SEARCH · Search PubMed

Results for “software tools”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 793 records · Page 44Linked to original sources

PubMed2006

Comparison between color Doppler cineloop- and conventional spectral Doppler-derived maximum velocity and flow in the umbilical vein.

OBJECTIVE: To compare the umbilical venous flow velocity derived from color Doppler cineloop recordings with that derived from conventional spectral Doppler in normal pregnancies. METHOD: In 18 uncomplicated pregnancies between 19 and 39 weeks' gestation, color Doppler was used to find the maximum velocity in the cross-sectional vessel area of a free-floating loop of the umbilical vein. The maximum velocity was determined using the software tool HDI_Lab (Philips Medical Systems) after tracing the vessel area of interest. Conventional spectral Doppler was then used to determine the maximum velocity with the High-Q machine option. The cross-sectional area of the umbilical vein was determined using B-mode imaging and was subsequently used to determine the umbilical volume flow from both Doppler methods. Assuming a parabolic flow profile in the umbilical vein, the mean velocity is equal to half the maximum velocity. The fetal weight was estimated from fetal biometry using the four-parameter Hadlock formula. RESULTS: Maximum velocity was significantly (P = 0.003) higher with color Doppler cineloop (14.3 +/- 2.5 cm/s) compared with spectral Doppler (12.7 +/- 3.2 cm/s). Therefore, using the same cross-sectional area for both methods, the umbilical blood flow was significantly higher (P = 0.001) with color Doppler cineloop (127.9 +/- 59.0 mL/min) than it was with spectral Doppler (112.8 +/- 54.1 mL/min). The umbilical blood flow expressed as volume flow per kg fetal weight was significantly (P = 0.01) higher with color Doppler cineloop (126.0 +/- 57.0 mL/min/kg) than it was with spectral Doppler (115.0 +/- 53.0 mL/min/kg). CONCLUSIONS: Umbilical venous flow velocity derived from color Doppler cineloops is approximately 10% higher than that derived from spectral Doppler-derived velocity. The reduced angle dependence of the color Doppler cineloop technique and the large sampling area of the cross-sectional vessel should allow better determination of the correct maximum velocity in the umbilical vein.

Blood Flow Velocity↗

PubMed1997

The mouse gene expression database GXD

The gene expression database (GXD) is being developed to store and integrate expression information for mouse development. GXD addresses many issues that apply to gene expression databases in general, and its data structures and supporting software tools are generalized in design and thus readily adaptable to other life stages and species. Integration of GXD with the mouse genome database (MGD) and interconnections with other relevant databases will place the gene expression data into the larger biological and analytical context. Here, we describe the design and implementation of GXD and illustrate, in particular, the gene expression annotator, an electronic system for submitting expression data to the database.Copyright 1997 Academic Press Limited Copyright 1997Academic Press Limited

Journal Article↗

PubMed2005

The BrainIT Group: concept and current status 2004.

Brain Injuries↗

PubMed1998

A DICOM document-oriented approach to PACS infrastructure.

The need for long-term storage requires the future migration of image data from a PACS to its successor system. This paper considers the cost of such migration It is proposed that storage of data as "documents" in DICOM Part 10 formats on industry-standard media could reduce the time and cost of data migration relative to on-line DICOM transfer. The relation to present efforts in developing document-oriented electronic patient records is discussed. DICOM Part 10 files are found to be a sufficient representation of image documents, but additional software tools will be needed to reach its full potential. There is a significant cost benefit of the document storage method, but it is one of many factors which must be balanced in the selection of a PACS.

Costs and Cost Analysis↗

PubMed1993

A modular method for evaluating the performance of picture archiving and communication systems.

Modeling can be used to predict the performance of picture archiving and communication system (PACS) configurations under various load conditions at an early design stage. This is important because choices made early in the design of a system can have a significant impact on the performance of the resulting implementation. Because PACS consist of many types of components, it is important to do such evaluations in a modular manner, so that alternative configurations and designs can be easily investigated. Stochastic activity networks (SANs) and reduced base model construction methods can aid in doing this. SANs are a model type particularly suited to the evaluation of systems in which several activities may be in progress concurrently, and each activity may affect the others through the results of its completion. Together with SANs, reduced base model construction methods provide a means to build highly modular models, in which models of particular components can be easily reused. In this article, we investigate the use of SANs and reduced base model construction techniques in evaluating PACS. Construction and solution of the models is done using UltraSAN, a graphic-oriented software tool for model specification, analysis, and simulation. The method is illustrated via the evaluation of a realistically sized PACS for a typical United States hospital of 300 to 400 beds, and the derivation of system response times and component utilizations.

