitude decorrelation. This package is in use at the Collaborative Research Group on Interfaces (CRG-IF) bending-magnet #32 X-ray line (BM-32) at the European Synchrotron Radiation Facility (ESRF) in Grenoble, France.

Journal Article↗
PubMed2000

Mobile software agents for Web-based medical image retrieval.

Mobile software agents are a new tool which may assist rural and remote physicians to obtain medical data from digital medical libraries on the Internet. Mobile agents are autonomous software objects that can move from digital library to digital library, analysing data to determine their usefulness to the user. A proof-of-concept system applied to mammography is proposed and a simplified prototype for this system is reported. Enhancement and development plans for the complete proof-of-concept system are suggested.

Information Storage and Retrieval↗
PubMed2000

DNASTAR's Lasergene sequence analysis software.

Lasergene's eight modules provide tools that enable users to accomplish each step of sequence analysis, from trimming and assembly of sequence data, to gene discovery, annotation, gene product analysis, sequence similarity searches, sequence alignment, phylogenetic analysis, oligonucleotide primer design, cloning strategies, and publication of the results. The Lasergene software suite provides the functions and customization tools needed so that users can perform analyses the software writers never imagined.

Base Sequence↗
PubMed2004

A complexity-scalable software-based MPEG-2 video encoder.

With the development of general-purpose processors (GPP) and video signal processing algorithms, it is possible to implement a software-based real-time video encoder on GPP, and its low cost and easy upgrade attract developers' interests to transfer video encoding from specialized hardware to more flexible software. In this paper, the encoding structure is set up first to support complexity scalability; then a lot of high performance algorithms are used on the key time-consuming modules in coding process; finally, at programming level, processor characteristics are considered to improve data access efficiency and processing parallelism. Other programming methods such as lookup table are adopted to reduce the computational complexity. Simulation results showed that these ideas could not only improve the global performance of video coding, but also provide great flexibility in complexity regulation.

Journal Article↗
PubMed1998

Flexible software architecture for user-interface and machine control in laboratory automation.

We describe a modular, layered software architecture for automated laboratory instruments. The design consists of a sophisticated user interface, a machine controller and multiple individual hardware subsystems, each interacting through a client-server architecture built entirely on top of open Internet standards. In our implementation, the user-interface components are built as Java applets that are downloaded from a server integrated into the machine controller. The user-interface client can thereby provide laboratory personnel with a familiar environment for experiment design through a standard World Wide Web browser. Data management and security are seamlessly integrated at the machine-controller layer using QNX, a real-time operating system. This layer also controls hardware subsystems through a second client-server interface. This architecture has proven flexible and relatively easy to implement and allows users to operate laboratory automation instruments remotely through an Internet connection. The software architecture was implemented and demonstrated on the Acapella, an automated fluid-sample-processing system that is under development at the University of Washington.

Automation↗
PubMed1995

Morphologic characteristics of oviducts from hens producing eggs of different Haugh units caused by genetics and by feeding vanadium as determined with computer software-integrated digitizing technology.

Magnum and isthmus morphologic characteristics (surface epithelium height, fold height and diameter, and periodic acid-Schiff-positive area and surface epithelium cells) of stained 6-micron tissue sections were measured by light microscopy, with data acquisition using a digitizing tablet interfaced to a microscope and to a personal computer with morphometric-dimensional software. Tissues were obtained from Leghorn layers in two separate experiments in which production of eggs with low and high Haugh unit (HU) values was induced by either genetic selection or by feeding V. Eggs produced by these hens had HU differences between the high and low groups of 11 to 14 units (both experiments, P = .0001) and had a greater volume of thick albumen fraction in high-HU groups (both experiments, P = .0001). The computer software-integrated digitizing system enabled rapid measurements of multiple characteristics. In the genetic lines, higher magnum fold height and magnum and isthmus surface epithelium height were detected at moderate significance (all at P < .05) in the tissues of the layers producing high-HU eggs than in tissues from the low-HU line. Other morphologic variables were not different between genetic lines. In response to feeding V, none of the morphological characteristics were affected, although magnum fold height approached difference at P < .07. Based on the observations in these two experiments, magnum fold height may be a further important factor related to egg albumen condition, in addition to surface epithelium height. It appears, however, that layers producing eggs of considerably different HU values, due in these experiments to genetics or V feeding, can have magnum or isthmus morphological characteristics that are indistinguishable, or only moderately different, as detected by integrated digitizing technology.

