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At least 307 records · Page 17Linked to original sources

PubMed2002

Software design for analysis of multichannel intracardial and body surface electrocardiograms.

Analysis of multichannel ECG recordings (body surface maps (BSMs) and intracardial maps) requires special software. We created a software package and a user interface on top of a commercial data analysis package (MATLAB) by a combination of high-level and low-level programming. Our software was created to satisfy the needs of a diverse group of researchers. It can handle a large variety of recording configurations. It allows for interactive usage through a fast and robust user interface, and batch processing for the analysis of large amounts of data. The package is user-extensible, includes routines for both common and experimental data processing tasks, and works on several computer platforms. The source code is made intelligible using software for structured documentation and is available to the users. The package is currently used by more than ten research groups analysing ECG data worldwide.

Algorithms↗

PubMed2003

Telemonitoring of patients at home: a software agent approach.

To address the issue of the increasing social, economical and medical needs of maintaining at home people in loss of autonomy while preserving privacy and quality of life, the authors present a software agent based telemonitoring and alarm raising system. The article describes the overall architecture, the various components of the model, and the methodology that has been used. It specifically addresses the issue of reflecting in the object oriented model of the system various dimensions including: the physical world of in-home bio-signal sensors, the numerical world of software agents and Internet-related technologies, and the medical and social worlds of patients, physicians and caregivers. In the model, the main stream of information goes from the biophysical world of patients at home to the socio-medical world of carers through a chain of devices including in-home sensors, local area network, home computer, remote server, and carers' computers. Each device hosts software agents with different levels of knowledge and complexity. Internet and Java technologies provide the building blocks of the designed telemonitoring software. Laboratory experiments have been realized using a fully equipped 'smart' demonstration home for telecare. The study takes place into a more general research project on 'smart' homes for telecare conducted at the Hospital Centre of Grenoble, France.

Computer Security↗

PubMed2004

Design and implementation of software for assembly and browsing of 3D brain atlases.

Visualization software for three dimensional digital brain atlases present many challenges in design and implementation. These challenges include the design of an effective human interface, management of large data sets, display speed when slicing the data set for viewing/browsing, and the display of delineated volumes of interest (VOI). We present a software design, implementation and storage architecture that addresses these issues, allowing the user to navigate through a reconstructed volume quickly and smoothly, with an easy-to-use human interface. The software (macostat, for use with Macintosh OS) allows the user to rapidly display slices of the digital atlas at any arbitrary slicing angle, complete with delineated VOIs. The VOIs can be assigned colors of the user's choosing. The entire atlas, or selected portions, may be resliced with slices stored as individual image files, complete with delineations. These delineations may be transferred to corresponding sections of experimental materials using our analysis program (brain). The software may be obtained from the laboratory's web site: http://www.neuroterrain.org

Brain↗

PubMedDate not supplied

3DVIEWNIX-AVS: a software package for the separate visualization of arteries and veins in CE-MRA images.

Our earlier study developed a computerized method, based on fuzzy connected object delineation principles and algorithms, for artery and vein separation in contrast enhanced Magnetic Resonance Angiography (CE-MRA) images. This paper reports its current development-a software package-for routine clinical use. The software package, termed 3DVIEWNIX-AVS, consists of the following major operational parts: (1) converting data from DICOM3 to 3DVIEWNIX format, (2) previewing slices and creating VOI and MIP Shell, (3) segmenting vessel, (4) separating artery and vein, (5) shell rendering vascular structures and creating animations. This package has been applied to EPIX Medical Inc's CE-MRA data (AngioMark MS-325). One hundred and thirty-five original CE-MRA data sets (of 52 patients) from 6 hospitals have been processed. In all case studies, unified parameter settings produce correct artery-vein separation. The current package is running on a Pentium PC under Linux and the total computation time per study is about 3 min. The strengths of this software package are (1) minimal user interaction, (2) minimal anatomic knowledge requirements on human vascular system, (3) clinically required speed, (4) free entry to any operational stages, (5) reproducible, reliable, high quality of results, and (6) cost effective computer implementation. To date, it seems to be the only software package (using an image processing approach) available for artery and vein separation of the human vascular system for routine use in a clinical setting.