Models, Theoretical↗

PubMed1997

[Data collection in anesthesia. Experiences with the inauguration of a new information system].

UNLABELLED: In many institutions information systems are used to process off-line anaesthesia data for invoices, statistical purposes, and quality assurance. Information systems are also increasingly being used to improve process control in order to reduce costs. Most of today's systems were created when information technology and working processes in anaesthesia were very different from those in use today. Thus, many institutions must now replace their computer systems but are probably not aware of how complex this change will be. Modern information systems mostly use client-server architecture and relational data bases. Substituting an old system with a new one is frequently a greater task than designing a system from scratch. This article gives the conclusions drawn from the experience obtained when a large departmental computer system is redesigned in an university hospital. METHODS: The new system was based on a client-server architecture and was developed by an external company without preceding conceptual analysis. Modules for patient, anaesthesia, surgical, and pain-service data were included. Data were analysed using a separate statistical package (RS/1 from Bolt Beranek), taking advantage of its powerful precompiled procedures. RESULTS: Development and introduction of the new system took much more time and effort than expected despite the use of modern software tools. Introduction of the new program required intensive user training despite the choice of modem graphic screen layouts. Automatic data-reading systems could not be used, as too many faults occurred and the effort for the user was too high. However, after the initial problems were solved the system turned out to be a powerful tool for quality control (both process and outcome quality), billing, and scheduling. The statistical analysis of the data resulted in meaningful and relevant conclusions. CONCLUSIONS: Before creating a new information system, the working processes have to be analysed and, if possible, made more efficient; a detailed programme specification must then be made. A servicing and maintenance contract should be drawn up before the order is given to a company. Time periods of equal duration have to be scheduled for defining, writing, testing and introducing the program. Modern client-server systems with relational data bases are by no means simpler to establish and maintain than previous mainframe systems with hierarchical data bases, and thus, experienced computer specialists need to be close at hand. We recommend collecting data only once for both statistics and quality control. To verify data quality, a system of random spot-sampling has to be established. Despite the large investments needed to build up such a system, we consider it a powerful tool for helping to solve the difficult daily problems of managing a surgical and anaesthesia unit.

Anesthesia↗

PubMedDate not supplied

Multidetector CT and virtual endoscopy in the evaluation of the esophagus.

In this prospective study, we assessed the diagnostic capabilities of multidetector computed tomography (CT) in various esophageal pathologic conditions. Thirty-three patients underwent a multidetector CT study after esophageal distention by means of effervescent powder administered after induction of pharmacologic esophageal hypotonia. All acquired images were post-processed with two- and three-dimensional software tools. The CT data were compared with the results of conventional radiology (33), endoscopy (28), endoscopy ultrasonography (14), or surgery (14). Follow-up ranged between 4 and 15 months. Esophageal distention in the upper and middle thirds was classified as "good" in 32 of 33 cases (97%); in the lower third, esophageal distention was "good" in 21 of 33 cases (64%). Final diagnoses were leiomyoma (six cases), squamous cell carcinoma (six), adenocarcinoma (four), esophageal infiltration by thyroid cancer (two), benign polyposis (two), chronic esophagitis (five), post-sclerotherapy stenosis (one), no abnormalities (seven). When good distention was achieved, the thickness of unaffected esophageal wall was less than 3 mm (range, 1.5-2.4 mm; mean, 1.9 mm). Pathologic wall thickening was observed in 25 of 33 cases (76%), with values ranging between 3.6 and 36 mm (mean, 9.6 mm). Spiral CT demonstrated 21 true positive cases, and seven true negative cases. There were four false negative cases and one false positive case. Sensitivity was 84%, specificity was 87%, diagnostic accuracy was 85%, positive predictive value was 95%, and negative predictive value was 64%. Evaluation of the esophagus with multidetector CT is a promising technique and easy to use, allowing panoramic exploration, virtual endoluminal visualization, accurate longitudinal and axial evaluations, and simultaneous evaluation of T and N parameters.

