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At least 253 records · Page 14Linked to original sources
PubMed2006

Internal radionuclide therapy: software for treatment planning using tomographic data.

AIM: Accurate dosimetry must be performed for each patient before therapy with unsealed radionuclides. Recently, the software tool ULMDOS was developed to facilitate planar dosimetric calculations and to support traceability and documentation as a prerequisite for good clinical practice. Here, the extended version of ULMDOS for processing of tomographic data is presented. METHODS: ULMDOS is developed in IDL 6.1 (Interactive Data Language) under Windows XP/2000. Serial tomographic data can be loaded in an ECAT7 or DICOM format, and presented as maximum intensity projection. The definition of volumes of interest is supported by various tools (e.g., freehand, isocontour, polygon), region growing, and cluster analysis. Residence times are calculated from fits of the time activity data to exponential functions. RESULTS, DISCUSSION: Quantitative 3-dimensional data allow performing a more individualized dosimetry, as problems due to organ overlay, insufficient attenuation and scatter correction in the planar approach can be avoided. For traceability, documentation, retrospective examination and later processing all data can be saved in binary or ASCII format. Dosimetric calculations can be conducted within a single environment, thus it spares the time-consuming transfer of data between different software tools.

Humans↗
PubMed2002

Interpretation and reporting of myocardial perfusion SPECT: a summary for technologists.

Interpretation of cardiac perfusion SPECT images, and the subsequent reporting of results to referring physicians, are sometimes taken to be outside the sphere of the nuclear medicine technologist. However, all personnel involved with nuclear medicine procedures contribute to the timeliness and usefulness of the final report. The goal of this article is to review the principles of scan interpretation and reporting, from the standpoint of what technologists need to understand about these processes. In addition, software tools to aid these processes will be discussed, including quantitative image analysis, telemedicine, computer-aided scan interpretation, databases, computer-aided reporting, and Internet-based reporting. Finally, the accuracy of the scan report will be related to the tasks normally performed by technologists, such as the acquisition and processing of images and the entry, transfer, and networking of data. After reading this article, the reader will be able to describe the principles of scan interpretation and reporting, the software tools for telemedicine and computer-aided interpretation, and the role of the technologist in this process.

Allied Health Personnel↗
PubMed2005

Application of a newly developed ARB software-integrated tool for in silico terminal restriction fragment length polymorphism analysis reveals the dominance of a novel pmoA cluster in a forest soil.

TRF-CUT, an ARB-implemented tool, was developed to predict in silico the terminal restriction fragments of aligned small-subunit rRNA gene or functional gene sequences. Application of this new tool to perform directed terminal restriction fragment length polymorphism analysis of pmoA products obtained from a forest soil revealed that novel cluster I methanotrophic bacteria were dominant.

Bacteria↗
PubMed2001

Correlation between nerve conduction studies and clinical scores in diabetic neuropathy.

Polyneuropathy, a frequent complication of diabetes, can be assessed clinically and electrophysiologically. Neurological examination can be quantified by validated scores, e.g., the neuropathy symptom score (NSS) or the neuropathy disability score (NDS). Such scores exclude electrophysiological aspects of the neuropathy. A software tool was designed to convert electrophysiological data into one single index of polyneuropathy (IPN). This index was calibrated to grade the severity of a polyneuropathy from 0.00 to 1.00. In a series of 38 diabetic patients, we have calculated NSS, NDS, and IPN. We found correlations between these variables, NDS and IPN exhibiting the more significant association. The use of IPN allowed us to demonstrate that nerve conduction values correlated with clinical scores in diabetic polyneuropathy. Such a software tool, by providing a single electrophysiological index, may facilitate clinico-electrophysiological assessment in large descriptive studies or therapeutic trials of diabetic polyneuropathy.

Adolescent↗
PubMed2004

An ontology for collaborative construction and analysis of cellular pathways.

