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At least 451 records · Page 25Linked to original sources
PubMed2005

Particle picking by segmentation: a comparative study with SPIDER-based manual particle picking.

Boxing hundreds of thousands of particles in low-dose electron micrographs is one of the major bottle-necks in advancing toward achieving atomic resolution reconstructions of biological macromolecules. We have shown that a combination of pre-processing operations and segmentation can be used as an effective, automatic tool for identifying and boxing single-particle images. This paper provides a brief description of how this method has been applied to a large data set of micrographs of ice-embedded ribosomes, including a comparative analysis of the efficiency of the method. Some results on processing micrographs of tripeptidyl peptidase II particles are also shown. In both cases, we have achieved our goal of selecting at least 80% of the particles that an expert would select with less than 10% false positives.

Algorithms↗
PubMed2005

Case study: an evaluation of user-assisted hierarchical watershed segmentation.

This paper evaluates the effectiveness of an interactive, three-dimensional image segmentation technique that relies on watersheds. This paper presents two user-based case studies, which include two different groups of domain experts. Subjects manipulate a graphics-based front end to a hierarchy of segmented regions generated from a watershed segmentation algorithm, which is implemented in the Insight Toolkit. In the first study, medical students segment several different anatomical structures from the Visible Human Female head and neck color cryosection data. In the second study, radiologists use the interactive tool to produce models of brain tumors from MRI data. This paper presents a quantitative and qualitative comparison against hand contouring. To quantify accuracy, we estimate ground truth from the hand-contouring data using the Simultaneous Truth and Performance Estimation algorithm. We also apply metrics from the literature to estimate precision and efficiency. The watershed segmentation technique showed improved subject interaction times and increased inter-subject precision over hand contouring, with quality that is visually and statistically comparable. The analysis also identifies some failures in the watershed technique, where edges were poorly defined in the data, and note a trend in the hand-contouring results toward systematically larger segmentations, which raises questions about the wisdom of using expert segmentations to define ground truth.

Algorithms↗
PubMed2004

Precentral gyrus discrepancy in electronic versions of the Talairach atlas.

Electronic versions of the atlas of Talairach and Tournoux, including the Talairach Daemon and the official versions published by Thieme, contain a discrepant region of the precentral gyrus on axial slice +35 mm that extends far forward into the frontal lobe. This area is anatomically incorrect and internally inconsistent within the digital atlas software applications using their multiplanar cross-referencing tools. By cross-referencing the axial, sagittal, and coronal plates from the original printed atlas, we demonstrate that the discrepant area should be labeled middle frontal gyrus. The mislabeled portion encompasses a 3 x 1.5-cm region in the axial plane and has significant implications for sensorimotor studies that rely on the digital atlases for anatomic labeling.

Brain Mapping↗
PubMed2001

The ergonomics of flight management systems: fixing holes in the cockpit certification net.

Recent air traffic control regulations mandate the installation of computer-based flight management systems in airliners across Europe. Integrating and certifying add-on cockpit systems is a long and costly process, which in its current form cannot meaningfully address ergonomics aspects. Two levels of problems occur: add-on systems carry many "classic" HCI failures, which could easily be addressed with modified certification requirements. Further, adding new technology changes practice, creates new skill and knowledge demands and produces new forms of error, which are more difficult to assess in advance. However, one innovative certification approach for add-on cockpit systems, based on the use of a representative population of user pilots, was found to be promising. This method minimizes the subjective bias of individual pilots in addition to defining pass/fail criteria in an operational environment.

Aviation↗
PubMed2001

Java-based graphical user interface for MRUI, a software package for quantitation of in vivo/medical magnetic resonance spectroscopy signals.

This article describes a Java-based graphical user interface for the magnetic resonance user interface (MRUI) quantitation package. This package allows MR spectroscopists to easily perform time-domain analysis of in vivo/medical MR spectroscopy data. We have found that the Java programming language is very well suited for developing highly interactive graphical software applications such as the MRUI system. We also have established that MR quantitation algorithms, programmed in the past in other languages, can easily be embedded into the Java-based MRUI by using the Java native interface (JNI).

Algorithms↗
PubMed1997

DullRazor: a software approach to hair removal from images.

Recently, there has been a growing number of studies applying image processing techniques to analyze melanocytic lesions for atypia and possible malignancy and for total-body mole mapping. However, such lesions can be partially obscured by body hairs. None of these studies has fully addressed the problem of human hairs occluding the imaged lesions. In our previous study we designed an automatic segmentation program to differentiate skin lesions from the normal healthy skin, and learned that the program performed well with most of the images, the exception being those with hairs, especially dark thick hairs, covering part of the lesions. These thick dark hairs confused the program, resulting in unsatisfactory segmentation results. In this paper, we present a method to remove hairs from an image using a pre-processing program we have called DullRazor. This pre-processing step enables the segmentation program to achieve satisfactory results. DullRazor can be downloaded as shareware from http:/(/)www.derm.ubc.ca.

