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At least 1,171 records · Page 65Linked to original sources
PubMed2002

Seafood Spoilage Predictor--development and distribution of a product specific application software.

To allow shelf-life prediction of a range of products, the Seafood Spoilage Predictor (SSP) software has been developed to include both kinetic models for growth of specific spoilage microorganisms and empirical relative rates of spoilage models. SSP can read and evaluate temperature profile data of different formats and in this way the software is a flexible device for electronic time-temperature integration. Predicted values of microbial growth and of remaining product shelf life can be exported from SSP as graphs and tables in ASCII, HTML and eXtensible Mark-up Language (XML) formats and this allows SSP to be used in combination with other programmes. More than 300 people have downloaded SSP and distribution of this software from the internet has been efficient in stimulating the application of predictive microbiology and of mathematical seafood shelf-life models within industry, research, seafood inspection and teaching.

Animals↗
PubMed1991

AuthorBase: a database of authoring systems software.

A working prototype database of authoring system software was developed as part of a study of authoring software conducted by the National Library of Medicine. The database and development issues ranging from the scope of the database to what information to document are described. The protype demonstrates that records of reasonable integrity can be derived from vendor supplied information as long as users understand the database is only an initial starting point in searching for authoring software and a resource for becoming generally familiar with the technology.

Authorship↗
PubMed2003

PyPop: a software framework for population genomics: analyzing large-scale multi-locus genotype data.

Software to analyze multi-locus genotype data for entire populations is useful for estimating haplotype frequencies, deviation from Hardy-Weinberg equilibrium and patterns of linkage disequilibrium. These statistical results are important to both those interested in human genome variation and disease predisposition as well as evolutionary genetics. As part of the 13th International Histocompatibility and Immunogenetics Working Group (IHWG), we have developed a software framework (PyPop). The primary novelty of this package is that it allows integration of statistics across large numbers of data-sets by heavily utilizing the XML file format and the R statistical package to view graphical output, while retaining the ability to inter-operate with existing software. Largely developed to address human population data, it can, however, be used for population based data for any organism. We tested our software on the data from the 13th IHWG which involved data sets from at least 50 laboratories each of up to 1000 individuals with 9 MHC loci (both class I and class II) and found that it scales to large numbers of data sets well.

Computational Biology↗
PubMed2005

[SSRHunter: development of a local searching software for SSR sites].

Progress in genome research has made it possible to develop new SSR markers by bioinformatics in a relatively narrow region of genome. To realize it, the first thing is to search for potential SSR sites. Any known methods have more or less defects. Efforts were made to develop a local SSR sites searching software in this study. The resultant software, SSRHunter, could accomplish this task perfectly. Furthermore, SSRHunter could provide automatic pretreatment of sequences, routine arrangement of sequences, sequence transformation and convenient report output.

Microsatellite Repeats↗
PubMed2006

Clinical, information and business process modeling to promote development of safe and flexible software.

Using a factorial vignette survey and modeling methodology, we developed clinical and information models - incorporating evidence base, key concepts, relevant terms, decision-making and workflow needed to practice safely and effectively - to guide the development of an integrated rule-based knowledge module to support prescribing decisions in asthma. We identified workflows, decision-making factors, factor use, and clinician information requirements. The Unified Modeling Language (UML) and public domain software and knowledge engineering tools (e.g. Protégé) were used, with the Australian GP Data Model as the starting point for expressing information needs. A Web Services service-oriented architecture approach was adopted within which to express functional needs, and clinical processes and workflows were expressed in the Business Process Execution Language (BPEL). This formal analysis and modeling methodology to define and capture the process and logic of prescribing best practice in a reference implementation is fundamental to tackling deficiencies in prescribing decision support software.

Asthma↗
PubMed2003

A methodology and implementation for annotating digital images for context-appropriate use in an academic health care environment.

