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PubMed2006

Automated detection of lung nodules in multidetector CT: influence of different reconstruction protocols on performance of a software prototype.

PURPOSE: To evaluate the accuracy of software for computer-aided detection (CAD) of lung nodules using different reconstruction slice thickness protocols in multidetector CT. MATERIALS AND METHODS: Raw image data sets for 15 patients who had undergone 16-row multidetector CT (MDCT) for known pulmonary nodules were reconstructed at a reconstruction thickness of 5.0, 2.0 and 1.0 mm with a reconstruction increment of 1.5, 1.0 and 0.5 mm, respectively. The "Nodule Enhanced Viewing" (NEV) tool of LungCare for computer-aided detection of lung nodules was applied to the reconstructed images. The reconstructed images were also blinded and then evaluated by 2 radiologists (A and B). Data from the evaluating radiologists and CAD was then compared to an independent reference standard established using the consensus of 2 independent experienced chest radiologists. The eligible nodules were grouped according to their size (diameter > 10, 5 - 10, < 5 mm) for assessment. Statistical analysis was performed using the receiver operating characteristic (ROC) curve analysis, t-test and two-rater Cohen's Kappa co-efficient. RESULTS: A total of 103 nodules were included in the reference standard by the consensus panel. The performance of CAD was marginally lower than that of readers at a 5.0-mm reconstruction thickness (AUC = 0.522, 0.517 and 0.497 for A, B and CAD, respectively). In the case of 2.0-mm reconstruction slices, the performance of CAD was better than that of the readers (AUC = 0.524, 0.524 and 0.614 for A, B and CAD, respectively). CAD was found to be significantly superior to radiologists in the case of 1.0-mm reconstruction slices (AUC = 0.537, 0.531 and 0.675 for A, B and CAD, respectively). The sensitivity at a reconstruction thickness of 1.0 mm was determined to be 66.99 %, 68.93 % and 80.58 % for A, B and CAD, respectively. The time required for detection was shortest for CAD at reconstruction slices of 1.0 mm (mean t = 4 min). The performance of radiologists was greatly enhanced when using CAD: sensitivity 91.26 % and 94.17 % for CAD+A and CAD+B, respectively (AUC = 0.889 and 0.917). CAD was most advantageous in the detection of nodules < 10 mm. CONCLUSION: At a 1.0-mm reconstruction thickness, CAD's ability to detect nodules < 10 mm is superior to that of radiologists and its relatively short evaluation time makes it a viable second reader.

Diagnosis, Computer-Assisted↗

PubMed1991

Denta Scan: CT software program used in the anatomic evaluation of the mandible and maxilla in the perspective of endosseous implant surgery.

A radiological technique, using a new CT software program for the evaluation of alveolar process height and width, is presented. Irradiation is kept within acceptable limits when this technique is used. Measurements obtained with this technique were compared with those obtained on panoramic radiographs in 40 "half-jaws" (21 maxillar and 19 mandibular). We found that new indications for implantation emerge in the mandibular region because 'Denta Scan' can sometimes show possibilities to place implants on the buccal side of the canal (2 of 19 mandibular cases) when no possibilities are present above the canal on both the panoramic radiographs and Denta Scan images. In the maxillar region Denta Scan avoids unnecessary interventions by demonstrating the insufficient width of the alveolar ridge, often missed on panoramic radiographs (4 of 21 maxillar cases). Moreover the use of Denta Scan allows the use of implants with optimal length and diameter (23 of the 40 cases), giving better long-term results.

Alveolar Process↗

PubMed1992

[PC software for evaluating the Farnsworth-Munsell 100-Hue test].

This computer program is designed for faster elaboration of the Farnsworth-Munsell 100-Hue test. It is thus made user friendly, in that faultless input of data can be achieved, even by an untrained person. Evaluation is facilitated by the opportunity of representing two results at the same time. Examples of typical colour vision deficiencies are stored in a file and can then also be called up. Storing the results in a special data file helps to avoid the time consuming printing process. However, a hardcopy is supported by storing the last grafic in a standard PostScript-file, thus giving easy access to any printer. This program is applicable for IBM- or compatible PCs. Extensive use is possible by means of a software interface with the wide spread database-system DBASE.

