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PubMed2007

Assessment of physical fitness in adults by field testing supported by the specific software for personal computer based use.

Physical inactivity is the second most important risk factor for development of cardiovascular diseases. Various field tests were developed for assessment of the fitness in general population. We aimed to assess the applicability and effectiveness of the specific software for UKK 2-km walking test data management. Descriptive results and statistical analysis on physical fitness of 383 adults are presented. The UKK 2-km walking test could be used as a feasible alternative for measurement of cardiovascular fitness. The test was integrated to exercise related health promotion programme, and widely available information technologies will be used for data management.

Adult↗

PubMed2006

Software for computational peptide identification from MS-MS data.

Protein identification in biological samples is an important task in drug discovery research. Protein identification is nowadays regularly performed by tandem mass spectrometry (MS-MS). Because of the difficulty of measuring intact proteins using MS-MS, typically a protein is enzymically digested into peptides and the MS-MS spectrum of each peptide is measured. Computational methods are then invoked to identify the peptides, which are later combined together to identify the protein. The most recognized peptide identification software packages can be classified into four categories: database searching, de novo sequencing, sequence tagging and consensus of multiple engines.

Databases, Protein↗

PubMed2005

Doppler US with perfusion software and contrast medium injection in the early evaluation of radiofrequency in breast cancer recurrences: a prospective phase II study.

INTRODUCTION: The aim of this study was to determine the efficacy of Doppler ultrasonography (US) with perfusion software and contrast agent injection (DUPC) during radiofrequency (RF) treatment of local recurrent breast cancer. MATERIALS AND METHODS: Ten patients were included in this monocentric prospective phase II study. DUPC was performed for each patient the day before treatment and immediately after RF in the operating suite. RF ablation was followed by a total mastectomy. The results of DUPC were compared to the histologic analysis of the operative specimen. RESULTS: Before RF, contrast uptake exceeded 70% in 5 lesions and was less than 50% in 5 lesions. Immediately after RF, no vascularization was detected with DUPC in 9 of the 10 lesions. Contrast uptake attaining 30% was depicted in the remaining lesion. At histologic analysis, complete tumour destruction was confirmed in 7 of the 10 operative specimens. CONCLUSION: In this study, DUPC is highly efficient and better adapted for the confirmation of tumour destruction in tumours that are hypervascularised before RF compared to hypovascularised lesions.

Adult↗

PubMed2005

Modeling and predicting non-isothermal microbial growth using general purpose software.

Published experimental isothermal growth curves of Clostridium perfringens cells in ground ham were fitted with a modified three-parameter version of the logistic equation as a primary model and the temperature dependence of the three parameters by ad hoc empirical secondary models. These were used to predict the organism's non-isothermal growth curves under three different cooling regimes. The assumption has been that the organism's instantaneous (or momentary) non-isothermal growth rate is the isothermal rate at the given temperature at a time that corresponds to its instantaneous population size. This could be translated into a differential rate model equation, whose coefficients are constructed from terms that reflect the changing growth parameters with temperature and hence with time. The continuous rate equation, however, can be solved incrementally by a numerical procedure that can be implemented in similar purpose software like Microsoft Excel(R). In all three cases, there was good agreement between the growth curves predicted by the model and those found experimentally. This demonstrated that the procedure can be used to generate growth curves under complicated thermal histories that may include regular and irregular temperature oscillations.

Animals↗

PubMed2005

Simultaneous quantification and identification using 18O labeling with an ion trap mass spectrometer and the analysis software application "ZoomQuant".