Use of digital medical images has become common over the last several years, coincident with the release of inexpensive, mega-pixel quality digital cameras and the transition to digital radiology operation by hospitals. One problem that clinicians, medical educators, and basic scientists encounter when handling images is the difficulty of using business and graphic arts commercial-off-the-shelf (COTS) software in multicontext authoring and interactive teaching environments. The authors investigated and developed software-supported methodologies to help clinicians, medical educators, and basic scientists become more efficient and effective in their digital imaging environments. The software that the authors developed provides the ability to annotate images based on a multispecialty methodology for annotation and visual knowledge representation. This annotation methodology is designed by consensus, with contributions from the authors and physicians, medical educators, and basic scientists in the Departments of Radiology, Neurobiology and Anatomy, Dermatology, and Ophthalmology at the University of Utah. The annotation methodology functions as a foundation for creating, using, reusing, and extending dynamic annotations in a context-appropriate, interactive digital environment. The annotation methodology supports the authoring process as well as output and presentation mechanisms. The annotation methodology is the foundation for a Windows implementation that allows annotated elements to be represented as structured eXtensible Markup Language and stored separate from the image(s).

Academic Medical Centers↗
PubMed2005

Noise-robust soft clustering of gene expression time-course data.

Clustering is an important tool in microarray data analysis. This unsupervised learning technique is commonly used to reveal structures hidden in large gene expression data sets. The vast majority of clustering algorithms applied so far produce hard partitions of the data, i.e. each gene is assigned exactly to one cluster. Hard clustering is favourable if clusters are well separated. However, this is generally not the case for microarray time-course data, where gene clusters frequently overlap. Additionally, hard clustering algorithms are often highly sensitive to noise. To overcome the limitations of hard clustering, we applied soft clustering which offers several advantages for researchers. First, it generates accessible internal cluster structures, i.e. it indicates how well corresponding clusters represent genes. This can be used for the more targeted search for regulatory elements. Second, the overall relation between clusters, and thus a global clustering structure, can be defined. Additionally, soft clustering is more noise robust and a priori pre-filtering of genes can be avoided. This prevents the exclusion of biologically relevant genes from the data analysis. Soft clustering was implemented here using the fuzzy c-means algorithm. Procedures to find optimal clustering parameters were developed. A software package for soft clustering has been developed based on the open-source statistical language R. The package called Mfuzz is freely available.

Algorithms↗
PubMed1998

Development of a computer-assisted learning software package on dental traumatology.

The development of computer-assisted learning software packages is a relatively new field of computer application. The progress made in personal computer technology toward more user-friendly operating systems has stimulated the academic community to develop computer-assisted learning for pre- and postgraduate students. The ability of computers to combine audio and visual data in an interactive form provides a powerful educational tool. The purpose of this study was to develop and evaluate a computer-assisted learning package on dental traumatology. This program contains background information on the diagnosis, classification, and management of dental injuries in both the permanent and the deciduous dentitions. It is structured into chapters according to the nature of the injury and whether injury has occurred in the primary or permanent dentition. At the end of each chapter there is a self-assessment questionnaire as well as references to relevant literature. Extensive use of pictures and video provides a comprehensive overview of the subject.

Computer-Assisted Instruction↗
PubMed2000

Quantitative real-time monitoring of dryer effluent using fiber optic near-infrared spectroscopy.

This paper describes a method for real-time quantitation of the solvents evaporating from a dryer. The vapor stream in the vacuum line of a dryer was monitored in real time using a fiber optic-coupled acousto-optic tunable filter near-infrared (AOTF-NIR) spectrometer. A balance was placed in the dryer, and mass readings were recorded for every scan of the AOTF-NIR. A partial least-squares (PLS) calibration was subsequently built based on change in mass over change in time for solvents typically used in a chemical manufacturing plant. Controlling software for the AOTF-NIR was developed. The software collects spectra, builds the PLS calibration model, and continuously fits subsequently collected spectra to the calibration, allowing the operator to follow the mass loss of solvent from the dryer. The results indicate that solvent loss can be monitored and quantitated in real time using NIR for the optimization of drying times. These time-based mass loss values have also been used to calculate "dynamic" vapor density values for the solvents. The values calculated are in agreement with values determined from the ideal gas law and could prove valuable as tools to measure temperature or pressure indirectly.

