Software for MS protein identification.
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Databases, Factual↗
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Results for “Software Validation”
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Analysis of genomic and proteomic data using advanced literature mining.
High-throughput technologies, such as proteomic screening and DNA micro-arrays, produce vast amounts of data requiring comprehensive analytical methods to decipher the biologically relevant results. One approach would be to manually search the biomedical literature; however, this would be an arduous task. We developed an automated literature-mining tool, termed MedGene, which comprehensively summarizes and estimates the relative strengths of all human gene-disease relationships in Medline. Using MedGene, we analyzed a novel micro-array expression dataset comparing breast cancer and normal breast tissue in the context of existing knowledge. We found no correlation between the strength of the literature association and the magnitude of the difference in expression level when considering changes as high as 5-fold; however, a significant correlation was observed (r = 0.41; p = 0.05) among genes showing an expression difference of 10-fold or more. Interestingly, this only held true for estrogen receptor (ER) positive tumors, not ER negative. MedGene identified a set of relatively understudied, yet highly expressed genes in ER negative tumors worthy of further examination.
Abstracting and Indexing↗
Comparison of two software versions for assessment of body-composition analysis by DXA.
OBJECTIVE: To compare two software versions provided by Lunar CO: for assessment of body composition analysis by DXA. RESEARCH METHODS AND PROCEDURES: Soft-tissue phantoms for lean tissue (water) and fat tissue (methanol) were repeatedly scanned using DXA machines (DPX-L; Lunar CO., Madison, WI) and analyzed using software version 1.33 and the updated year 2000-compatible version 1.35. For the intersoftware comparison, the phantoms were scanned 10 times (each scan was analyzed once) with both software versions using all three scanning modes (slow, medium, and fast) for a total of 60 scans and analyses. For the intermachine comparison, the same phantoms were scanned three times (each scan was analyzed once) with a second machine from the same manufacturer using all three scanning modes and version 1.35 only. Percentage of fat was the variable of interest. RESULTS: For version 1.33, fat was 9.9 +/- 0.4%, 10.0 +/- 0.5%, and 11.0 +/- 0.5% (mean +/- SD) for the lean-tissue phantom and 50.8 +/- 0.3%, 50.9 +/- 0.5%, and 51.1 +/- 0.6% for the fat-tissue phantom using the slow, medium, and fast scanning modes, respectively. For version 1.35, the respective fat values were 9.8 +/- 0.7%, 9.9 +/- 0.4%, and 10.3 +/- 0.7%, and 50.6 +/- 0.5%, 50.9 +/- 0.6%, and 50.8 +/- 0.8%, respectively. For the lean-tissue phantom, the estimation of percentage of fat was significantly (p < 0.05) affected by scanning mode but not by software version. For the fat-tissue phantom, the estimation of percentage of fat was not affected by either scanning mode or software version. The use of version 1.35 did not effect intermachine variability. DISCUSSION: Versions 1.33 and 1.35 of the Lunar body composition software appear to be comparable. Soft-tissue phantoms, such as the ones described in this paper, may be useful in monitoring the reproducibility of body composition analyses within and between DXA machines, particularly in longitudinal studies.
Absorptiometry, Photon↗
Initial experience of the ORATEL computerised information tools in general practice.
ORATEL (a telematic system for quality assurance indicators in oral health care) is a three-year project with the ultimate objective of improving the quality of oral health care through the use of appropriate computerised information systems. These tools are designed to promote quality assurance and quality of care development in oral health care by using common quality indicators/standards. ORATEL has developed three prototypes of computerised information systems: an interactive multimedia teach software on quality assurance in oral health care, ORATEL-TEACH; a proactive quality assurance support tool for real time use at the dental unit, ORATEL-PROACT; and an integrated set of modules for monitoring and self assessment at the clinical level and for the computerised reporting of aggregated data for evaluation at higher levels, ORATEL-REVAL. The initial experiences of using these tools was assessed during 1993 in general dental practice locations in Liverpool and clinics in for other European countries. Overall, the dentists were positive about the potential usefulness of the ORATEL tools but further improvements were considered necessary. Finding has been approved by the European Commission for further development under a new project called ORQUEST.
Computer Communication Networks↗
Specialized spring design in segmented edgewise orthodontics: further verification of dedicated software.
