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The measure analysis and QA system for gamma knife dose field and its pivotal techniques are described in this paper. By using our own measuring tools and analysis software, we have made a testing analysis about the HuaYuan Gamma Knife dose field with a satisfactory result.
At the Giessen University Hospital electronic data processing systems have been in routine use since 1975. In the early years developments were focused on ADT functions (admission/discharge/transfer) and laboratory systems. In the next decade additional systems were introduced supporting various functional departments. In the mid-eighties the need to stop the ongoing trend towards more and more separated stand-alone systems was realized and it was decided to launch a strategic evaluation and planning process which sets the foundation for an integrated hospital information system (HIS). The evaluation of the HELP system for its portability into the German hospital environment was the first step in this process. Despite its recognized capabilities in integrating decision support and communication technologies, and its powerful HIS development tools, the large differences between American and German hospital organization, influencing all existing HELP applications, and the incompatibility of the HELP tools with modern software standards were two important factors forcing the investigation of alternative solutions. With the HELP experience in mind, a HIS concept for the Giessen University Hospital was developed. This new concept centers on the idea of a centralized relational patient database on a highly reliable database server, and clinical front-end applications which might be running on various other computer systems (mainframes, departmental UNIX satellites or PCs in a LAN) integrated into a comprehensive open HIS network. The first step towards this integrated approach was performed with the implementation of ADT and results reporting functions on care units.
Internet teleconferencing software can be used to hold "virtual" meetings, during which participants around the world can share ideas. A core group of anesthetic medical practitioners, largely consisting of the Society for Advanced Telecommunications in Anesthesia (SATA), has begun to hold regularly scheduled "virtual grand rounds." This paper examines currently available software and offers impressions of our own early experiences with this technology. Two teleconferencing systems have been used: White Pine Software CU-SeeMe and Microsoft NetMeeting. While both provided acceptable results, each had specific advantages and disadvantages. CU-SeeMe is easier to use when conferences include more than two participants. NetMeeting provides higher quality audio and video signals under crowded network conditions, and is better for conferences with only two participants. While some effort is necessary to get these teleconferencing systems to work well, we have been using desktop conferencing for six months to hold virtual Internet meetings. The sound and video images produced by Internet teleconferencing software are inferior to dedicated point-to-point teleconferencing systems. However, low cost, wide availability, and ease of use make this technology a potentially valuable tool for clinicians and researchers.
We have developed a distributed software package which allows neurophysiologists to have at hand a set of network and graphic tools in order to perform the analysis of data collected from the electrical activity of neurons, studied in the experimental laboratory. This system is built around three major components. First, the experimental data are processed in order to select specific data files from the networked computer and display the spike trains as raster dots. The second part selects one type of analysis (e.g., cross-correlation, out of a set of possible choices) after configuration of some specific parameters. Finally, the third component deals with the results of data analyses, which are selected and displayed on a multi-parameter graphic "ring binder." We have used the Java programming language to implement this application. This recent object-oriented language offers platform-independent software tools including graphic package and standard network protocols.
System development projects in health care have not properly addressed the issues of availability, confidentiality and integrity. The safety critical aspects of health care have not been well recognised in the context of information systems, as opposed to medical devices where considerable effort has been made to ensure the 'correctness' of the device before it is authorized for use. Consideration should be given at the start of the development process to the particular requirements of the project and the project should be structured to ensure that the specific functional requirements for security are satisfied. In addition the development process itself must be conducted in a rigorous fashion in order to ensure-and to demonstrate--that the end product has the appropriate degree of 'correctness'. Suitable tools and techniques will be required to assist the efficiency and the integrity of this process.
Transcription Regulatory Regions Database (TRRD) is an informational resource containing an integrated description of the gene transcription regulation. An entry of the database corresponds to a gene and contains the data on localization and functions of the transcription regulatory regions as well as gene expression patterns. TRRD contains only experimental data that are inputted into the database through annotating scientific publication. TRRD release 6.0 comprises the information on 1167 genes, 5537 transcription factor binding sites, 1714 regulatory regions, 14 locus control regions and 5335 expression patterns obtained through annotating 3898 scientific papers. This information is arranged in seven databases: TRRDGENES (general gene description), TRRDLCR (locus control regions); TRRDUNITS (regulatory regions: promoters, enhancers, silencers, etc.), TRRDSITES (transcription factor binding sites), TRRDFACTORS (transcription factors), TRRDEXP (expression patterns) and TRRDBIB (experimental publications). Sequence Retrieval System (SRS) is used as a basic tool for navigating and searching TRRD and integrating it with external informational and software resources. The visualization tool, TRRD Viewer, provides the information representation in a form of maps of gene regulatory regions. The option allowing nucleotide sequences to be searched for according to their homology using BLAST is also included. TRRD is available at http://www.bionet.nsc.ru/trrd/.