Calibration↗
PubMed1995

The Electronic View Box: a software tool for radiation therapy treatment verification.

PURPOSE: We have developed a software tool for interactively verifying treatment plan implementation. The Electronic View Box (EVB) tool copies the paradigm of current practice but does so electronically. A portal image (online portal image or digitized port film) is displayed side by side with a prescription image (digitized simulator film or digitally reconstructed radiograph). The user can measure distances between features in prescription and portal images and "write" on the display, either to approve the image or to indicate required corrective actions. The EVB tool also provides several features not available in conventional verification practice using a light box. METHODS AND MATERIALS: The EVB tool has been written in ANSI C using the X window system. The tool makes use of the Virtual Machine Platform and Foundation Library specifications of the NCI-sponsored Radiation Therapy Planning Tools Collaborative Working Group for portability into an arbitrary treatment planning system that conforms to these specifications. The present EVB tool is based on an earlier Verification Image Review tool, but with a substantial redesign of the user interface. A graphical user interface prototyping system was used in iteratively refining the tool layout to allow rapid modifications of the interface in response to user comments. RESULTS: Features of the EVB tool include 1) hierarchical selection of digital portal images based on physician name, patient name, and field identifier; 2) side-by-side presentation of prescription and portal images at equal magnification and orientation, and with independent grayscale controls; 3) "trace" facility for outlining anatomical structures; 4) "ruler" facility for measuring distances; 5) zoomed display of corresponding regions in both images; 6) image contrast enhancement; and 7) communication of portal image evaluation results (approval, block modification, repeat image acquisition, etc.). CONCLUSION: The EVB tool facilitates the rapid comparison of prescription and portal images and permits electronic communication of corrections in port shape and positioning.

Hospital Records↗
PubMed1993

Dynamic computed tomographic imaging of regional cerebral blood flow and blood volume. A clinical pilot study.

BACKGROUND AND PURPOSE: The advent of faster computed tomography scanners has evoked considerable interest in using this technology as a more practical method of regional cerebral hemodynamic evaluation than the currently available positron emission and single-photon emission computed tomography. The theoretical concepts have been worked out and validated in the laboratory by several groups. The aim of the present study was the development of a clinically useful system. METHODS: Software was developed for dynamic computed tomography-based calculation and color-coded representation of regional cerebral blood flow and blood volume. Normal values, reproducibility, and sensitivity to acetazolamide challenge were established in 13 volunteers. The method was applied to an additional three patients with internal carotid artery occlusion and known decreased vascular reserve capacity as diagnosed by transcranial Doppler ultrasonography. RESULTS: Normal regional cerebral blood flow was determined as 50 +/- 13 ml/100 ml per minute and normal fractional cerebral blood volume as 58 +/- 12 ml/1,000 ml (mean +/- SD). In five volunteers, two examinations were performed within 15 minutes for determination of reproducibility. Intermeasurement variability of hemispheric blood flow and blood volume was determined as +/- 23% and +/- 16%, respectively. Intravenous administration of 1 g acetazolamide resulted on the average in a 75% increase of blood flow and a 65% increase of fractional blood volume. In the patients with decreased cerebrovascular reserve capacity, baseline fractional blood volume in the ischemic hemispheres was significantly increased. Baseline regional cerebral blood flow in the ischemic territories was overestimated. Reactivity to acetazolamide of both regional blood flow and fractional blood volume was clearly reduced in the ischemic hemispheres. CONCLUSIONS: The present results demonstrate that the method is a simple and effective means of determining regional cerebral blood volume. Spatial resolution is superior to that of the radioactive tracer methods. Hemodynamic evaluation of ischemic conditions can be performed on the basis of increased resting cerebral blood volume and a diminished increase after acetazolamide. Accuracy of cerebral blood flow measurements, on the other hand, is affected by abnormal cerebral blood volume, and corresponding adjustments need to be made in pathological conditions.