Color Perception Tests↗

PubMed2003

The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT and tandem mass spectrometry to proteins copurifying with T cell lipid rafts.

Lipid rafts were prepared according to standard protocols from Jurkat T cells stimulated via T cell receptor/CD28 cross-linking and from control (unstimulated) cells. Co-isolating proteins from the control and stimulated cell preparations were labeled with isotopically normal (d0) and heavy (d8) versions of the same isotope-coded affinity tag (ICAT) reagent, respectively. Samples were combined, proteolyzed, and resultant peptides fractionated via cation exchange chromatography. Cysteine-containing (ICAT-labeled) peptides were recovered via the biotin tag component of the ICAT reagents by avidin-affinity chromatography. On-line micro-capillary liquid chromatography tandem mass spectrometry was performed on both avidin-affinity (ICAT-labeled) and flow-through (unlabeled) fractions. Initial peptide sequence identification was by searching recorded tandem mass spectrometry spectra against a human sequence data base using SEQUEST software. New statistical data modeling algorithms were then applied to the SEQUEST search results. These allowed for discrimination between likely "correct" and "incorrect" peptide assignments, and from these the inferred proteins that they collectively represented, by calculating estimated probabilities that each peptide assignment and subsequent protein identification was a member of the "correct" population. For convenience, the resultant lists of peptide sequences assigned and the proteins to which they corresponded were filtered at an arbitrarily set cut-off of 0.5 (i.e. 50% likely to be "correct") and above and compiled into two separate datasets. In total, these data sets contained 7667 individual peptide identifications, which represented 2669 unique peptide sequences, corresponding to 685 proteins and related protein groups.

Amino Acid Sequence↗

PubMed2003

The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the application of statistical tools for data analysis and interpretation.

Proteomic approaches to biological research that will prove the most useful and productive require robust, sensitive, and reproducible technologies for both the qualitative and quantitative analysis of complex protein mixtures. Here we applied the isotope-coded affinity tag (ICAT) approach to quantitative protein profiling, in this case proteins that copurified with lipid raft plasma membrane domains isolated from control and stimulated Jurkat human T cells. With the ICAT approach, cysteine residues of the two related protein isolates were covalently labeled with isotopically normal and heavy versions of the same reagent, respectively. Following proteolytic cleavage of combined labeled proteins, peptides were fractionated by multidimensional chromatography and subsequently analyzed via automated tandem mass spectrometry. Individual tandem mass spectrometry spectra were searched against a human sequence database, and a variety of recently developed, publicly available software applications were used to sort, filter, analyze, and compare the results of two repetitions of the same experiment. In particular, robust statistical modeling algorithms were used to assign measures of confidence to both peptide sequences and the proteins from which they were likely derived, identified via the database searches. We show that by applying such statistical tools to the identification of T cell lipid raft-associated proteins, we were able to estimate the accuracy of peptide and protein identifications made. These tools also allow for determination of the false positive rate as a function of user-defined data filtering parameters, thus giving the user significant control over and information about the final output of large-scale proteomic experiments. With the ability to assign probabilities to all identifications, the need for manual verification of results is substantially reduced, thus making the rapid evaluation of large proteomic datasets possible. Finally, by repeating the experiment, information relating to the general reproducibility and validity of this approach to large-scale proteomic analyses was also obtained.

Amino Acid Sequence↗

PubMed1998

Task analysis for the investigation of human error in safety-critical software design: a convergent methods approach.

An investigation was conducted into sources of error within a safety-critical software design task. A number of convergent methods of task- and error-analysis were systematically applied: hierarchical task analysis (HTA), error log audit, error observation, work sample and laboratory experiment. HTA, which provided the framework for the deployment of subsequent methods, revealed possible weaknesses in the areas of task automation and job organization. Application of other methods within this more circumscribed context focused on the impact of task and job design issues. The use of a convergent methods approach draws attention to the benefits and shortcomings of individual analysis methods, and illustrates the advantages of combining techniques to analyse complex problems. The features that these techniques should possess are highlighted.

Ergonomics↗

PubMed2006

Comparison of a camera - software system and typical farm management for detecting oestrus in dairy cattle at pasture.