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.
Many studies of neuronal activity require isolation of the extracellular wave form (spike) of a single neuron from the potentials generated by nearby cells. A variety of methods for spike sorting exists, but most are expensive and require specialized hardware and software. Moreover, there is no easy and objective way for evaluating and comparing the performance of spike sorting devices. We describe here a system for on-line spike sorting that is implemented on an IBM PC/AT computer using commercially available hardware and C-language software. Spikes are detected after crossing an amplitude threshold and are sorted or rejected by template matching. The templates are constructed in a learning phase, using a fast manual sorting of all detected spikes. Later, each detected spike is matched against all defined templates. A detected spike which does not match any template, or matches more than one, is rejected. A continuous display of the wave forms of the last 256 sorted, double-matched, and rejected spikes is used as the main tool for parameter adjustment and error detection. Also described is a new and highly versatile tool for generating appropriate wave forms for critical evaluation of sorter performance. Using the same hardware and software tools, a simulation program mimics the extra-cellular activity of several neurons by linear combination of two vectors and added random noise. The size, shape and the variability of the action potential, as well as its firing pattern, can be adjusted. Comparison of the sorter output with the known simulated activity is used to examine the sorter performance and limitations.
BACKGROUND: Study end-points in microcirculation research are usually video-taped images rather than numeric computer print-outs. Analysis of these video-taped images for the quantification of microcirculatory parameters usually requires computer-based image analysis systems. Most software programs for image analysis are custom-made, expensive, and limited in their applicability to selected parameters and study end-points. METHODS AND RESULT: We demonstrate herein that an inexpensive, commercially available computer software (Adobe Photoshop), run on a Macintosh G3 computer with inbuilt graphic capture board provides versatile, easy to use tools for the quantification of digitized video images. Using images obtained by intravital fluorescence microscopy from the pre- and postischemic muscle microcirculation in the skinfold chamber model in hamsters, Photoshop allows simple and rapid quantification (i) of microvessel diameters, (ii) of the functional capillary density and (iii) of postischemic leakage of FITC-labeled high molecular weight dextran from postcapillary venules. We present evidence of the technical accuracy of the software tools and of a high degree of interobserver reliability. CONCLUSION: Inexpensive commercially available imaging programs (i.e., Adobe Photoshop) provide versatile tools for image analysis with a wide range of potential applications in microcirculation research.
Quality assurance of biostatistical data analysis is becoming mandatory. The aim of this review of statistical software was to guide uses who are faced with the increasing number of these tools. A list of softwares was obtained from statisticians and computer scientists, computerized databases, computer science lay press, and commercial documents. The softwares were described and their possibilities measured. The following functions were studied: functions considered as essential (descriptive analysis, Student's t, Mann-Whitney or Wilcoxon, ANOVA, Kruskall-Wallis, Pearson's chi 2, Fisher's exact test, Pearson's r), survival and multivariate analysis (logistic regression, proportional hazards modelling, times series). User-friendliness and quality of graphs were also studied. Among the 220 listed softwares, 26 could be considered as general softwares and were extensively analyzed. Statistical softwares may be classified into four categories: easy-to-use general public softwares with limited functions, such as EPI INFO; simple reference softwares with satisfactory user-friendliness and performing most of the statistical analyses, such as PCSM, STATISTICA or STATA; complex reference softwares intended for statisticians (EPILOG PLUS, SAS); specific cases such as EGRET performing only multivariate analysis or SUPERANOVA performing only analysis of variance. Such a review should be regularly updated.