Esophageal Diseases↗

PubMed2002

The seated man: geometry acquisition and three-dimensional reconstruction.

A three-dimensional (3D) virtual human body in seated position can be used in a wide range of applications such as basic or clinical research. A male cadaver placed in the driving position in a car cockpit was frozen. Strictly parallel 5 mm thickness serial sections were then performed. Both sides of the slices were photographed, scanned and analyzed by anatomists with software tools, in order to produce accurate contours of the identified anatomical structures. A 3D reconstruction of organs, based on the marching cubes method, was achieved except for thin structures. This allowed an anatomical validation of these reconstructed elements. The result of this work is a complete geometrical database of a seated human body in the driving position including skin, all bones, internal organs and main muscle groups.

Aged↗

PubMed2004

Study of carpal bone morphology and position in three dimensions by image analysis from computed tomography scans of the wrist.

The morphology and positioning of the carpal bones were studied in three dimensions in 18 normal adults on computed tomography (CT) scans of the wrist. The digital data from each CT scan were processed to extract the carpal bones and to automatically characterize their geometry (geometric centroid, principal axes of inertia) using specific software tools. Biometric and angular parameters were defined for this purpose, and most of these parameters showed a normal distribution. The mean distance between the geometric centroid of the capitate and that of the triquetrum, expressed as a relationship to the length of the first principal axis of inertia of the capitate, was found to be the greatest (157.6%+/-8.4%), whereas the smallest mean distance was between the hamate and triquetrum (91.4%+/-7.3%). In the sagittal plane, the first principal axis of inertia of the bones of the first carpal row projected in front of the vertical axis of the orthogonal reference system, whereas the first principal axis of the capitate projected behind it. Measurements using this methodology are far more numerous than those from standard plain radiographs and have the additional advantage of being independent of the examiner. Future investigations on normal wrists should provide a normal range for each quantitative parameter, and comparative study of normal and pathologic wrist measurements should help to define the most relevant parameters for specific traumatic pathologies of the wrist.

Adult↗

PubMed2005

Inter- and intraobserver assessment of periacetabular osteodensitometry after cemented and uncemented total hip arthroplasty using computed tomography.

INTRODUCTION: This study was initiated to evaluate the reproducibility of a novel method for measuring the periacetabular bone density after insertion of cemented and uncemented acetabular cups using CT in vivo. MATERIALS AND METHODS: CT scans were obtained from 20 patients after cemented polyethylene cup implantation (ZCA, Zimmer, USA) and 20 patients after uncemented titanium alloy cup fixation (Cerafit, Ceraver, France). A manual segmentation of cancellous and cortical pelvic bone ventral, dorsal and cranial to the cup was undertaken. Values are given in Hounsfield units. Inter- and intraobserver studies were conducted using a special analysis software tool. To define the reproducibility of the method, all measurements were evaluated according to Bland and Altman. RESULTS: For both cemented and uncemented acetabular cups, reproducibility of bone density measurement for cortical and cancellous bone cranial, ventral and dorsal to the cup was high. There was no significant difference between the intraobsever study (two repeated measurements) and the interobserver study (two investigators), indicating the reproducibility of the method independent of the investigator. CONCLUSION: In conclusion, the periacetabular bone density measurement as conducted in this CT study is a new reproducible method for in vivo evaluation of cortical and cancellous pelvic bone after cemented and uncemented acetabular cup implantation. In vivo CT measurements will allow a thorough assessment of periacetabular stress-shielding phenomena.

Acetabulum↗

PubMed2004

Multiple transcripts of a gene for a leucine-rich repeat receptor kinase from morning glory (Ipomoea nil) originate from different TATA boxes in a tissue-specific manner.