Algorithms↗

PubMed2006

Optimizing the use of open-source software applications in drug discovery.

Drug discovery is a time consuming and costly process. Recently, a trend towards the use of in silico computational chemistry and molecular modeling for computer-aided drug design has gained significant momentum. This review investigates the application of free and/or open-source software in the drug discovery process. Among the reviewed software programs are applications programmed in JAVA, Perl and Python, as well as resources including software libraries. These programs might be useful for cheminformatics approaches to drug discovery, including QSAR studies, energy minimization and docking studies in drug design endeavors. Furthermore, this review explores options for integrating available computer modeling open-source software applications in drug discovery programs.

Computer-Aided Design↗

PubMed2001

Towards integration of clinical decision support in commercial hospital information systems using distributed, reusable software and knowledge components.

PROBLEM: Clinicians' acceptance of clinical decision support depends on its workflow-oriented, context-sensitive accessibility and availability at the point of care, integrated into the Electronic Patient Record (EPR). Commercially available Hospital Information Systems (HIS) often focus on administrative tasks and mostly do not provide additional knowledge based functionality. Their traditionally monolithic and closed software architecture encumbers integration of and interaction with external software modules. Our aim was to develop methods and interfaces to integrate knowledge sources into two different commercial hospital information systems to provide the best decision support possible within the context of available patient data. METHODS: An existing, proven standalone scoring system for acute abdominal pain was supplemented by a communication interface. In both HIS we defined data entry forms and developed individual and reusable mechanisms for data exchange with external software modules. We designed an additional knowledge support frontend which controls data exchange between HIS and the knowledge modules. Finally, we added guidelines and algorithms to the knowledge library. RESULTS: Despite some major drawbacks which resulted mainly from the HIS' closed software architectures we showed exemplary, how external knowledge support can be integrated almost seamlessly into different commercial HIS. This paper describes the prototypical design and current implementation and discusses our experiences.

Abdominal Pain↗

PubMed2002

Image processing and enhancement provided by commercial dental software programs.

OBJECTIVES: To identify and analyse methods/algorithms for image processing provided by various commercial software programs used in direct digital dental imaging and to map them onto a standardized nomenclature. METHODS: Twelve programs presented at the 28th International Dental-Show, March, 2001, Cologne, Germany and the Emago advanced software were included in this study. An artificial test image, comprised of gray scale ramps, step wedges, fields with Gaussian-distributed noise, and salt and pepper noise, was synthesized and imported to all programs to classify algorithms for display; linear, non-linear and histogram-based point processing; pseudo-coloration; linear and non-linear spatial filtering; frequency domain filtering; measurements; image analysis; and annotations. RESULTS: The 13 programs were found to possess a great variety of image processing and enhancement facilities. All programs offer gray-scale image display with interactive brightness and contrast adjustment and gray-scale inversion as well as calibration and length measurements. While Emago enables arbitrary spatial filtering with user-defined masks up to 7x7 pixels in size, most programs sparsely include filters and tools for image analysis and comparison. Moreover, the naming and implementation of provided functions differ. Some functions inappropriately use standardized image processing terms to describe their operations. CONCLUSIONS: Image processing and enhancement functions are rarely incorporated in commercial software for direct digital imaging in dental radiology. Until now, comparison of software was limited by the arbitrary naming used in each system. Standardized terminology and increased functionality of image processing should be offered to the dental profession.

Algorithms↗

PubMed1998

The role of computer software in the analysis of qualitative data: efficient clerk, research assistant or Trojan horse?