This paper presents a new software developed for analyzing single strand conformation polymorphism (SSCP) electrophoresis patterns delivered by the genetic analyzer ABI310 (Applied Biosystems). SSCP is a molecular typing technique based on the PCR amplification of microbial 16S rDNA and used for the monitoring of complex microbial ecosystems dynamics. The software--a home-made MATLAB toolbox called MODIMECO--developed for the analysis of SSCP patterns is presented. MODIMECO includes a number of basic signal processing abilities as well as largely used statistical tools such as the well known principal component analysis. The use of the SSCP for assessing the hypothesis of the existence of a microbial signature of drinking waters illustrates the typical advantages of using such software tools. Results are discussed and conclusions drawn.
BACKGROUND: Uncovering the key sequence elements in gene promoters that regulate the expression of plant genomes is a huge task that will require a series of complementary methods for prediction, substantial innovations in experimental validation and a much greater understanding of the role of combinatorial control in the regulation of plant gene expression. RESULTS: To add to this larger process and to provide alternatives to existing prediction methods, we have developed several tools in the statistical package R. ModuleFinder identifies sets of genes and treatments that we have found to form valuable sets for analysis of the mechanisms underlying gene co-expression. CoReg then links the hierarchical clustering of these co-expressed sets with frequency tables of promoter elements. These promoter elements can be drawn from known elements or all possible combinations of nucleotides in an element of various lengths. These sets of promoter elements represent putative cis-acting regulatory elements common to sets of co-expressed genes and can be prioritised for experimental testing. We have used these new tools to analyze the response of transcripts for nuclear genes encoding mitochondrial proteins in Arabidopsis to a range of chemical stresses. ModuleFinder provided a subset of co-expressed gene modules that are more logically related to biological functions than did subsets derived from traditional hierarchical clustering techniques. Importantly ModuleFinder linked responses in transcripts for electron transport chain components, carbon metabolism enzymes and solute transporter proteins. CoReg identified several promoter motifs that helped to explain the patterns of expression observed. CONCLUSION: ModuleFinder identifies sets of genes and treatments that form useful sets for analysis of the mechanisms behind co-expression. CoReg links the clustering tree of expression-based relationships in these sets with frequency tables of promoter elements. These sets of promoter elements represent putative cis-acting regulatory elements for sets of genes, and can then be tested experimentally. We consider these tools, both built on an open source software product to provide valuable, alternative tools for the prioritisation of promoter elements for experimental analysis.
For most medical informatics software products, insufficient effort is spent on the design phase of production. However, poor design often leads to systems that are either not well accepted, or far less effective than they could be. In this paper, we describe the ideas of participatory design and discuss why these ideas are especially applicable to medical informatics systems. In particular, we present a case study in the area of clinical trial protocol management. We designed and developed a tool aimed at increasing accrual to clinical trial protocols at an oncology center. However, the design evolved over time, and features of this design were only discovered through iterative development and interaction with the users within the context of the workplace.
Analysis of single nucleotide polymorphisms (SNPs) is a rapidly growing field of research that provides insights into the most common type of differences between individual genomes. The resulting information has a strong impact in the fields of pharmacogenomics, drug development, forensic medicine, and diagnostics of specific disease markers. The technique of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) has been shown to be a highly suitable tool for the analysis of DNA. It supplies a very versatile method for addressing a high-throughput SNP genotyping approach. Here, we present the Bruker genotools SNP MANAGER, a new software tool suitable for highly automated MALDI-TOF MS SNP genotyping. The genotools SNP MANAGER administers the sample preparation data, calculates masses of allele-specific primer extension products, performs genotyping analysis, and displays the results. In the current study, we have used the genotools SNP MANAGER to perform an automated duplex SNP analysis of two biallelic markers from the promoter of the gene encoding the inflammatory mediator interleukin-6.
This study explores the Patient Record Information System (PaRIS) for primary health care centers in a developing country such as Indonesia. The specific geography of the thousand islands country Indonesia is the reason for transportation difficulties as well as communication problems. This causes a serious adverse effect on the public healthcare service especially in the rural area within the country. Hence, a sustainable system is required that makes use of appropriate Information and Communication Technology (ICT). We developed a clinical information system with modest communication technology combined with a unique database distribution system. The Internet and its free software are the main tools for this system. It is a good opportunity for a developing country such as Indonesia to apply open free software in regard to the healthcare sector. This cost effective and sustainable system can enhance the work of physicians in order to provide better and applicable public health care service.