Animals↗
PubMed2004

Monte Carlo Commissioning of Low Energy Electron Radiotherapy Beams using NXEGS Software.

This work is a report on the commissioning of low energy electron beams of a medical linear accelerator for Monte Carlo dose calculation using NXEGS software (NXEGS version 1.0.10.0, NX Medical Software, LLC). A unique feature of NXEGS is automated commissioning, a process whereby a combination of analytic and Monte Carlo methods generates beam models from dosimetric data collected in a water phantom. This study uses NXEGS to commission 6, 9, and 12 MeV electron beams of a Varian Clinac 2100C using three applicators with standard inserts. Central axis depth-dose, primary axis and diagonal beam profiles, and output factors are the measurements necessary for commissioning of the code. We present a comparison of measured dose distributions with the distributions generated by NXEGS, using confidence limits on seven measures of error. We find that confidence limits are typically less than 3% or 3 mm, but increase with increasing source to surface distance (SSD) and depth at or beyond R(50). We also investigate the dependence of NXEGS' performance on the size and composition of data used to commission the program, finding a weak dependence on number of dose profiles in the data set, but finding also that commissioning data need be measured at only two SSDs.

Journal Article↗
PubMed1997

E-CELL: Software Environment for Whole Cell Simulation.

We present E-CELL, a generic computer software environment for modeling a cell and conducting experiments in silico. The E-CELL system allows a user to define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation of gene expression and other features of cellular metabolism, in terms of a set of reaction rules. The system then executes those reactions iteratively, and the user can observe, through a computer display, dynamic changes in concentrations of proteins, protein complexes and other chemical compounds in the cell. Using this software, we constructed a model of a hypothetical cell with only 127 genes sufficient for transcription, translation, energy production and phospholipid synthesis. Most of the genes are taken from Mycoplasma genitalium, the organism having the smallest known chromosome, whose complete 580kb genome sequence was determined at TIGR in 1995. We discuss future applications of the E-CELL system with special respect to genome engineering.

Journal Article↗
PubMed2003

[Nonlinear regression analysis of cardiac enzyme kinetic model with modified simplex method and DUD method using SAS software].

OBJECTIVE: To compare the efficacy of modified simplex method and DUD method using SAS software for nonlinear regression analysis of cardiac enzyme kinetic model. METHOD: By using cardiac enzyme kinetic one-compartment mathematical model, nonlinear regression results obtained from DUD methods using SAS software and modified simplex method were compared with the same starting values to fit the creatine kinase curves in 22 patients with acute myocardial infarction. RESULTS: The parameters calculated by DUD method and modified simplex method were the same in 4 cases, and smaller least square was resulted from DUD method in 4 cases. In the other 14 cases, modified simplex method yielded smaller least square. The mean value of the least square calculated by modified simplex method was less than that by DUD method (867 747 vs 6 712 989, P=0.013). CONCLUSION: Modified simplex method appears to be more adequate than DUD method in estimating circulatory parameters of the one-compartment model.

Humans↗
PubMed2003

Metcalfe's law predicts reduced power of Electronic Medical Record software.

Error reduction, quality improvement and lowering of cost can all be achieved through electronic integration of health care providers. Despite the existence of clinical computing software for decades, meaningful linkage between health care providers has not occurred. We hypothesize that a major reason is reduction in network value through incompatible clinical software among hundreds of health care entities.

Adult↗
PubMed2004

Patient-specific dosimetry for 131I thyroid cancer therapy using 124I PET and 3-dimensional-internal dosimetry (3D-ID) software.

UNLABELLED: Compared with conventional, whole-organ, S-factor-based dosimetry, 3-dimensional (3D), patient-specific dosimetry better accounts for radionuclide distribution and anatomic patient variability. Its accuracy, however, is limited by the quality of the cumulated activity information that is provided as input. This input has typically been obtained from SPECT and planar imaging studies. The objective was to implement and evaluate PET-based, patient-specific, 3D dosimetry for thyroid cancer patients. METHODS: Three to 4 PET imaging studies were obtained over a 7-d period in 15 patients with metastatic thyroid carcinoma after administration of (124)I-NaI. Subsequently, patients were treated with (131)I on the basis of established clinical parameters. Retrospective dosimetry was performed using registered (124)I PET images that were corrected for the half-life difference between (124)I and (131)I. A voxel-by-voxel integration, over time, of the resulting (131)I-equivalent PET-derived images was performed to provide a single 3D dataset representing the spatial distribution of cumulated activity values for each patient. Image manipulation and registration were performed using Multiple Image Analysis Utility (MIAU), a software package developed previously. The software package, 3D-Internal Dosimetry (3D-ID), was used to obtain absorbed dose maps from the cumulated activity image sets. RESULTS: Spatial distributions of absorbed dose, isodose contours, dose-volume histograms (DVHs), and mean absorbed dose estimates were obtained for a total of 56 tumors. Mean absorbed dose values for individual tumors ranged from 1.2 to 540 Gy. The absorbed dose distribution within individual tumors was widely distributed ranging from a minimum of 0.3 to a maximum of 4,000 Gy. CONCLUSION: (124)I PET-based, patient-specific 3D dosimetry is feasible, and sequential PET can be used to obtain cumulated activity images for 3D dosimetry.