MOTIVATION: As the scientific curiosity in genome studies shifts toward identification of functions of the genomes in large scale, data produced about cellular processes at molecular level has been accumulating with an accelerating rate. In this regard, it is essential to be able to store, integrate, access and analyze this data effectively with the help of software tools. Clearly this requires a strong ontology that is intuitive, comprehensive and uncomplicated. RESULTS: We define an ontology for an intuitive, comprehensive and uncomplicated representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information via collaboration, and supports manipulation of the stored data. In addition, it facilitates concurrent modifications to the data while maintaining its validity and consistency. Furthermore, novel structures for representation of multiple levels of abstraction for pathways and homologies is provided. Lastly, our ontology supports efficient querying of large amounts of data. We have also developed a software tool named pathway analysis tool for integration and knowledge acquisition (PATIKA) providing an integrated, multi-user environment for visualizing and manipulating network of cellular events. PATIKA implements the basics of our ontology.

Biopolymers↗
PubMed1998

New software provides tool for managing contact capitation.

The main drawback to contact capitation has been its administrative complexity. Now, a San Francisco managed care firm has released an Internet-based system that offers a simple process for determining contact values and payment amounts.

California↗
PubMed2002

Use of three-dimensional computer graphic animation to illustrate cleft lip and palate surgery.

OBJECTIVE: Three-dimensional (3D) computer animation is not commonly used to illustrate surgical techniques. This article describes the surgery-specific processes that were required to produce animations to teach cleft lip and palate surgery. MATERIALS AND METHODS: Three-dimensional models were created using CT scans of two Chinese children with unrepaired clefts (one unilateral and one bilateral). We programmed several custom software tools, including an incision tool, a forceps tool, and a fat tool. RESULTS: Three-dimensional animation was found to be particularly useful for illustrating surgical concepts. Positioning the virtual "camera" made it possible to view the anatomy from angles that are impossible to obtain with a real camera. Transparency allows the underlying anatomy to be seen during surgical repair while maintaining a view of the overlaying tissue relationships. Finally, the representation of motion allows modeling of anatomical mechanics that cannot be done with static illustrations. The animations presented in this article can be viewed on-line at http://www.smiletrain.org/programs/virtual_surgery2.htm. CONCLUSIONS: Sophisticated surgical procedures are clarified with the use of 3D animation software and customized software tools. The next step in the development of this technology is the creation of interactive simulators that recreate the experience of surgery in a safe, digital environment.

Child↗
PubMed2004

Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting.

UNLABELLED: A set of new algorithms and software tools for automatic protein identification using peptide mass fingerprinting is presented. The software is automatic, fast and modular to suit different laboratory needs, and it can be operated either via a Java user interface or called from within scripts. The software modules do peak extraction, peak filtering and protein database matching, and communicate via XML. Individual modules can therefore easily be replaced with other software if desired, and all intermediate results are available to the user. The algorithms are designed to operate without human intervention and contain several novel approaches. The performance and capabilities of the software is illustrated on spectra from different mass spectrometer manufacturers, and the factors influencing successful identification are discussed and quantified. MOTIVATION: Protein identification with mass spectrometric methods is a key step in modern proteomics studies. Some tools are available today for doing different steps in the analysis. Only a few commercial systems integrate all the steps in the analysis, often for only one vendor's hardware, and the details of these systems are not public. RESULTS: A complete system for doing protein identification with peptide mass fingerprints is presented, including everything from peak picking to matching the database protein. The details of the different algorithms are disclosed so that academic researchers can have full control of their tools. AVAILABILITY: The described software tools are available from the Halmstad University website www.hh.se/staff/bioinf/ SUPPLEMENTARY INFORMATION: Details of the algorithms are described in supporting information available from the Halmstad University website www.hh.se/staff/bioinf/

Algorithms↗
PubMed2005

Internal radionuclide therapy: the ULMDOS software for treatment planning.