The Quebec Patient Smart Card Project is a Provincial Government initiative under the responsibility of the Rgie de l'assurance-maladie du Québec (Quebec Health Insurance Board). Development, implementation, and assessment duties were assigned to a team from Université Laval, which in turn joined a group from the Direction de la santé publique du Bas-St-Laurent in Rimouski, where the experiment is taking place. The pilot project seeks to evaluate the use and acceptance of a microprocessor card as a way to improve the exchange of clinical information between card users and various health professionals. The card can be best described as a résumé containing information pertinent to an individual's health history. It is not a complete medical file; rather, it is a summary to be used as a starting point for a discussion between health professionals and patients. The target population is composed of persons 60 years and over, pregnant women, infants under 18 months, and the residents of a small town located in the target area, St-Fabien, regardless of age. The health professionals involved are general practitioners, specialists, pharmacists, nurses, and ambulance personnel. Participation in the project is on a voluntary basis. Each health care provider participating in the project has a personal identification number (PIN) and must use both an access card and a user card to access information. This prevents unauthorized access to a patient's card and allows the staff to sign and date information entered onto the patient card. To test the microprocessor card, we developed software based on a problem-oriented approach integrating diagnosis, investigations, treatments, and referrals. This software is not an expert system that constrains the clinician to a particular decisional algorithm. Instead, the software supports the physician in decision making. The software was developed with a graphical interface (Windows 3.1) to maximize its user friendliness. A version of the software was developed for each of the four groups of health care providers involved. In addition we designed an application to interface with existing pharmaceutical software. For practical reasons and to make it possible to differentiate between the different access profiles, the information stored on the card is divided in several blocks: Identification, Emergency, History (personal and family), Screening Tests, Vaccinations, Drug Profile, General follow-up, and some Specific follow-ups (Pregnancy, Ophthalmology, Kidney failure, Cardiology, Pediatrics, Diabetes, Pneumology, Specific parameters). Over 14,000 diagnoses and symptoms are classified with four levels of precision, the codification being based on the ICPC (International Classification for Primary Care). The software contains different applications to assist the clinician in decision making. A "Drug Advisor" helps the prescriber by detecting possible interactions between drugs, giving indications (doses) and contraindications, cautions, potential side-effects and therapeutic alternatives. There is also a prevention module providing recommendations for vaccination and periodic examinations based on the patient's age and sex. The pharmaceutical, vaccination, and screening tests data banks are updated every six months. These sections of the software are accessible to access card holders at any times, even without a patient card, and constitute in themselves an interesting clinical tool. We developed a software server (SCAM) allowing the different applications to access the data in a memory card regardless of the type of memory card used. Using a single high level command language, this server provides a standardized utilization of memory cards from various manufacturers. It ensures the compatibility of the applications using the card as a storage medium. (abstract truncated)
The Biomek 2000 Laboratory Automation Workstation is used for liquid handling and other repetitive operations in many laboratories. Since it has very good spatial positioning capabilities, we have modified this workstation to deliver samples at high densities onto microscope slides to produce DNA microarrays. The workstation tool, originally designed for bacterial colony replication, was adapted to carry special printing pins and was further modified to improve its positional accuracy. Software written in the Tool Command Language was concurrently developed to control the movements of the workstation arm during the process of printing. With these modifications, the workstation can reliably deliver individual samples at a spacing of 0.5 mm, corresponding to a total of more than 3000 samples on a single slide. Arrays prepared in this way were successfully tested in hybridization experiments.
Amino acid sequence alignment is an extremely useful tool in protein family analysis. Most family characteristics, such as the localization of functional residues, structural constraints and evolutionary relationships may be retrieved through the observation of the conservation pattern highlighted by the alignments. A quantitative score for the conservation in the alignment allows different stages of an alignment to be compared and consequently the alignment information to be efficiently exploited. Many scoring methods have been proposed during the last three decades. Claude Shannon's theory of communication (1948) paved the way for a consistent scoring of protein alignments by considering the residue (or symbol) frequency. A number of modifications have been proposed since that time, but the core statistical approach is still considered one of the best. By combining many database managing tools for treatment of protein sequences, a ClustalW software integration, a flexible symbols treatment and gap normalization functions, Entropy Calculator software has been developed. This new tool provides a global and optimal approach to multiple sequence alignment scoring by offering an easy graphic interface and a series of modification options that help in interpreting alignments and allow conservation pattern inferences to be performed.