A software program for use in the investigation of specialized springs used in the segmented arch technique has previously been developed and an example of its clinical application has been shown. The purpose of this study was to further assess the reliability of the software in 4 tests using T-loop springs. A numerical simulation of a determined experimental condition relative to a T-loop spring was carried out in each test. Numerical and experimental results were compared, and the precision of the analytical tool was assessed relative to a variety of parameters of the spring. Since the comparison between numerical and experimental results showed good agreement along the entire range of activation of the spring, the reliability of the software is sufficient for the clinical purposes of the segmented arch technique.
Computer Simulation↗
Mathematical shape matching as a tool in tooth wear assessment--development and conduct.
The quantitative assessment of restoration and tooth wear usually requires fixed reference points from which measurements are made. In longitudinal patient follow-up the loss or erosion of such points may preclude measurement and an alternative approach is to seek regions of coincidence and conflict in digital models of before and after wear surfaces, with a continuous refinement of the parameters of the coordinate transformations, until the closest correspondence between them is found. A computer program has been written to implement the algorithm and assess the technique's capacity to find the match between surfaces both artificially generated and from tooth replicas recorded from patients at different epochs. The program was able to achieve the desired ends, demonstrating the utility of the technique in tooth wear assessment but identifying the need to refine the program further to enhance both its difference detection capabilities and level of automation. Examination of the theory and practical experience highlighted certain situations when user understanding is invaluable to ensure a satisfactory solution. This strengthened the investigators' resolve against reliance upon commercially based surface fitting programs whose basis may not be fully understood. Notwithstanding this surface matching is a powerful tool in the investigation of dental wear.
Algorithms↗
Intermittent mode reversion to VOO of a dual chamber pacemaker model.
This report describes an asymptomatic patient with a DDDR pacemaker system (Inos Cls, Biotronik) that showed intermittent mode reversion to VOO and sometimes to VVI without a detectable source of electromagnetic interference and oversensing. Patients with this Biotronik model should be carefully assessed along with a surface ECG before placing the programming head.
Cardiac Pacing, Artificial↗
Impaired detection of ventricular tachyarrhythmias by a rate-smoothing algorithm in dual-chamber implantable defibrillators: intradevice interactions.
INTRODUCTION: Rate smoothing is an algorithm initially designed to prevent rapid changes in pacemaker rates. In this study, we sought to determine the potential of the rate-smoothing mechanism in preventing detection of ventricular tachyarrhythmias. METHODS AND RESULTS: Clinical testing of rate smoothing was performed at the time of defibrillator arrhythmia induction in 16 patients with implantable defibrillators during 65 episodes of ventricular tachyarrhythmias. We also performed simulator-based testing to assess detection of ventricular tachycardia between 170 and 220 beats/min with systematic sequential change of rate-smoothing percent, AV delay, and maximal rate. During clinical testing of 54 ventricular fibrillation/polymorphic ventricular tachyarrhythmia episodes, there were no cases of nondetection and 3 episodes (5%) of minimally delayed detection. Of 10 monomorphic ventricular tachyarrhythmias, 6 had either delayed (2 cases) or absent (4 cases) detection. During simulator testing, complex interrelationships were demonstrated in AV delay, upper rate, and rate-smoothing percent in determining the severity of the effect on detection. Generally, long AV delay, higher upper rate, and smaller (more aggressive) rate smoothing were associated with increased risk of ventricular tachyarrhythmia underdetection. Importantly, use of parameters that impaired detection was always accompanied by a programmer warning message. CONCLUSION: Rate smoothing may result in delay or failure of ventricular tachycardia detection. It is important to consider warning messages when programming rate smoothing and to test for appropriate detection when rate smoothing is used despite warning messages.
Algorithms↗
Feasibility and reliability of on-line automated microemboli detection after carotid endarterectomy. A transcranial Doppler study.