Stable isotope labeling with (18)O is a promising technique for obtaining both qualitative and quantitative information from a single differential protein expression experiment. The small 4 Da mass shift produced by incorporation of two molecules of (18)O, and the lack of available methods for automated quantification of large data sets has limited the use of this approach with electrospray ionization-ion trap (ESI-IT) mass spectrometers. In this paper, we describe a method of acquiring ESI-IT mass spectrometric data that provides accurate calculation of relative ratios of peptides that have been differentially labeled using(18)O. The method utilizes zoom scans to provide high resolution data. This allows for accurate calculation of (18)O/(16)O ratios for peptides even when as much as 50% of a (18)O labeled peptide is present as the singly labeled species. The use of zoom scan data also provides sufficient resolution for calculating accurate ratios for peptides of +3 and lower charge states. Sequence coverage is comparable to that obtained with data acquisition modes that use only MS and MS/MS scans. We have employed a newly developed analysis software tool, ZoomQuant, which allows for the automated analysis of large data sets. We show that the combination of zoom scan data acquisition and analysis using ZoomQuant provides calculation of isotopic ratios accurate to approximately 21%. This compares well with data produced from (18)O labeling experiments using time of flight (TOF) and Fourier transform-ion cyclotron resonance (FT-ICR) MS instruments.

Amino Acid Sequence↗

PubMed2005

Development of a software tool for in silico simulation of Escherichia coli using a visual programming environment.

This study describes the development of a software tool, EcoSim, to assist users in implementing quantitative in silico simulation easily. It consists of four parts: extracellular environment and constraints setting mode, table for optimal metabolic flux distribution and chart for changes of substrate concentration, dynamic flux distribution viewer and dynamic hierarchical regulatory network viewer. Representation of a hierarchical regulatory network was constructed with defined modeling symbols and weight in the central Escherichia coli metabolism. All programming procedures for EcoSim were accomplished in a visual programming environment (LabVIEW). To illustrate quantitative in silico simulation with EcoSim, this program was performed on E. coli using glucose and acetate as carbon sources. The simulation results were in agreement with the experimental data obtained from the literature. EcoSim can be used to assist biologists and engineers in predicting and interpreting dynamic behaviors of E. coli under a variety of environmental conditions.

Acetates↗

PubMed2005

An in-vitro and in-vivo methodology study of alveolar bone measurement using extra-oral radiographic alignment apparatus, Image Pro-Plus software and a subtraction programme.

OBJECTIVES: (a) To validate a method for acquiring reproducible radiographic images and repeatable measurements of digital images. (b) To investigate the clinical and radiographic changes following periodontal surgery and in a periodontally healthy control group. METHODS: In-vitro study. Sixteen dried human skulls had replicate intra-oral radiographs taken using an extra-oral alignment apparatus under simulated clinical conditions, and measurements were made on the images using Image Pro-Plus analysis software. In-vivo study. Seven subjects, aged 38-63 years with chronic periodontitis, were treated using replaced flap surgery. Nine patients with healthy periodontal tissues were recruited as a control group. Clinical measurements and radiographs were taken pre-surgery and 6 months afterwards, and at the same interval for untreated healthy controls using the alignment apparatus. Radiographs were analysed using Image Pro-Plus and subtraction radiography. RESULTS: Radiographs had a high degree of reliability (ICC 0.98-0.99) for the in-vitro study and intra-operator repeatability of measurements was high (ICC 0.65-0.99) for the in-vivo study. Over this interval there were both significant clinical improvements and in bone gain within infra-bony defects on radiographs. Subtracted images showed that out of 17 surgically treated sites, 13 showed evidence of bone gain, one showed no change, two showed bone loss and one could not be interpreted due to poor alignment. Overall there were no significant clinical or radiographic changes in the control group. CONCLUSIONS: Radiographic images were highly reproducible. Measurements had a high degree of repeatability. The methods used allowed accurate quantitative and qualitative measurement of change in alveolar bone. This technique would allow accurate measurement of any changes in alveolar bone levels in patients with periodontal disease.

Adult↗

PubMed2005

Computer software tool REALM for sustainable water allocation and management.