TATA boxes are the most common regulatory elements found in the promoters of eukaryotic genes because they are associated with basal transcription initiation by RNA polymerase II. Often only a single TATA element is found in a given promoter, and tissue-, stage- and/or stimulus-specific expression occurs because the TATA box is associated with other cis -acting elements that enhance or repress transcription. We used software tools for gene analysis to assist in locating potential TATA box(es) in an AT-rich region of the promoter of a gene, inrpk1, which codes for a leucine-rich receptor protein kinase in morning glory (Ipomoea nil). Through the use of RT-PCR and various combinations of forward primers bracketing most of the promoter region we were able to define the 5'-ends of transcripts in this region. The region was then targeted for analysis by RNA Ligase-Mediated-5' Rapid Amplification of cDNA Ends (RLM-5' RACE) to identify the transcript initiation site(s). Positioning of initiation sites with respect to TATA boxes identified by gene analysis tools allowed us to identify three operational TATA elements which regulate basal transcription from this gene. Two TATA boxes were responsible for all of the inrpk1 transcripts found in leaves and cotyledons, and about 25-30% of the transcripts in roots. A third TATA box was involved only in expression in roots and accounted for the remaining 50-70% of root transcripts. RNAs expressed from this element lack two potentially functional upstream AUG codons, and may be translated more efficiently than transcripts originating from the other TATA boxes.

Alternative Splicing↗

PubMed2003

The BrainIT group: concept and core dataset definition.

INTRODUCTION: An open collaborative international network has been established which aims to improve inter-centre standards for collection of high-resolution, neurointensive care data on patients with traumatic brain injury. The group is also working towards the creation of an open access, detailed and validated database that will be useful for post-hoc hypothesis testing. In Part A, the underlying concept, the group coordination structure, membership guidelines and database access and publication criteria are described. Secondly, in part B, we describe a set of meetings funded by the EEC that allowed us to define a "Core Dataset" and we present the results of a feasibility exercise for collection of this core dataset. METHODS: Four group meetings funded by the EEC have enabled definition of a "Core Dataset" to be collected from all centres regardless of specific project aim. A paper based pilot collection of data was conducted to determine the feasibility for collection of the core dataset. Specially designed forms to collect the core dataset demographic and clinical information as well as sample the time-series data elements were distributed by both email and standard mail to 22 BrainIT centres. A deadline of two months was set to receive completed forms back from centres. A pilot data collection of minute by minute physiological monitoring data was also performed. FINDINGS: A core-dataset was defined and can be downloaded from the BrainIT web-site (go to "Core dataset" link at: www.brainit.org). Eighteen centres (82%) returned completed forms by the set deadline. Overall the feasibility for collection of the core data elements was high with only 10 of the 64 questions (16%) showing missing data. Of those 10 fields with missing data, the average number of centres not responding was 12% and the median 6%. An SQL database to hold the data has been designed and is being tested. Software tools for collection of the core dataset have been developed. Ethics approval has been granted for collection of multi-centre data as part of a pilot data collection study. INTERPRETATION: The BrainIT network provides a more standardised and higher resolution data collection mechanism for research groups, organisations and the device industry to conduct multi-centre trials of new health care technology in patients with traumatic brain injury.

Brain Injuries↗

PubMed2002

Is reject analysis necessary after converting to computed radiography?

Reject analysis is an accepted standard of practice for quality assurance in conventional radiology. The need for reject analysis has been challenged by the introduction of computed radiography (CR) because of low reported reject rates and because criteria for improperly exposed images were lacking. Most CR systems include quality control (QC) workstations that are capable of modifying the appearance of images before release, and also of deleting poor images before they are analyzed. Texas Children's Hospital has been using computed radiography since October 1995, and now conducts essentially filmless imaging operations using a large-scale picture archival and communications system (PACS) with fourteen CR units. The QC workstation is a key element of our CR operation; however, the extensive software tools of the workstation are limited in terms of avoiding repeated examinations. Neither the QC workstation nor the PACS itself is designed to support reject analysis, so our task was to design a system that accommodates identification, isolation, and archiving of repeated examinations, making use of our electronic imaging systems. We had already developed transcription codes for our radiologist's examination critique, so we adopted these as codes for rejected images. The technologist at the QC workstation appends the critique code to patient demographic information, modifies other fields to indicate that the image is rejected, and archives as usual. Modified routing tables prevent the release of rejected images but ensure they are available for review. Our frequency and reasons for repeated examinations are comparable to other reports of reject analysis in the literature. The most frequent cause of a repeated examination is mis-positioning. The process of developing the method for capturing repeat, collecting the data, and analyzing it is only one-half of the battle; to achieve an improvement in services, it is necessary to feed back the results to management and staff and to implement training as indicated. It is our intention to share our results with PACS and CR vendors in the hope that they will incorporate some mechanisms for reject analysis into the design of their systems.