OBJECTIVES: recently, a new algorithm for transcranial Doppler (TCD) ultrasound detection of microembolic signals (MES) was developed. In the present study, we investigated its on-line performance in TCD monitoring after carotid endarterectomy (CEA) and assessed off-line its accuracy in detecting MES. MATERIALS AND METHODS: first, the feasibility of MES detection in TCD monitoring after CEA in a routine clinical setting was evaluated in 50 patients. Second, to test the reliability of the software a 2-h digital audio study tape was made and analysed by the algorithm and five human experts. The "gold standard" was defined as the agreement between human experts: a MES was considered to be present if at least three human observers agreed. RESULTS: TCD monitoring for emboli detection after CEA was well tolerated by the patients and could be performed reliably. In the study tape, the human gold standard detected 107 MES, with 93 MES having an intensity of > or =7 dB. The software detected 81 and 77 MES, respectively. Using the 7 dB intensity threshold, the software had no false positives and 16 false negatives. The kappa value between the human gold standard and the software was 0.91, the proportion of specific agreement was 0.83. CONCLUSIONS: the tested algorithm provides a reliable method for automated on-line microemboli detection after CEA. This makes monitoring of the effectiveness of antiplatelet agents in the prevention of stroke after CEA more practicable.
Algorithms↗
Infection control training: evaluation of a computer-assisted learning package.
An evaluation of the training module of an interactive infection control computer-assisted learning (CAL) software program was carried out with ward-based nurses, third-year medical students and infection control personnel. All nursing staff, 87% of the medical students and all infection control staff found the programme easy and enjoyable to use. The module was accessed 3101 times on the hospital network in 18 months with usage settling to between 100-150 times per month. There was a higher level of use by night-duty and weekend staff. Medical students gained as much infection control knowledge from using the CAL package (increase in correct responses from 63.5% to 83.4%;P<0.0001) as they did from a formal lecture (increase in correct responses from 62.1% to 79.5%;P<0.0001). We conclude the training module which is accessible on the hospital wards and across the academic network, is a convenient and effective way for staff and students to gain a basic understanding in evidence-based infection control practices, at locations and times suitable for them.
Attitude of Health Personnel↗
A computer-based method for calculation of orbital floor fractures from coronal computed tomography scans.
PURPOSE: A computer program recently developed for the calculation of the orbital floor and fracture areas from coronal computed tomography (CT) scans was used in a study to evaluate the accuracy and ability of this new method. MATERIAL AND METHODS: The size of orbital floors and fabricated fractures in 14 dried, anatomic specimens were measured in coronal CT scans by 3 independent observers. Based on this data set, the orbital floor and fracture regions were calculated with the newly developed computer program. These calculated regions were then compared with a direct measurement of the specimens that had been obtained by digital photography. The accuracy of the computer-based calculations was assessed using Lin's concordance correlation coefficient. RESULTS: The size of the orbital floor (mean +/- SD) was found to be 5.21 +/- 0.39 cm(2) by direct measurement of the specimens and 5.30 +/- 0.52 cm(2) by calculation with the computer program. The region of the fracture (mean +/- SD) was 1.05 +/- 0.64 cm(2) by direct measurement and 1.01 +/- 0.62 cm(2) by computer calculation. The between-method mean difference (direct measurement minus computer based calculation) was -0.09 cm(2) (or 1.7% of mean orbital floor region) for orbital floor region and 0.04 cm(2) (or 3.8% of mean fracture region) for fracture region. CONCLUSIONS: This accurate and time-saving method is practicable for determining the size and location of orbital floor fractures. This calculation program can be advantageously applied in the clinical management of blowout fractures of the orbit.
Algorithms↗
The Y2K problem and management strategies for the individual practitioner.
This article will detail concisely the nature of the Y2K problem, how it could affect your computer systems and your business, and what measures you can institute to minimize and/or eliminate computer failure as you enter the year 2000.
Chronology as Topic↗
Quantitative analysis of apical root resorption by means of digital subtraction radiography.
OBJECTIVE: This study was performed to assess the diagnostic and quantifying ability of digital subtraction images for simulated apical root resorption, as well as to compare the diagnostic accuracy of conventional intraoral radiographs with digital subtraction images for this condition. STUDY DESIGN: Digital and intraoral radiographs of 10 sound maxillary central incisors and those with simulated apical root resorption were taken with varying horizontal and vertical angulations of the x-ray beam. Paired t tests were used to compare the lengths of the sound teeth on the images with their actual lengths, and the estimated amount of simulated apical root resorption was compared with the actual amount of tooth loss by means of Emago software. The diagnostic accuracy for detecting lesions was also evaluated on conventional intraoral radiographs and digital subtraction images through receiver operating characteristic (ROC) analysis. RESULTS: There were no statistically significant differences between the actual lengths and those measured on the reconstructed images of the sound teeth. The calculated amounts of apical root resorption showed no statistically significant differences in comparison with the actual amounts (P >.05). The diagnostic accuracy of the conventional intraoral radiographs in detecting the lesions was low (ROC area = 0.6446). CONCLUSION: A quantitative analysis of small amounts of apical root resorption can be performed by means of digital subtraction radiography.