In the last 15 years there has been a proliferation of computer software packages designed to facilitate qualitative data analysis. The programs can be classified, according to function, into a number of broad categories such as: text retrieval; text base management; coding and retrieval; code-based theory building; and conceptual-network building. The programs vary enormously in the extent to which they can facilitate the diverse analytical processes involved. The decision to use computer software to aid analysis in a particular project may be influenced by a number of factors, such as the nature of the data and the researcher's preferred approach to data analysis which will have as its basis certain epistemological and ontological assumptions. This paper illustrates the way in which a package called NUD.IST facilitated analysis where grounded theory methods of data analysis were also extensively used. While highlighting the many benefits that ensued, the paper illustrates the limitations of such programs. The purpose of this paper is to encourage researchers contemplating the use of computer software to consider carefully the possible consequences of their decision and to be aware that the use of such programs can alter the nature of the analytical process in unexpected and perhaps unwanted ways. The role of the Computer Assisted Qualitative Data Analysis (CAQDAS) Networking Project, in providing up-to-date information and support for researchers contemplating the use of software, is discussed.

Humans↗

PubMed2000

Use of free-hand three-dimensional ultrasound software in the study of the fetal heart.

OBJECTIVE: To propose a new approach to the study of the fetal heart using free-hand three-dimensional (3D) ultrasound software. METHODS: We studied a total of 28 fetuses, of which 26 were normal and two were known to have heart pathology. In all of them a B-mode scan was performed. After obtaining a four-chamber view, and keeping the transducer in the same position, the free-hand 3D-View software was activated. A sequence of frames was stored. Additional information was recorded looking from the four-chamber view towards the outflow tract, and also adding color Doppler. RESULTS: We obtained a multiplanar display of one B-mode and two perpendicular M-modes in all cases studied. In this multiplanar mode, Y and X axes represent distance and Z axis represents time. We were able to obtain M-modes and a variation of color-M-mode in any desired position. Moving the information along the Z axis, a frame sequence of the B-mode was obtained. Using this approach we observed one case of fetal supraventricular extrasystoles and other having an interventricular septum defect. CONCLUSIONS: This modality gives a new perspective of fetal heart scanning using the free-hand 3D-View software, in which there is benefit from many of the advantages of the 3D software, although the power of this procedure must be improved.

Fetal Diseases↗

PubMed2004

Analysis of mice tumor models using dynamic MRI data and a dedicated software platform*.

PURPOSE: To implement a software platform (DynaVision) dedicated to analyze data from functional imaging of tumors with different mathematical approaches, and to test the software platform in pancreatic carcinoma xenografts in mice with severe combined immunodeficiency disease (SCID). MATERIALS AND METHODS: A software program was developed for extraction and visualization of tissue perfusion parameters from dynamic contrast-enhanced images. This includes regional parameter calculation from enhancement curves, parametric images (e. g., blood flow), animation, 3D visualization, two-compartment modeling, a mode for comparing different datasets (e. g., therapy monitoring), and motion correction. We analyzed xenograft tumors from two pancreatic carcinoma cell lines (BxPC3 and ASPC1) implanted in 14 SCID mice after injection of Gd-DTPA into the tail vein. These data were correlated with histopathological findings. RESULTS: Image analysis was completed in approximately 15 minutes per data set. The possibility of drawing and editing ROIs within the whole data set makes it easy to obtain quantitative data from the intensity-time curves. In one animal, motion artifacts reduced the image quality to a greater extent but data analysis was still possible after motion correction. Dynamic MRI of mice tumor models revealed a highly heterogeneous distribution of the contrast-enhancement curves and derived parameters, which correlated with differences in histopathology. ASPC1 tumors showed a more hypervascular type of curves with faster and higher signal enhancement rate (wash-in) and a faster signal decrease (wash-out). BXPC3 tumors showed a more hypovascular type with slower wash-in and wash-out. This correlated with the biological properties of the tumors. CONCLUSION: With the described software, it was possible to analyze tissue perfusion parameters in small xenograft tumor models in mice. Our data correlated with histopathological data, and the qualitative and quantitative perfusion parameters could distinguish two tumor entities with different growth characteristics.