AIM: To compare the sensitivity, specificity, predictive values and accuracy of detection of oestrus using a novel oestrus detection strip (ODS) and a camera-software device (CSD) with typical farm management practices of visual observation and use of tail paint in dairy cattle at pasture. METHODS: Dairy cows (n = 480) in a seasonal-calving herd managed at pasture under typical commercial conditions in New Zealand were stratified by age, body condition score and days in milk, then randomly allocated to one of two groups prior to the planned start of mating (PSM). Tail paint was applied to all cows and oestrus detected by visual observation of oestrous behaviour and removal of paint, by farm staff. One group (n = 240) was fitted with ODS and also monitored for signs of oestrus using a CSD, while the Control group (n = 240) was monitored using tail paint and visual observations only. Cows detected in oestrus were artificially inseminated (AI), and pregnancy status determined using rectal palpation and ultrasonography, 51-52 days after the end of a 55-day A period. Results of pregnancy diagnosis were used to confirm the occurrence of oestrus, and the sensitivity, specificity, predictive value and accuracy of detection of oestrus compared between oestrus detection methods. RESULTS: The sensitivity and accuracy of oestrus detection in the Control group, using visual observation and tail paint, were low. Compared with the Control group, detection of oestrus using the ODS and CSD resulted in greater sensitivity (85% vs 78%; p = 0.006), specificity (99.6% vs 98.0%; p < 0.001), positive predictive value (PPV; 88% vs 51%; p < 0.001) and overall accuracy (99.0% vs 98.0%; p < 0.001). Negative predictive value (NPV) did not differ significantly between groups (99.4% vs 99.3%; p = 0.28). Pregnancy rate to first service was higher in the CSD group than in the Control group (72% vs 39%; p < 0.05). Use of the CSD significantly increased the cumulative proportion of cows pregnant to AI over the breeding period (p = 0.044). CONCLUSION AND CLINICAL RELEVANCE: The ODS and CSD was satisfactory for detection of oestrus in seasonal calving dairy herds grazing on pasture and could improve the sensitivity and accuracy of detection of oestrus in herds where these are low.

Animals↗

PubMed2001

Quality evaluation of spiral CT-directed skull base coordinate assignment using the Leibinger 'Z-D' frame and 'STP' software.

We employed a phantom model to evaluate the accuracy and precision of spiral CT-directed intracranial skull base coordinate assignment using the Leibinger 'ZD' frame and 'stp' stereotactic software. Whilst the difference between the true and computed coordinates was in the perimillimeter range for anteroposterior, lateral and vertical measurements in a 1-mm slice thickness series of scans, errors of greater than 4 mm were encountered in 60% of vertical measurements in a 2-mm slice thickness series. Potential explanations for this clinically significant observation are discussed.

Humans↗

PubMed2002

Software and scan acquisition technique-related discrepancies in bone mineral assessment using dual-energy X-ray absorptiometry in neonates.

AIM: In adults, whole-body mineralization assessment by dual-energy X-ray absorptiometry can be affected by the densitometer and/or the software used. As there are no published data on neonates, the aim of this study was to evaluate the magnitude of such effects in growing preterm infants. METHODS: We analysed the absorptiometry results obtained from 44 preterm infants scanned at discharge and again 6 wk later using densitometers from the same manufacturer equipped with "Pediatric" (Group A, n = 24) or with "Infant" (Group B, n = 20) packages. Results of bone mineral content assessment were compared using an unpaired t-test and a linear regression analysis. RESULTS: At the time of the first absorptiometry (body weight = 2119 +/- 144 g, n = 44), the bone mineral content was three times lower in Group A (10 +/- 3 g) than in Group B (29 +/- 4 g) (p < 0.001). Subsequently, on the second absorptiometry (body weight = 4037 +/- 236 g, n = 44) such significant differences in bone mineral content (A: 65 +/- 19 g, B: 66 +/- 9 g, p = 0.85) were no longer in evidence. The differences in bone mineral content were related to differences in analysis algorithms between the two programs, which can lead to an overestimation of bone mineral content accretion when two successive measurements are made using the "Pediatric"package. CONCLUSION: Considering that significant differences in bone mineral assessment may depend upon which program is used, data previously collected in low birthweight infants using the "Pediatric" package should be analysed with caution. Data obtained using the "Pediatric" and "Infant" packages are not directly comparable. Careful validation studies of future densitometers and programs are required before their use in clinical paediatric studies.