Humans↗
Computerized charting: from dream to reality.
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Alberta↗
The year 2000 problem: hiccough or approaching Armageddon.
The complexity of information technology systems has increased to approximate that of biological organisms, with a similar unpredictability of behaviour. With several million lines of code, a modern computer operating system, still can only be compared in complexity to a bacterial genome. However, just as unpredictable mutations continuously arise in the 3000 million haploid base pairs of human code and cause much misery and disease, undiscovered errors lie buried in the accumulated machine code which make up our world. As in human genetics, the difficulty is often distinguishing the harmless polymorphisms from the dangerous or lethal mutations. Similarly there is uncertainty about the impact of errors in data-handling code, which make up the "Year 2000 Problem". Over the remaining months it is vital that critical systems are checked for year 2000 compliance so as to avoid potentially serious disruption.
Chronology as Topic↗
An associative model of rat serial pattern learning in three-element sequences.
Hypotheses ranging from subsymbolic to symbolic have been proposed to account for rat sequential behaviour, and in the subsymbolic domain alone there are multiple proposed subsymbolic processes or factors thought to affect serial behaviour. A behavioural study and computer simulations were conducted to evaluate these hypotheses, and a new computational associative model based on pairwise associations and generalization was evaluated. Seven 3-element sequences were selected for study that systematically (1) varied sequence discriminability, (2) varied reward magnitude, and (3) manipulated the order of food quantities. Neither element discriminability nor response enhancement subsymbolic processes in isolation were able to account for the behavioural data; however, simulations from the computational model known as the sequential pairwise associative memory (SPAM) model with a log-linear mapping of stimulus dimension items to food quantities correlated well with the behavioural data. SPAM accounts for differential element anticipation in different sequences by appealing to pairwise association of sequence events and generalization between cues as the principal factors mediating pattern tracking in three-element sequences.
Animals↗
Talk your way round--a speech interface to a virtual museum.
PURPOSE: To explore the development of a speech interface to a virtual world and to consider its relevance for disabled users. METHOD: The system was developed using mainly software that is available at minimal cost. How well the system functioned was assessed by measuring the number of times a group of users with a range of voices had to repeat commands in order for them to be successfully recognized. During an initial session, these users were asked to use the system with no instruction to see how easy this was. RESULTS: Most of the spoken commands had to be repeated less than twice on average for successful recognition. For a set of 'teleportation' commands this figure was higher (2.4), but it was clear why this was so and could easily be rectified. The system was easy to use without instruction. Comments on the system were generally positive. CONCLUSIONS: While the system has some limitations, a virtual world with a reasonably reliable speech interface has been developed almost entirely from software which is available at minimal cost. Improvements and further testing are considered. Such a system would clearly improve access to virtual reality (VR) technologies for those without the skills or physical ability to use a standard keyboard and mouse. It is an example of both assistive technology (AT) and universal design.
Computer Graphics↗
Visualization tools for blind people using multiple modalities.
PURPOSE: There are many problems when blind people need to access visualizations such as graphs and tables. Current speech or raised-paper technology does not provide a good solution. Our approach is to use non-speech sounds and haptics to allow a richer and more flexible form of access to graphs and tables. METHOD: Two experiments are reported that test out designs for both sound and haptic graph solutions. In the audio case a standard speech interface is compared to one with non-speech sounds added. The haptic experiment compares two different graph designs to see which was the most effective. RESULTS: Our results for the sound graphs showed a significant decrease in subjective workload, reduced time taken to complete tasks and reduced errors as compared to a standard speech interface. For the haptic graphs reductions in workload and some of the problems that can occur when using such graphs are shown. CONCLUSIONS: Using non-speech sound and haptics can significantly improve interaction with visualizations such as graphs. This multimodal approach makes the most of the senses our users have to provide access to information in more flexible ways.
Blindness↗