Animals↗

PubMed2005

[Eva-Reha: a computer software supporting outcome-based quality management in medical rehabilitation].

PURPOSE: Development of a computer software for supporting medical quallity management by documenting progression and results of medical rehabilitation in neurologic, orthopaedic, and geriatric patients. METHODS: The software "Eva-Reha" (Evaluation of Medical Rehabilitation) was generated using C ++ in a client-server structure with Interbase being the underlying relational database management system. The software is network-compatible and runs under Windows NT and Windows 2000. RESULTS: "Eva-Reha", developed by the "Medizinischer Dienst der Krankenversicherung Rheinland-Pfalz (MDK RLP)" supports quality management systems in medical rehabilitation. Since 2003 the MDK RLP provides neurologic and geriatric rehabilitation centres with the software free of charge. With the help of "Eva-Reha" progression and results of medical rehabilitation can be displayed metrically, thus facilitating individual rehabilitation planning and supporting motivation of the rehabilitation team. Therapeutic strategies can be evaluated for different ICD-10-diagnoses or impairment groups. Moreover, "Eva-Reha" provides valuable data for administration and controlling purposes, e. g. age structure, case mix, impairment on admission and medical as well as rehabilitative procedures. The system generates a request for extension in a set form which facilitates communication between rehabilitation centres and sponsors.

Aged↗

PubMed2005

[Assessment of two different software solutions for the evaluation of CT colonography].

PURPOSE: To compare a commercial CT colonography software ("Colonography", Siemens, Forchheim) with a non-commercial post-processing system ("Colotux", Department of Informatics). MATERIAL AND METHODS: Identical data sets of 10 patients, who underwent an ultra-low-dose multi-detector CT colonography (ULD-MDCTC) (4x1 mm collimation, 8 mm pitch, 120 kVp, 10 mAs) were analyzed retrospectively. Assessment was performed using both software solutions by two resident radiologists, who did not have any experience with any colonography software tool before and who did not know the clinical symptoms of the patients or the results of the conventional colonoscopy. Both systems were analyzed using several subjective quality criteria including workflow, handling, image quality, endoluminal navigation and analysis of lesions with grading on a 5-point-scale. Results concerning polyps were compared between the two systems as well as with conventional colonoscopy. RESULTS: Both colonography systems detected the same number of polyps. Although both showed some advantages for single criteria, no relevant difference was noted in general for subjective assessment. The time for calculation of three dimensional interactive volumes was three times longer for "Colotux" compared to "Colonography." Linux-based "Colotux" showed a trend towards better subjective image quality and easier measurement of polyp size. An intuitive desktop and "Syngo"-workflow integration were advantages of "Colonography." CONCLUSION: The analysis of CT colonographies (4-detector-row-CT-scanner, ultra low dose technique, supine position) can adequately be achieved by both software solutions. There was no significant subjective or objective difference of quality between a "stand-alone" individual system and a commercial workflow-integrated solution. A relevant factor for decision between the two systems may be the difference in time needed for the 3D volume calculation, especially in institutes with a high frequency of examinations.

Aged↗

PubMedDate not supplied

Lessons from a randomized controlled trial designed to evaluate computer decision support software to improve the management of asthma.