Algorithms↗
PubMed2000

Volumetric measurements of right cerebral hemisphere infarction: use of a semiautomatic MRI segmentation technique.

The applications of a new segmentation software, Anatomatic, in the evaluation of volumetric measurements of brain infarctions and the new Medimag 3D software in the evaluation of 3D image representation of infarctions are described. These programs are applied to magnetic resonance imaging. The aim of this study is to evaluate the use of these software packages in making accurate volumetric measurements in 40 patients with right cerebral infarctions, in determining the correlations between the quantitated lesions and neurological/neuropsychological dysfunctions and in creating realistic 3D views of the infarctions. Using Anatomatic, reproducible infarction volumes were achieved with ease and within a reasonably fast time. Medimag helped achieve realistic 3D representations of the infarctions. When compared, the semiautomatic segmentation proved to be much faster and yielded higher infarction volumes than the manual segmentation technique. Significantly positive correlations between the infarction volumes and neurological dysfunctions and neuropsychological deficit (neglect) helped to explain the effect of volumes on the clinical status of the patients.

Adult↗
PubMed2000

Soft-testing of industrial control systems programmed in IEC 1131-3 languages.

This paper presents a technique and the means for testing PLC-based control software outside the actual plant environment with the purpose of increasing the confidence level on the compliance of the software to functional and temporal requirements. The need to obtain a high confidence level on the correct software operation arises from the fact that in most of the cases it is quite dangerous and expensive to test unproved PLC operation by linking it with the actual facilities that it is going to control. The proposed technique relies on a combined simulation of the controlled plant and the PLC system and an analysis of the plant responses. The PLC system simulation imitates the way software is executed on a PLC that is programmed in the languages of the IEC1131-3 standard. It is based on the programming model of the IEC standard and analytical formulae for estimating the program runtime. The simulation of the plant is based on a discrete convolution model that is solved at the same rate with the rate determined by the control algorithms. A tool realizing these concepts has been developed and its use in testing the control software of three critical outputs of a distillation column is demonstrated.

Computer Simulation↗
PubMed2002

Improving the development of event-driven control systems in the batch processing industry. A case study.

This paper presents the results of an academia-industry collaborative project whose main objective was to test novel techniques for the development of event-driven control systems in the batch processing (e.g., pharmaceutical, fine chemicals, food) industries. Proposed techniques build upon industrial standards and focus on (i) formal synthesis of phase control logic and its automatic translation into procedural code, and (ii) verification of the complete discrete-event control system via dynamic simulation. In order to test the techniques in an engineering environment, a complete discrete-event control system was produced for a benchmark batch process plant based on a standard development method employed by one of the industrial partners. The control system includes functional process specification, control architecture, distributed control system (DCS) proprietary programming code for procedural control at equipment, unit, and process cell levels, and human-machine interfaces: A technical assessment of the development method and the obtained control system was then carried out. Improvements were suggested using the proposed techniques in the specification, code generation and, verification steps. The project assessed the impact of these techniques from both an engineering and economic point of view. Results suggest that the introduction of computer aided engineering (CAE) practices based on the benchmarked techniques and a structured approach could effect a 75% reduction of errors produced in the development process. This translates into estimated overall savings of 7% for green-field projects. Figures were compared with other partners' experience. It is expected that the work load on a given project will shift, increasing the load on process engineers during the specification stage and decreasing the load on the software engineers during the code writing.

Algorithms↗
PubMed1999

Three-dimensional dynamical capabilities of the human masticatory muscles.

Many habitual human jaw movements are non-symmetrical. Generally, it is observed that when the lower incisors move to one side the contralateral condyle moves forwards onto the articular eminence, whereas the ipsilateral condyle stays in the mandibular fossa, moving slightly to the ipsilateral side. These jaw movements are the result of contractions of active masticatory muscles and guided by the temporomandibular joints, their ligaments and passive elastic properties of the muscles. It is not known whether the movements are primarily dependent on passive guidance, active muscle control or both. Therefore, the objective of this study was to analyse the interplay between these factors during non-symmetrical jaw movements. A six-degrees-of-freedom dynamical biomechanical model of the human masticatory system was used. The movements were not restricted to a priori defined joint axes. Jaw movement simulations were performed by unilateral activity of the muscles. The ligaments or the passive elastic properties of the muscles could be removed during these simulations. Laterodeviations conform to naturally observed ones could be generated by unilateral muscle contractions. The movement of the lower incisors was hardly affected by the absence of passive elastic muscle properties or temporomandibular ligaments. The latter, however, influenced the movement of the condyles. The movements could be understood by analysing the combination of forces and torques with respect to the centre of gravity of the lower jaw. In addition, the loading of the condyles appeared to be an important determinant for the movement. This analysis emphasizes that the movements of the jaw are primarily dependent on the orientation of the contributing muscles with respect to this centre of gravity and not on the temporomandibular ligaments or passive elastic muscle properties.