Quality Control↗

PubMed2002

Quantitative evaluation of acquisition parameters in three-dimensional imaging with multidetector computed tomography using human skull phantom.

This study evaluated the quantitative measurements of three-dimensional (3D) volume images using multidetector row computed tomography (MDCT) and one skull specimen. Twenty-one linear distances were measured five times each by vernier caliper. A dry human skull was imaged with MDCT for various acquisition parameters at slice thicknesses of 1.25, 2.50, 3.75, and 5.00 mm for the different acquisition modes of axial and spiral scan. The distance of each corresponding item displayed on 3D rendered images was measured seven times by an uninvolved observer using a 3D software tool. Data analysis was performed to determine if there were any statistically significant differences in acquisition parameters. No significant image differences were found among the scan modes for each slice thickness. For a given scan mode, acquisition slice thickness was the important factor for quantitative measurement of 3D rendered CT images.

Humans↗

PubMed2006

Computation of individual latent variable scores from data with multiple missingness patterns.

Latent variable models are used in biological and social sciences to investigate characteristics that are not directly measurable. The generation of individual scores of latent variables can simplify subsequent analyses. However, missing measurements in real data complicate the calculation of scores. Missing observations also result in different latent variable scores having different degrees of accuracy which should be taken into account in subsequent analyses. This manuscript presents a publicly available software tool that addresses both these problems, using as an example a dataset consisting of multiple ratings for ADHD symptomatology in children. The program computes latent variable scores with accompanying accuracy indices, under a 'user-specified' structural equation model, in data with missing data patterns. Since structural equation models encompass factor models, it can also be used for calculating factor scores. The program, documentation and a tutorial, containing worked examples and specimen input and output files, is available at http://statgen.iop.kcl.ac.uk/lsc .

Attention Deficit Disorder with Hyperactivity↗

PubMed2005

Reliable classification and recombination analysis of porcine endogenous retroviruses.

Prevention of cross-species infection with porcine endogenous retroviruses (PERV) is crucial for xenotransplantation. Previous studies described the potential risk of infection for the PERV gamma1 subfamilies A, B and C. Replication competent PERV gamma1 proviruses designated to a particular subfamily and hybrid viruses originating from retroviral recombination events between the subfamilies were observed. Future pig genome sequencing projects will reveal multiple novel PERV proviruses from additional breeds and animals. Evaluation of these viral genomes has to be carried out to assess the potential risk of retroviral cross-species infection. In this study, we tested common sequence comparison methods for the classification of PERV sequences and the detection of hybrid clones. The examination of the polymorphic nucleotide positions was found to be the most suitable procedure. We describe a fast and simple method using bioinformatic software tools which can also be applied to analogous analyses of other viral genomes.

Animals↗

PubMed1995

Spatial analysis of Honolulu motor vehicle crashes: I. Spatial patterns.

This study describes spatial patterns in Honolulu motor vehicle accidents for 1990. A method for geo-coding accident locations is utilized with approximately 98% of the crash locations being identified. Spatial software tools are developed for describing the degree of spatial concentration. The spatial patterns of different types of accidents and accidents for every hour of the day, weekdays and weekends separately, are analyzed. Accidents spatially fluctuate dynamically, as a response to changing traffic patterns and volume. Generally, most accidents are closer to employment centers than to residential areas. In the suburban and rural areas, however, accidents are more likely to involve fatalities or serious injuries and be related to night-time driving and alcohol. It is shown that these conditions spatially correlate with single-vehicle crashes and crashes with opposite direction vehicles. The spatial patterns point to the limits of "blackspot" analysis.

Accidents, Traffic↗

PubMed1995

A software toolkit for hierarchical task analysis.

This paper describes a prototype software tool that offers support to the human factors specialist using hierarchical task analysis (HTA). The tool provides a direct manipulation diagram editor for HTA and provides high-quality output of analyses, in both graphic and automatically generated tabular form. The tool is implemented in Smalltalk-80 and currently runs on Macintosh computers.

Journal Article↗