PRIMARY OBJECTIVE: To investigate whether computer decision support software used in the management of patients with asthma improves clinical outcomes. RESEARCH DESIGN: Randomized controlled trial with practices each reporting on 30 patients with asthma over a 6 month period. METHODS AND PROCEDURES: 447 patients were randomly selected from practice asthma registers managed by 17 general practices from throughout the UK. Intervention practices used the software during consultations with these patients throughout the study while control practices did not. MAIN OUTCOMES AND RESULTS: Practice consultations, acute exacerbations of asthma, hospital contacts, symptoms on assessment and medication use. A smaller proportion of patients within the intervention group initiated practice consultations for their asthma: 34 (22%) vs 111 (34%), odds ratio (OR) = 0.59, 95% confidence interval (CI) (0.37-0.95); and suffered acute asthma exacerbations: 12 (8%) vs 57 (17%), OR = 0.43, 95% CI = 0.21-0.85 six months after the introduction of the computer decision support software. There were no discernable differences in reported symptoms, maintenance prescribing or use of hospital services between the two groups. CONCLUSION: The use of computer decision support software that implements guidelines during patient consultations may improve clinical outcomes for patients with asthma.

Asthma↗

PubMed1999

staffTRAK-TB: software for surveillance of tuberculosis infection in healthcare workers.

The Centers for Disease Control and Prevention (CDC) recommends periodic tuberculin skin testing of healthcare workers with potential exposure to Mycobacterium tuberculosis. However, many healthcare facilities have neither a system to identify workers due for their skin test nor a means of analyzing aggregate data. To illustrate some of the complexities involved in tuberculin skin test (TST) tracking and analysis, and how these might be addressed, this report describes a software package called staffTRAK-TB, developed by the CDC to facilitate surveillance of tuberculosis infection in healthcare workers. staffTRAK-TB records data for each healthcare worker, including demographic information, occupation, work location, multiple TST results, and results of evaluations to determine if clinically active tuberculosis is present. Programmed reports include lists of workers due and overdue for skin tests, and skin test conversion rates by occupation or worksite. Standardization of types of occupations and locations allows data from multiple facilities to be aggregated and compared. Data transfer to the CDC can be performed via floppy diskettes. staffTRAK-TB illustrates important issues in software structure, standardization of occupation and work-location information, relevant data items, and reports and analyses that would be useful in practice. Developing software that adequately addresses the epidemiological issues is complex, and the lessons learned may serve as a model for hospital epidemiologists, infection control personnel, occupational health personnel, and computer programmers considering software development in this area or trying to optimize their facility's TST surveillance.

Adult↗

PubMed2002

Why are people downloading the freeware AIDA diabetes computing software program: a pilot study.

The purpose of this paper is to report a pilot survey about why people are downloading the AIDA interactive educational diabetes simulator. AIDA is a diabetes computer program that permits the interactive simulation of plasma insulin and blood glucose profiles for teaching, demonstration, and self-learning purposes. It has been made freely available, without charge, on the Internet as a noncommercial contribution to continuing diabetes education. Since its launch in 1996 well over 200,000 visits have been logged at the main AIDA Website--www.2aida.org--and over 40,000 copies of the AIDA program have been downloaded free-of-charge. This article documents a pilot survey of comments left by Website visitors while they were downloading the AIDA software, before they had a chance to actually use the program. The overall paradigm adopted for this study has endeavored to establish why people are resorting to the Internet to obtain diabetes information. Specific intended goals of the study were: (1) to demonstrate ongoing use of the World Wide Web for surveying diabetes software users by obtaining their free-text comments; (2) to identify what sort of things people were planning to do with the AIDA software simulator; and (3) to more generally gain some insight into why people are turning to the Web for healthcare-related information. The Internet-based survey methodology was found to be robust and reliable. Over an 8-month period (from February 2, 2001 to October 1, 2001) 642 responses were received. During the corresponding period 2,248 actual visits were made to the Website survey page--giving a response rate to this pilot study of 28.6%. Responses were received from participants in over 56 countries--although over half of these (n = 343; 53.4%) originated from the United States and United Kingdom. Two hundred forty-four responses (38.0%) were received from patients with diabetes, and 73 (11.4%) from relatives of patients, with fewer responses from doctors, students, diabetes educators, nurses, pharmacists, and other end users. This pilot survey has confirmed the feasibility of using the Internet to obtain free-text comments, at no real cost, from a large number of medical software downloaders/users. The survey has also offered a valuable insight into why members of the public are turning to the Internet for medical information. Furthermore it has provided useful information about why people are actually downloading the AIDA interactive educational "virtual diabetes patient" simulator.