REALM (REsource ALlocation Model) is a generalised computer simulation package that models harvesting and bulk distribution of water resources within a water supply system. It is a modeling tool, which can be applied to develop specific water allocation models. Like other water resource simulation software tools, REALM uses mass-balance accounting at nodes, while the movement of water within carriers is subject to capacity constraints. It uses a fast network linear programming algorithm to optimise the water allocation within the network during each simulation time step, in accordance with user-defined operating rules. This paper describes the main features of REALM and provides potential users with an appreciation of its capabilities. In particular, it describes two case studies covering major urban and rural water supply systems. These case studies illustrate REALM's capabilities in the use of stochastically generated data in water supply planning and management, modelling of environmental flows, and assessing security of supply issues.

Australia↗

PubMed2004

Radioecological software package: an interactive computational system to simulate the behaviour of radionuclides in semi-natural environments.

RSP (Radioecological Software Package) is an interactive support system that simulates the behaviour of radionuclides in semi-natural environments and the consequences on the population in terms of the external exposure. RSP consists of three modules: the first one, soil mobility, simulates the vertical transport of radionuclide in soil using the mathematical model RABES. The second module, soil -to-plant transfer, simulates the radionuclide soil-to-plant transfer factor reported in the literature. Soil properties, vegetation types and environmental conditions are taken into consideration in the simulation process. In the third module, dose assessment, the dose-rate factor in air at a height of 1 m above ground can be calculated for sources distributed in a slab of finite thickness dn sources which are exponentially distributed with depth. The calculations are performed using DAGES Model, a Monte Carlo algorithm developed to simulated the photon transport for the soil/air configuration. A free copy of RSP can be downloaded from the website: http://imasl-apat.unsl.edu.ar.

Air Pollutants, Radioactive↗

PubMed2005

Quantitative immunohistochemistry of fluorescence labelled probes using low-cost software.

This paper describes simple procedures to process digital images in quantitative immunofluorescence microscopy. Monoclonal antibodies directed against the sarcoplasmic myosin heavy chain isoforms and against laminin, located on the basement membranes, were applied to sections of human skeletal muscle. The localisation and staining intensity of a fluorescent secondary antibody were recorded using an indirect histochemical method. The digitised images were pre-processed and the luminosities of appropriate structures were determined using existing tools in the widely used image processing software Photoshop from Adobe. Procedures to obtain a quantitative measure for the specific fluorescence signal (the background corrected fluorescence in the object) were developed. In addition, antibody binding to individual cells could be quantified whether these cells are well separated or not. The relation between the specific fluorescence signal and the dilution factor of the primary antibody could be measured to determine a suitable concentration of the antibody for incubation of the sections. The potential fading of the fluorescence signal with time and prolonged exposure to light from the microscope was explored and analysed. With the tools described in the present report it is thus possible also to optimize the topical immunohistochemical protocol in order to quantify the fluorescence signal.

Adenosine Triphosphatases↗

PubMed2004

A multichannel electronic monitor of acoustic behaviors, and software to parse individual channels.

We designed an electronic device to monitor calling behavior in male crickets. The device and its associated software can record to disk the activity of as many as 16 individuals simultaneously. The data recorded contain detailed information about the temporal structure of each individual's calls. The temporal resolution achieved with an ordinary PC is good enough to detect and record the occurrence of every pulse of sound from each cricket. The resulting data files are efficient and compact, and so the system is appropriate for experiments lasting many days.

Acoustics↗

PubMed2006

MPScope: a versatile software suite for multiphoton microscopy.

MPScope is a software suite to control and analyze data from custom-built multiphoton laser scanning fluorescence microscopes. The acquisition program MPScan acquires, displays and stores movies, linescans, image stacks or arbitrary regions from up to four imaging channels and up to two analog inputs, while plotting the intensity of regions of interest in real-time. Bidirectional linescans allow 256 x 256 pixel frames to be acquired at up to 10 fps with typical galvanometric scanners. A fast stack mode combines movie acquisition with continuous z-focus motion and adjustment of laser intensity for constant image brightness. Fast stacks can be automated by custom programs running in an integrated scripting environment, allowing a 1 mm(3) cortical volume to be sampled in 1 billion voxels in approximately 1 h. The analysis program MPView allows viewing of stored frames, projections, automatic detection of cells and plotting of their average intensity across frames, direct frame transfer to Matlab, AVI movie creation and file export to ImageJ. The combination of optimized code, multithreading and COM (Common Object Model) technologies enables MPScope to fully take advantage of custom-built two-photon microscopes and to simplify their realization.