Absorptiometry, Photon↗

PubMed1984

Optimization methods and available software. Part 1.

Optimization theories and generally applied optimization techniques are reviewed. The versatility and the complexity anticipated in actual problems are simplified to enable the food practitioners interested in the subject to overcome some of the barriers which prevented full utilization of optimization. The paper summarizes the various mathematical methods available for solving problems of product and process optimization and provides information and advice concerning the advantages and limitations of each technique. A compiled list of optimization subroutines, guidelines and criteria for choosing the proper software are furnished.

Computers↗

PubMedDate not supplied

Zherlock: an open source data analysis software.

Zherlock is an open source software that provides state-of-the-art data analysis tools to the user in an intuitive and flexible way. It is a front-end to different numerical "engines" to produce a seamless integration of algorithms written in different computer languages. Of particular interest is creating an interface to high-level scientific languages such as Octave (a Matlab clone) and R (an S-PLUS clone) to enable efficient porting of new data analytical methods. Zherlock uses advanced scientific visualization tools in 2-D and 3-D and has been extended to work on virtual reality (VR) systems. Central to Zherlock is a visual programming environment (VPE) which enables diagram based programming. These diagrams consist of nodes and connection lines where each node is an operator or a method and lines describe the flow of data between nodes. A VPE is chosen for Zherlock because it forms an effective way to control the processing pipeline in complex data analyses. The VPE is similar in functionality to other programs such as IRIS Explorer, AVS or LabVIEW.

Algorithms↗

PubMed1984

Enhancing the usability of safety software for microcomputers.

With the proliferation of microcomputers, increasing effort is being made to write programs dealing with occupational safety and health. So as to assure the widespread use of this material, it is important that it be prepared in a manner easy to use. Ignoring this consideration may cause the potential users to be repelled by it from the start, or that its use will be difficult and error-prone. This article dwells on some of the points that need to be borne in mind when writing such software to make it easy and pleasant to use. Additionally, a project, carried out by the author, is described, which makes use of a free-form program access approach, as opposed to a purely menu-driven one. Two potential extensions of this approach are then described.

Computers↗

PubMedDate not supplied

Improved quality data systems through the use of standard electronic data deliverables (EDDs) and environmental data assessment software.

One of the challenges facing professionals in the environmental arena today is the collection and assessment of large amounts of environmental analytical data. The assessment of the quality of that data is essential as multi-million dollar decisions for environmental site cleanups and/or long term monitoring efforts are made based on the analytical results. Also critical to environmental programs is the sharing and access of data across multiple data users. The ability to share data allows for better use of the limited resources available to clean up and monitor contaminated environmental sites. Standardization of electronic deliverables allows for collection of data from multiple data collectors into a single database for use by numerous data users and stakeholders on a project. This paper discusses the benefits of using a standard EDD deliverable format and use of environmental data assessment software tools to do project planning and data assessment throughout the duration of the environmental project.

Database Management Systems↗

PubMed1999

A control systems approach for the simulation of renal dynamic software phantoms for nuclear medicine.

For renal dynamic studies, the COST B2 hybrid phantom is an example of an artificially created software phantom. Although this phantom is useful, it is not possible to implement the phantom in a self-consistent fashion to produce, for example, a collection of tracer in the bladder which is related to the flow from the kidneys. In this study control systems are used to provide a self-consistent model. A feed-forward control system was designed for the transport of DTPA in the human body using SIMULINK. The system is based on a three-compartment model described by a set of differential equations with flow rates which may be set by the operator. The differential uptake in the kidneys may also be specified, while the flow of tracer through the renal parenchyma and collecting system of each kidney is determined using two-parameter retention functions. Curves corresponding to normal or pathological conditions may be simulated for plasma, parenchyma, collecting system and bladder by appropriate selection of parameters. The system is user-friendly and can be used to simulate almost all conditions seen in patient studies. The next stage of using this information to design dynamic image simulations is in progress.