Adenocarcinoma, Follicular↗
PubMed2004

Evaluation of a novel, integrated approach using functionalized magnetic beads, bench-top MALDI-TOF-MS with prestructured sample supports, and pattern recognition software for profiling potential biomarkers in human plasma.

The advantage of using proteins and peptides as biomarkers is that they can be found readily in blood, urine, and other biological fluids. Such sample types are easily obtained and represent a potentially rich palette of biologically informative molecules. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) represents a key tool for rapidly interrogating such sample types. The goal of clinical proteomics is to harness the power of this tool for identifying novel, condition-specific protein fingerprints that may, in turn, lead to the elucidation and use of diseasespecific biomarkers that may be used to diagnose disease as well as to evaluate disease severity, disease progression, and intervention efficacy. Here we have evaluated a simple, affordable bench-top MALDI-TOF mass spectrometer to generate protein profiles from human plasma samples of asthma patients and healthy individuals. We achieve this profiling by using C8-functionalized magnetic beads that enrich a specific subset of plasma proteins based on their absorption by this resin. This step is followed by elution, transfer onto a prestructured sample support (AnchorChip technology), and analysis in a bench-top MALDI-TOF mass spectrometer (OmniFLEX) with AutoXecute acquisition control which enables automated operation with reproducible results. Resulting spectra are compiled and analyzed through the pattern recognition component of ClinProTools software. This approach in combination with ClinProTools software permits the investigator to rapidly scan for potential biomarker peptides/proteins in human plasma. The reproducibility of plasma profiles within and between days has been evaluated. The results show that the novel and facile approach with manual magnetic-bead sample preparation and a low-cost bench-top MALDI-TOF mass spectrometer is suitable for preliminary biomarker discovery studies.

Algorithms↗
PubMed2005

[Diagnostic application of serum protein pattern and artificial neural network software in breast cancer].

BACKGROUND & OBJECTIVE: The progress in proteomics provides a novel platform for early diagnosis of cancer, and screening for new tumor biomarkers. This study was designed to develop and evaluate a diagnostic model of breast cancer with surface enhanced laser desorption/ionization-time of flight-mass spectrometry (SELDI-TOF-MS) ProteinChip array technology and artificial neural network software. METHODS: SELDI-TOF-MS ProteinChip was used to detect serum protein patterns of 49 patients with breast cancer, and 33 healthy women. Diagnostic model was developed, and validated using artificial neural network software. RESULTS: An intact diagnostic model from all 253 discrepant protein peaks, and a terse model from the top-scored 4 peaks were built. The diagnostic sensitivity, and specificity of the intact model were 83.33% (15/18), and 88.89% (8/9)u the detection rates of breast cancer of stage I, and stage II-IV using the intact model were 90.00% (9/10), and 75.00% (6/8). The diagnostic sensitivity, and specificity of the terse model were 76.47% (13/17), and 90.00% (9/10)u the detection rates of breast cancer of stage I, and stage II-IV using the terse model were 100.00% (3/3), and 71.43% (10/14). The diagnostic values of these 2 models were similar (P>0.05). Their diagnostic abilities to breast cancer of stage I were not worse than those to breast cancer of stage II-IV (P>0.05). CONCLUSION: High sensitivity and specificity achieved by this method show great potential for early diagnosis of breast cancer, and screening for new tumor biomarkers.

Adult↗
PubMed1997

[Curvefit, an overlapping bands resolving software for IR spectra].

A Curvefit software has been developed for resolving the overlapping band of the vibartional spectra in our lab . Various functions and a friendly interface are equipped in the software. The testing results showed that both the speed of the calculation and the reliability of the final results are satisfactory.

English Abstract↗