Acetazolamide↗
PubMed1998

Image based renal stone tracking to improve efficacy in extracorporeal lithotripsy.

PURPOSE: We describe a method to reduce the number of shocks necessary to fragment renal stones during extracorporeal shock wave lithotripsy by automatically taking into account stone movements. MATERIALS AND METHODS: Echotrack computer software was developed and implemented on a lithotriptor. One software module uses image processing to detect instantaneous stone location based on ultrasound images generated by the lithotriptor. A second module uses the detected location to control the shock wave generator position, and automatically adjusts it to improve coincidence between the focal volume and stone. The reliability of the tracking algorithm was clinically tested in 65 patients with renal stones. These in vivo tests were qualitative and the goal was to assess software ability to track stones during actual treatments. A quantitative evaluation of the reduction in shocks necessary for fragmentation was performed in vitro. Artificial stones were moved according to computer generated trajectories. Each trajectory was applied once with and once without automatic adjustment of the generator position. RESULTS: The in vivo tests demonstrated software ability to track stones as far as they were visible in the images. During in vitro tests automatic adjustments of the generator position reduced the number of shocks necessary to fragment stones completely by a factor of 1.64. CONCLUSIONS: Image based renal stone tracking software that automatically adjusts the shock wave generator position according to the displacement of renal stones is useful during extracorporeal shock wave lithotripsy. Treatment time was significantly shorter with this software.

Humans↗
PubMed2006

[An interactive and evolutive software program to personalize treatment schedule : implication on daily life: the Centre Léon Bérard experience].

The second plan against cancer, initiated by the French President in 2003, has introduced a two-step procedure to announce cancer to the patient. During initial visit, the doctor tells the patient about his disease. On the second visit, the doctor elaborates the treatment strategy and proposes an individualized treatment plan for each patient. The objective of this plan is to offer to patients and caregivers an accurate, precise and personalized treatment schedule. The Centre Léon Bérard (Regional Cancer Center) has implemented a computerized model to manage all different treatment schedules. We developed a software program based on two different steps. Firstly, standard treatment schedules are programmed for each type of disease. To offer a better view of the influence of treatment on daily life, we added information such as place of treatment (ambulatory, inpatient, outpatient) impact on well being (side effects, risk of aplasia...), future evaluations and medical acts (CT scan, MRI, lumbar puncture...) as well as actions the patient should take (blood cell count, to have eaten nothing...). Secondly, it tailors these standard treatments as well as all complementary information's to the specific needs of each patient, based on the medical information available in their computerized records. This personalized plan may be modified and adjusted at any time including therefore more and more real details and insights for each patient (delay of chemotherapy, dates of CT scan....). This would help patients and caregivers to better understand the different phases of the treatment and, thus, improve patient follow-up and information at every step of patient management. This tool is currently being tested at the Centre Léon Bérard.

Case Management↗
PubMedDate not supplied

Approaching the millennium: perinatal problems and software solutions.