Computer-Assisted Instruction↗

PubMed2003

Why people download the freeware AIDA v4.3a diabetes software program: a proof-of-concept semi-automated analysis.

AIDA is a diabetes-computing program freely available at www.2aida.org on the Web. The software is intended to serve as an educational support tool and can be used by anyone who has an interest in diabetes, whether they be patients, relatives, health-care professionals, or students. In previous "Diabetes Information Technology & WebWatch" columns various indicators of usage of the AIDA program have been reviewed, and various comments from users of the software have been documented. The purpose of this column is to overview a proof-of-concept semi-automated analysis about why people are downloading the latest version of the AIDA educational diabetes program. AIDA permits the interactive simulation of plasma insulin and blood glucose profiles for teaching, demonstration, self-learning, and research purposes. It has been made freely available, without charge, on the Internet as a noncommercial contribution to continuing diabetes education. Since its launch in 1996 over 300,000 visits have been logged at the main AIDA Website-www.2aida.org-and over 60,000 copies of the AIDA program have been downloaded free-of-charge. This column documents the results of a semi-automated analysis of comments left by Website visitors while they were downloading the AIDA software, before they had a chance to use the program. The Internet-based survey methodology and semi-automated analysis were both found to be robust and reliable. Over a 5-month period (from October 3, 2001 to February 28, 2002) 400 responses were received. During the corresponding period 1,770 actual visits were made to the Website survey page-giving a response rate to this proof-of-concept study of 22.6%. Responses were received from participants in over 54 countries-with nearly half of these (n = 194; 48.5%) originating from the United States, United Kingdom, and Canada; 208 responses (52.0%) were received from patients with diabetes, 50 (12.5%) from doctors, 49 (12.3%) from relatives of patients, with fewer responses from students, diabetes educators, nurses, pharmacists, and other end users. The semi-automated analysis adopted for this study has re-affirmed the feasibility of using the Internet to obtain free-text comments, at no real cost, from a substantial number of medical software downloaders/users. The survey has also offered some insight into why members of the public continue to turn to the Internet for medical information. Furthermore it has provided useful information about why people are actually downloading the AIDA v4.3a interactive educational "virtual diabetes patient" simulator.

Automation↗

PubMed1997

Software for the analysis of DNA sequence elements of transcription.

The detection of transcription control elements in DNA sequences became both more important and more complicated by the completion of the first full genome sequencing projects. Rapid evaluation of potential regulatory elements in large amounts of sequence data requires specific methods preferably available as user-friendly computer programs. However, many more algorithms and methods have been published than programs are available, creating problems for scientists who try to select an appropriate method for their needs from the literature. The Internet provides a worldwide and relatively easy access to computer software if the user knows where to look. One of the major problems remaining is how to find the appropriate software. We have compiled a guide detailing where software is available and what is to be expected in terms of interface and data compatibility with other programs. We also show results obtained with each program for several examples. The summarized features of each program should allow scientists to select quickly the method of their choice and inform them where to download the software.

Algorithms↗

PubMed2006

arrayQCplot: software for checking the quality of microarray data.

UNLABELLED: arrayQCplot is a software for the exploratory analysis of microarray data. This software focuses on quality control and generates newly developed plots for quality and reproducibility checks. It is developed using R and provides a user-friendly graphical interface for graphics and statistical analysis. Therefore, novice users will find arrayQCplot as an easy-to-use software for checking the quality of their data by a simple mouse click. AVAILABILITY: arrayQCplot software is available from Bioconductor at http://www.bioconductor.org. A more detailed manual is available at http://bibs.snu.ac.kr/software/arrayQCplot CONTACT: tspark@stats.snu.ac.kr.

Algorithms↗