Animals↗

PubMed2005

A public software for energy filtering transmission electron tomography (EFTET-J): application to the study of granular inclusions in bacteria from Riftia pachyptila.

Energy-filtering transmission electron microscopy (EFTEM) allows the determination of elemental distributions out of a sequence of energy filtered images. Combined with electron tomography, EFTEM is a powerful tool to obtain three-dimensional chemical maps from sub-cellular structures. However, there is no existing software in the public-domain for the computation and analysis of 3D-chemical maps. Here, we present a Java-based program to compute 3D-elemental distribution. This program is available as a set of plug-ins for the public-domain Java image processing program Image J inspired by NIH Image. Its implemented algorithms have been successfully applied to the three-dimensional localization of iron granules in semi thin (200 nm) epon sections from the vent worm Riftia pachyptalia.

Algorithms↗

PubMed2004

Bizarre alterations of the morphology of pineal synaptic bodies under constant light and an evaluation of suitable 3D-reconstruction software.

Three dimensional (3D) reconstruction and modelling software was evaluated to find a procedure suitable for visualization of small subcellular structures in transmission electron microscope images. The method applied in this study demonstrates bizarre alterations of the structure of synaptic bodies (SBs) in pinealocytes of the guinea-pig pineal gland caused by constant illumination. It can, in general, be used for any 3D reconstruction from serial sections. Pineal glands of five guinea-pigs (two kept under a LD cycle of 12:12 h; three kept in constant light, for 4 months) were investigated. SBs consist of an electron-dense centre with attached vesicles. Under normal lighting conditions most SBs are flat plates (about 35 nm in thickness), which eventually may be bent. The proteins comprising the molecular basis of SBs, mainly RIBEYE A and B are polymerised in a regular manner in these plates. This is not the case in other SBs, which appear as spheres or irregular lumps. SBs lie in groups in which usually some of the plates are arranged in parallel arrays Constant illumination caused different changes in morphology: many of the SBs lie in 'paired fields', i.e. appear in groups attached to the cell membranes of two pinealocytes directly opposite to each other. Some of the SBs in such groups are strongly bent, showing blebs and irregular thickened areas, others seem to aggregate and show inclusions of cytoplasm. Further goblet-like, shield-like and other bizarre forms of SBs occurred and the relative number of spheroid and lump-like SBs increased. Protrusions on larger SBs suggest detachment or fusion of SB material to a greater extent than in the control animals. There is a reduction of areas in which the polymerisation of the SB proteins remains well ordered, i.e. where the typical thickness of 35 nm is maintained. It remains unclear why this polymerisation pattern is only partly affected by constant light.

Animals↗

PubMed2004

Development and validation of evolutionary algorithm software as an optimization tool for biological and environmental applications.

A flexible, extendable tool for the optimization of (micro)biological processes and protocols using evolutionary algorithms was developed. It has been tested using three different theoretical optimization problems: 2 two-dimensional problems, one with three maxima and one with five maxima and a river autopurification optimization problem with boundary conditions. For each problem, different evolutionary parameter settings were used for the optimization. For each combination of evolutionary parameters, 15 generations were run 20 times. It has been shown that in all cases, the evolutionary algorithm gave rise to valuable results. Generally, the algorithms were able to detect the more stable sub-maximum even if there existed less stable maxima. The latter is, from a practical point of view, generally more desired. The most important factors influencing the convergence process were the parameter value randomization rate and distribution. The developed software, described in this work, is available for free.

Algorithms↗

PubMed2004

Development of public toxicogenomics software for microarray data management and analysis.