Before therapy with unsealed radionuclides, a dosimetry assessment must be performed for each patient. We present the interactive software tool ULMDOS, which facilitates dosimetric calculations, enhances traceability, and adequate documentation. ULMDOS is developed in IDL 6.1 (Interactive Data Language) under Windows XP/2000. First the patient data, the radiotracer data, and optionally urine and serum data are entered. After loading planar gamma camera images and drawing regions of interest, the residence times can be calculated using fits of the time activity data to exponential functions. Data can be saved in ASCII format for retrospective examination and further processing. ULMDOS allows one to process the dosimetric calculations within a standardized environment, spares the time-consuming transfer of data between different software tools, enables the documentation of ROI and raw data, and reduces intraindividual variability. ULMDOS satisfies the required conditions for traceability and documentation as a prerequisite to routine use in clinical settings.

Algorithms↗
PubMed2005

Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation.

The oligonucleotide specificity for microarray hybridization can be predicted by its sequence identity to non-targets, continuous stretch to non-targets, and/or binding free energy to non-targets. Most currently available programs only use one or two of these criteria, which may choose 'false' specific oligonucleotides or miss 'true' optimal probes in a considerable proportion. We have developed a software tool, called CommOligo using new algorithms and all three criteria for selection of optimal oligonucleotide probes. A series of filters, including sequence identity, free energy, continuous stretch, GC content, self-annealing, distance to the 3'-untranslated region (3'-UTR) and melting temperature (T(m)), are used to check each possible oligonucleotide. A sequence identity is calculated based on gapped global alignments. A traversal algorithm is used to generate alignments for free energy calculation. The optimal T(m) interval is determined based on probe candidates that have passed all other filters. Final probes are picked using a combination of user-configurable piece-wise linear functions and an iterative process. The thresholds for identity, stretch and free energy filters are automatically determined from experimental data by an accessory software tool, CommOligo_PE (CommOligo Parameter Estimator). The program was used to design probes for both whole-genome and highly homologous sequence data. CommOligo and CommOligo_PE are freely available to academic users upon request.

Algorithms↗
PubMed2005

Conservation analysis of large biochemical networks.

MOTIVATION: Large biochemical networks pose a unique challenge from the point of view of evaluating conservation laws. The computational problem in most cases exceeds the capability of available software tools, often resulting in inaccurate computation of the number and form of conserved cycles. Such errors have profound effects on subsequent calculations, particularly in the evaluation of the Jacobian which is a critical quantity in many other calculations. The goal of this paper is to outline a new algorithm that is computationally efficient and robust at extracting the correct conservation laws for very large biochemical networks. RESULTS: We show that our algorithm can perform the conservation analysis of large biochemical networks, and can evaluate the correct conserved cycles when compared with other similar software tools. Biochemical simulators such as Jarnac and COPASI are successful at extracting only a subset of the conservation laws that our algorithm can. This is illustrated with examples for some large networks which show the advantages of our method.

Algorithms↗
PubMed1998

[A comparison of the monitor and alternator findings of digital thoracic images with the aid of a computer-supported procedure].

PURPOSE: To compare softcopy and hardcopy reading of chest radiographs a software tool was designed for creating lesions with clearly defined size, location and contrast. METHOD: An ROC study was performed using a set of chest radiographs with 300 simulated small nodules and linear details displayed on film and on a 1 K monitor. Six observers participated in the study. ROC curves were generated on the basis of 7200 decisions. RESULTS: There was no significant difference in observer performance overall (AUC = Area under curve). Monitor: 0.84 +/- 0.08 vs. AUC, Film: 0.84 +/- 0.08). Slight, but not statistical significant differences were found in the detection of low-contrast lung nodules and of linear lung details. CONCLUSION: Soft-copy reading using a high quality 1 K CRT display provides the same accuracy for the detection of subtle computer-simulated lesions as hardcopy reading. A software tool could be used for assigning optimal characteristics of CRT- and hardcopy displays using clearly defined lesions as a gold standard.

Computer Simulation↗
PubMed2004

MetaCyc: a multiorganism database of metabolic pathways and enzymes.