Computer Simulation↗

PubMed2000

Estimation of the radiation dose from radiotherapy for skin haemangiomas in childhood: the ICTA software for epidemiology.

Radium applicators and pure beta emitters have been widely used in the past to treat skin haemangioma in early childhood. A well defined relationship between the low doses received from these applicators and radiation-induced cancers requires accurate dosimetry. A human-based CT scan phantom has been used to simulate every patient and treatment condition and then to calculate the source target distance when radium and pure beta applicators were used. The effective transmission factor psi(r) for the gamma spectrum emitted by the radium sources applied on the skin surface was modelled using Monte Carlo simulations. The well-known quantization approach was used to calculate gamma doses delivered from radium applicators to various anatomical points. For 32P, 90Sr/90Y applicators and 90Y needles we have used the apparent exponential attenuation equation. The dose calculation algorithm was integrated into the ICTA software (standing for a model that constructs an Individualized phantom based on CT slices and Auxological data), which has been developed for epidemiological studies of cohorts of patients who received radium and beta-treatments for skin haemangioma. The psi(r) values obtained for radium skin applicators are in good agreement with the available values in the first 10 cm but higher at greater distances. Gamma doses can be calculated with this algorithm at 165 anatomical points throughout the body of patients treated with radium applicators. Lung heterogeneity and air crossed by the gamma rays are considered. Comparison of absorbed doses in water from a 10 mg equivalent radium source simulated by ICTA with those measured at the Radiumhemmet, Karolinska Hospital (RAH) showed good agreement, but ICTA estimation of organ doses did not always correspond those estimated at the RAH. Beta doses from 32P, 90Sr/90Y applicators and 90Y needles are calculated up to the maximum beta range (11 mm).

Algorithms↗

PubMed2000

An intelligent diabetes software prototype: predicting blood glucose levels and recommending regimen changes.

Maintaining optimal blood glucose (BG) control is difficult for type 1 diabetes mellitus (T1DM) patients when typical daily regimens of food, insulin and exercise are altered. Artificial intelligence (AI) systems consisting of treatment algorithms calibrated through large datasets of patient specific information may offer a solution. Such a system can predict BG level changes resulting from regimen disturbances and recommend regimen changes for compensation. A software prototype based on neural network, fuzzy logic, and expert system concepts was developed and evaluated to determine feasibility and efficacy of a patient specific prediction model. BG data are the primary driver for adapting existing functions to patient specific prediction algorithms. Mean absolute percent error (MAPE) between actual and predicted BG values from inputs of daily insulin, food, and exercise information for an T1DM test subject was 10.5% using a calibrated model. The prototype is limited by the requirement for a rigid testing schedule, human error and situational circumstances such as alcohol consumption, illness, infection, stress, and significant hormonal imbalances. No significant conclusions regarding model validity can be drawn due to limited evaluation process and subject sample size, although the prototype has demonstrated viability as a learning tool for diabetes patients. Increased impetus for further development of this prototype and similar AI models may materialize when more effective diagnostic and data capture tools become available to reduce testing and improve accuracy of the model with more input data.

Algorithms↗

PubMed2003

A software package for cDNA microarray data normalization and assessing confidence intervals.

DNA microarray data are affected by variations from a number of sources. Before these data can be used to infer biological information, the extent of these variations must be assessed. Here we describe an open source software package, lcDNA, that provides tools for filtering, normalizing, and assessing the statistical significance of cDNA microarray data. The program employs a hierarchical Bayesian model and Markov Chain Monte Carlo simulation to estimate gene-specific confidence intervals for each gene in a cDNA microarray data set. This program is designed to perform these primary analytical operations on data from two-channel spotted, or in situ synthesized, DNA microarrays.

Bayes Theorem↗

PubMed1993

An overview of computer software developed to search biological sequence databases.

The scientific community has established a number of databases to receive and maintain the abundant biological sequence information being generated by research investigators worldwide. For researchers in an increasing number of biological disciplines, the information stored in these databases has become an invaluable tool in their daily research endeavors. This article reviews the organization of the largest nucleic acid and protein sequence databases and discusses some of the commonly available computer software that has been developed for searching them.

Amino Acid Sequence↗