A robust bioinformatics capability is widely acknowledged as central to realizing the promises of toxicogenomics. Successful application of toxicogenomic approaches, such as DNA microarray, inextricably relies on appropriate data management, the ability to extract knowledge from massive amounts of data and the availability of functional information for data interpretation. At the FDA's National Center for Toxicological Research (NCTR), we are developing a public microarray data management and analysis software, called ArrayTrack. ArrayTrack is Minimum Information About a Microarray Experiment (MIAME) supportive for storing both microarray data and experiment parameters associated with a toxicogenomics study. A quality control mechanism is implemented to assure the fidelity of entered expression data. ArrayTrack also provides a rich collection of functional information about genes, proteins and pathways drawn from various public biological databases for facilitating data interpretation. In addition, several data analysis and visualization tools are available with ArrayTrack, and more tools will be available in the next released version. Importantly, gene expression data, functional information and analysis methods are fully integrated so that the data analysis and interpretation process is simplified and enhanced. ArrayTrack is publicly available online and the prospective user can also request a local installation version by contacting the authors.

Databases, Genetic↗

PubMed2006

Application of public-domain statistical analysis software for evaluation and comparison of comet assay data.

A novel approach for statistical analysis of comet assay data (i.e.: tail moment) is proposed, employing public-domain statistical software, the R system. The analytical strategy takes into account that the distribution of comet assay data, like the tail moment, is usually skewed and do not follow a normal distribution. Probability distributions used to model comet assay data included: the Weibull, the exponential, the logistic, the normal, the log normal and log-logistic distribution. In this approach it was also considered that heterogeneity observed among experimental units is a random feature of the comet assay data. This statistical model can be characterized with a location parameter m(ij), a scale parameter r and a between experimental units variability parameter theta. In the logarithmic scale, the parameter m(ij) depends additively on treatment and random effects, as follows: log(m(ij)) = a0 + a1x(ij) + b(i), where exp(a0) represents approximately the mean value of the control group, exp(a1) can be interpreted as the relative risk of damage with respect to the control group, x(ij) is an indicator of experimental group and exp(b(i)) is the individual risk effects assume to follows a Gamma distribution with mean 1 and variance theta. Model selection is based on Akaike's information criteria (AIC). Real data coming from comet analysis of blood samples taken from the flounder Paralichtys orbignyanus (Teleostei: Paralichtyidae) and from samples of cells suspension obtained from the estuarine polychaeta Laeonereis acuta (Nereididae) were employed. This statistical approach showed that the comet assay data should be analyzed under a modeling framework that take into account the important features of these measurements. Model selection and heterogeneity between experimental units play central points in the analysis of these data.

Animals↗

PubMed2004

Software-enabled CT analysis of optic nerve position and paranasal sinus pneumatization patterns.

OBJECTIVE: Delineate the relationships among the optic nerve (CN II), the sphenoid sinus, and the sphenoethmoid cell. STUDY DESIGN: High-resolution CT scans of 64 frozen human cadavers were obtained on a Siemens VolumeZoom CT scanner (Munich, Germany) and transferred to a CBYON Suite Doctor Station version 2.6 (CBYON, Mountain View CA) for standardized review. RESULTS: Pneumatization around CN II was categorized into 5 types: no adjacent pneumatization (type 0), pneumatization adjacent to CN II (type 1), adjacent pneumatization with indentation (type 2), pneumatization of <50% CN II circumference (type 3), and pneumatization of >50% CN II circumference (type 4). The prevalence of types 0 to 4 CN II position relative to the sphenoid sinus was 4.7%, 25.8%, 39.8%, 14.1%, and 15.6%, respectively. The prevalence of sphenoethmoid cells was 28.1%. The prevalences of types 0, 1, 2, 3, and 4 CN II positions relative to the sphenoethmoid cell was 5.6%, 58.3%, 25%, 2.8%, and 8.3% respectively. CONCLUSIONS: Software-enabled CT review facilitated precise study of the anatomic relationships of CN II. Caution must be exercised during sinonasal surgery to minimize the risk of inadvertent CN II injury. EBM RATING: D.

Adult↗