The MetaCyc database (see URL http://MetaCyc.org) is a collection of metabolic pathways and enzymes from a wide variety of organisms, primarily microorganisms and plants. The goal of MetaCyc is to contain a representative sample of each experimentally elucidated pathway, and thereby to catalog the universe of metabolism. MetaCyc also describes reactions, chemical compounds and genes. Many of the pathways and enzymes in MetaCyc contain extensive information, including comments and literature citations. SRI's Pathway Tools software supports querying, visualization and curation of MetaCyc. With its wide breadth and depth of metabolic information, MetaCyc is a valuable resource for a variety of applications. MetaCyc is the reference database of pathways and enzymes that is used in conjunction with SRI's metabolic pathway prediction program to create Pathway/Genome Databases that can be augmented with curation from the scientific literature and published on the world wide web. MetaCyc also serves as a readily accessible comprehensive resource on microbial and plant pathways for genome analysis, basic research, education, metabolic engineering and systems biology. In the past 2 years the data content and the Pathway Tools software used to query, visualize and edit MetaCyc have been expanded significantly. These enhancements are described in this paper.

Biochemical Phenomena↗
PubMed2006

Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data.

A novel software tool named PTM-Explorer has been applied to LC-MS/MS datasets acquired within the Human Proteome Organisation (HUPO) Brain Proteome Project (BPP). PTM-Explorer enables automatic identification of peptide MS/MS spectra that were not explained in typical sequence database searches. The main focus was detection of PTMs, but PTM-Explorer detects also unspecific peptide cleavage, mass measurement errors, experimental modifications, amino acid substitutions, transpeptidation products and unknown mass shifts. To avoid a combinatorial problem the search is restricted to a set of selected protein sequences, which stem from previous protein identifications using a common sequence database search. Prior to application to the HUPO BPP data, PTM-Explorer was evaluated on excellently manually characterized and evaluated LC-MS/MS data sets from Alpha-A-Crystallin gel spots obtained from mouse eye lens. Besides various PTMs including phosphorylation, a wealth of experimental modifications and unspecific cleavage products were successfully detected, completing the primary structure information of the measured proteins. Our results indicate that a large amount of MS/MS spectra that currently remain unidentified in standard database searches contain valuable information that can only be elucidated using suitable software tools.

Amino Acid Sequence↗
PubMed2003

Software for automated analysis of DNA fingerprinting gels.

Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the restriction fragments as a function of fragment size, with model parameters determined empirically from "marker" lanes containing molecular size standards. Automated identification of restriction fragments involves several steps, including: image preprocessing, to put the data in a form consistent with a linear model; marker lane analysis, for determination of the model parameters; and data lane analysis, a procedure for detecting restriction fragment multiplets while simultaneously determining the amplitude curve that describes restriction fragment amplitude as a function of mobility. In validation experiments conducted on fingerprinted and sequenced Bacterial Artificial Chromosome (BAC) clones, sensitivity and specificity of restriction fragment identification exceeded 96% on restriction fragments ranging in size from 600 base pairs (bp) to 30,000 bp. The integrated suite of software tools, written in MATLAB and collectively called BandLeader, is in use at the BC Cancer Agency Genome Sciences Centre (GSC) and the Washington University Genome Sequencing Center, and has been provided to the Wellcome Trust Sanger Institute and the Whitehead Institute. Employed in a production mode at the GSC, BandLeader has been used to perform automated restriction fragment identification for more than 850,000 BAC clones for mouse, rat, bovine, and poplar fingerprint mapping projects.

Animals↗
PubMed2003

Cone beam computed tomography in craniofacial imaging.