Strategic planning for rational development of perinatal computing capabilities for the year 2000 should be driven by anticipated trends in (1) the health care business, (2) computer technology and (3) medicine, as well as (4) the needs of perinatal practitioners. In the USA, health care is the fastest growing segment of the economy. This will produce increasing attention from hardware and software developers, and vendors, and will lead to a proliferation of computing platforms, operating systems and specific medical application software. Desktop computers, already capable of 20 million instructions per second (MIPS) with massive storage capacities, will continue to evolve and fall in price. Increasingly, perinatologists will develop software packages to facilitate patient care in their own environments. All of these trends will lead to severe fragmentation in medical computing. Simultaneously, however, the need for integrated institutional computer-based data access for quality assurance and fiscal and operations management will increase. Perinatal care will be more regionalized, complex and rigorous with new clinical trial- and effectiveness research-based interventions, as well as molecular diagnosis and therapy. To practice appropriately, clinicians will need to be familiar with computer capabilities. Having been exposed to computer-aided instruction (CAI) at the undergraduate and postgraduate levels, they will except on-line access to detailed and accurate patient information with linkage to laboratory, radiology and other medical databases, as well as to reference databases, such as Medlines and the Oxford Database of Perinatal Trials. Artificial intelligence (AI) software may support perinatal decision making; computerized professional and facility billing will be available.

Forecasting↗
PubMed2003

Construction of patient-specific surface models from MR images: application to bioelectromagnetism.

Patient-specific geometric models are needed in many engineering problems. This work reports a novel software tool developed to construct individualized triangulated surface models from MR images. The program consists of three main parts: segmentation, triangulation and registration. The software tool was developed under the UNIX operating system. The application area demonstrated in this work is bioelectromagnetism but the program can be used as well in other engineering problems. The tool has been successfully applied in numerous cases, both for the thorax and the head.

Algorithms↗
PubMed1994

Native American youths and cancer risk reduction. Effects of software intervention.

PURPOSE: Toward developing attractive and effective means to reduce cancer risks faced by Native American people, this study developed and tested interactive computer software to improve dietary choices and prevent tobacco use among Native American adolescents. METHODS: Based on a legend of the Seneca Nation, a cancer prevention lesson was developed and programmed for software. A sample of 368 Native American adolescents were divided randomly into intervention and control arms. Youths in both arms were pre-tested, youths in the intervention arm interacted with the software, and all youths were post-tested. Pre-test and post-test measures covered information and attitudes about cancer risks from dietary practices and tobacco use. RESULTS: Pre-test scores differed between the two arms on youths' age and on one outcome variable. Relative to their counterparts in the control arm, youths in the intervention arm increased their post-test scores on 8 of 12 outcome measurement variables. Process data gathered during intervention delivery indicated that nearly all youths were involved with the interactive software and lesson. CONCLUSION: Interactive computer software holds promise for delivering cancer risk reduction intervention aimed at modifying dietary habits and preventing tobacco use among Native American youth.

Adolescent↗
PubMed2004

Detection of chromosomal regions showing differential gene expression in human skeletal muscle and in alveolar rhabdomyosarcoma.

BACKGROUND: Rhabdomyosarcoma is a relatively common tumour of the soft tissue, probably due to regulatory disruption of growth and differentiation of skeletal muscle stem cells. Identification of genes differentially expressed in normal skeletal muscle and in rhabdomyosarcoma may help in understanding mechanisms of tumour development, in discovering diagnostic and prognostic markers and in identifying novel targets for drug therapy. RESULTS: A Perl-code web client was developed to automatically obtain genome map positions of large sets of genes. The software, based on automatic search on Human Genome Browser by sequence alignment, only requires availability of a single transcribed sequence for each gene. In this way, we obtained tissue-specific chromosomal maps of genes expressed in rhabdomyosarcoma or skeletal muscle. Subsequently, Perl software was developed to calculate gene density along chromosomes, by using a sliding window. Thirty-three chromosomal regions harbouring genes mostly expressed in rhabdomyosarcoma were identified. Similarly, 48 chromosomal regions were detected including genes possibly related to function of differentiated skeletal muscle, but silenced in rhabdomyosarcoma. CONCLUSION: In this study we developed a method and the associated software for the comparative analysis of genomic expression in tissues and we identified chromosomal segments showing differential gene expression in human skeletal muscle and in alveolar rhabdomyosarcoma, appearing as candidate regions for harbouring genes involved in origin of alveolar rhabdomyosarcoma representing possible targets for drug treatment and/or development of tumor markers.

Chromosome Mapping↗