Cone beam computed tomography (CT) has the potential to reduce the size and cost of CT scanners. Because this emerging technology produces images with isotropic submillimeter spatial resolution, it is ideally suited for dedicated dentomaxillofacial CT scanning. When combined with application-specific software tools, cone beam computed tomography can provide dentomaxillofacial practitioners with a complete solution for performing specific diagnostic and surgical tasks, such as dental implant planning. In this paper, we provide a brief overview of cone beam scanning technology and compare it with the fan beam scanning used in conventional CT scanners. We introduce 'DentoCAT', a relatively small, low-cost cone beam CT scanner dedicated for dentomaxillofacial imaging developed at Xoran Technologies. We present images generated by the DentoCAT scanner and provide an assessment of its performance in terms of spatial resolution and effective radiation dose. Finally, we illustrate the clinical utility of the scanner by presenting the results we have obtained to date using the DentoCAT scanner in conjunction with an implant planning software tool.

Dental Implants↗
PubMed2004

Multi-layered representation for cell signaling pathways.

To understand complex signaling pathways and networks, it is necessary to develop a formal and structured representation of the available information in a format suitable for analysis by software tools. Due to the complexity and incompleteness of the current biological knowledge about cell signaling, such a device must be able to represent cellular pathways at differing levels of details, one level of information abstract enough to convey an essential signaling flow while hiding its details and another level of information detailed enough to explain the underlying mechanisms that account for the signaling flow described at a more abstract level. We have defined a formal ontology for cell-signaling events that allows us to describe these cellular pathways at various levels of abstraction. Using this formal representation, ROSPath (reactive oxygen species-mediated signaling pathway) database system has been implemented and made available on the web (rospath.ewha.ac.kr). ROSPath is a database system for reactive oxygen species (ROS)-mediated cell signaling pathways and signaling processes in molecular detail, which facilitates a comprehensive understanding of the regulatory mechanisms in signaling pathways. ROSPath includes growth factor-, stress-, and cytokine-induced signaling pathways containing about 500 unique proteins (mostly mammalian) and their related protein states, protein complexes, protein complex states, signaling interactions, signaling steps, and pathways. It is a web-based structured repository of information on the signaling pathways of interest and provides a means for managing data produced by large-scale and high-throughput techniques such as proteomics. Also, software tools are provided for querying, displaying, and analyzing pathways, thus furnishing an integrated web environment for visualizing and manipulating ROS-mediated cell-signaling events.

Cell Physiological Phenomena↗
PubMed2002

Dynamic computed tomography: a novel technique to study lung aeration and atelectasis formation during experimental CPR.

OBJECTIVE: To develop an image based technique to study the effect of different ventilatory strategies on lung ventilation and alveolar recruitment during cardiopulmonary resuscitation (CPR). DESIGN: (1) Technical development of the following components: (a) construction of an external chest compression device, which does not interfere with CT imaging, and (b) development of a software tool to detect lung parenchyma automatically and to calculate radiological density parameters. (2) Feasibility studies: three strategies of CPR ventilation were performed and imaged in one animal each (pigs, 25 kg): volume-constant ventilation (VCV), no ventilation, or continuous airway pressure (CPAP). One minute after induction of circulatory arrest inside the CT scanner, external chest compressions started at a rate of 100 cpm, and one of the ventilation modes was initiated. After 1 min, intravenous epinephrine was added as a bolus (40 microg/kg), followed by a continuous infusion (13 microg/kg per min). Six minutes later, dynamic CT acquisitions (temporal resolution: 100 ms) commenced. Simultaneously, arterial blood gases, acid base status and haemodynamics were sampled. RESULTS: Using a modified chest compression device, dynamic CT acquisitions are feasible during closed-chest CPR. In three pilot experiments with different ventilation strategies, the dedicated software tool allowed to quantify ventilated, atelectatic and over-distended fractions of total lung area. VCV showed a large amount of atelectasis, which was recruited during every respiratory cycle. No ventilation led to atelectasis to govern over 50% of the total lung area. CPAP caused less atelectasis as VCV, and no cyclic recruitment and de-recruitment phenomena were observed. CONCLUSIONS: We demonstrate a novel experimental set up, which allows quantification of different lung compartments during ongoing CPR and may become useful in comparing the direct pulmonary effects of different ventilatory strategies in the settings of Basic and Advanced Cardiac Life Support.

Animals↗