Biomechanical Phenomena↗
PubMed1998

Detecting subtle differences in behavior using waveform display analysis.

We have devised a method, behavioral waveform display analysis, to analyze complex ethological information by measuring behavior in real time and visualizing it as a time-dependent, multistate waveform. To facilitate the generation and statistical analysis of behavioral waveform displays, we have designed a simple Macintosh-based software program. When keystrokes coded to particular behavioral states are entered in real time, this software measures and collates the time, frequency, and duration of each behavioral state. These data can then be displayed either in a tabular format for statistical analysis of behavioral duration and frequency or as graphical coordinates for creating waveform displays by direct importing into graphing programs. An illustration of the use of waveform display analysis to detect anomalous behaviors in cocaine- and amphetamine-treated mice, some of which are not detectable by a standard time-sampling assay, is shown. Both waveform display and time-sampling analysis detected drug-induced changes in sniffing, bar hanging, digging, and rearing. However, unlike time-sampling analysis, waveform display analysis also detected changes in the total duration, frequency, and average duration of these behaviors as well as additional changes in gnawing and locomotion. Additionally, visual scanning of behavioral waveform displays detected drug-induced changes in the patterns of behavior not detectable by time-sampling, including 1) a staged progression to a limited behavioral repertoire consisting of sniffing, locomotion, and rearing; 2) rapid switching between these remaining few behaviors; 3) a delayed onset of postinjection rearing relative to sniffing and locomotion; and 4) the absence of other transient stereotypies during the onset of drug action. These data indicate that behavioral waveform display provides an approach for the detection, visualization, and statistical analysis of aspects of complex behavior not amenable to detection by time-sampling methods.

Amphetamine↗
PubMed1996

Evaluation of iohexol as a marker for the clinical measurement of glomerular filtration rate in dogs.

The contrast medium iohexol can be used as a marker for the measurement of glomerular filtration rate. It has the advantages of sample stability and the availability of a simple, automated (though expensive) analyser. The clearance of iohexol was compared with the clearance of Tc-DTPA in 24 dogs with known or suspected renal impairment. The results were comparable but fractionally lower with iohexol. The correction factors developed for human beings were found to be satisfactory in the dogs, thus validating the software routines used in the automated analyser with the canine samples.

Animals↗
PubMed2003

Predicting logP of pesticides using different software.

We compared experimental and calculated logP values using a data set of 235 pesticides and experimental values from four different sources: The Pesticide Manual, Hansch Manual, ANPA and KowWin databases. LogP were calculated with four softwares: HyperChem, Pallas, KowWin and TOPKAT. Crossed comparison of the experimental and calculated values proved useful, especially for pesticides. These are harder to study than simpler organic compounds. Structurally they are complex, heterogeneous and similar to drugs from a chemical point of view. They offer an interesting way to verify the goodness of the different methods. Other studies compared several logP predictors using a single set of experimental values taken as a reference. Here we discuss the utility of the different logP predictors, with reference to experimental data found in different databases. This offers three advantages: (1) it avoids bias due to the assumption that one single data set is correct; (2) a given predictor can be developed on the same data set used for evaluation; (3) it takes account of experimental variability and can compare it with the predictor's variability. In our study Pallas and KowWin gave the best results for prediction, followed by TOPKAT.

1-Octanol↗
PubMed2001

Prediction of the subcellular location of prokaryotic proteins based on the hydrophobicity index of amino acids.

An algorithm of predicting the subcellular location of prokaryotic proteins is proposed in this paper. In addition to the amino acid composition, the auto-correlation functions based on the hydrophobicity profile of amino acids along the primary sequence of the query protein have been used. Consequently, the best predictive accuracy to date has been achieved. Of the 997 prokaryotic proteins in the database used here, 688 cytoplasmic, 107 extracellular and 202 periplasmic proteins, the overall predictive accuracies are as high as 97.7 and 90.4% in the resubstitution and jackknife tests, respectively, using the hydrophilicity value of Hopp and Woods. The underlying mechanism of the improvement is also discussed. This work would be useful for a systematic analysis of the great amounts of prokaryotic genome sequences. The computer programs used in this paper are available on request via email.

Algorithms↗
PubMed2003

Darting behavior: a quantitative movement pattern designed for discrimination and replicability in mouse locomotor behavior.

In the open-field behavior of rodents, Software for Exploring Exploration (SEE) can be used for an explicit design of behavioral endpoints with high genotype discrimination and replicability across laboratories. This ability is demonstrated here in the development of a measure for darting behavior. The behavior of two common mouse inbred strains, C57BL/6J (B6) and DBA/2J (D2), was analyzed across three different laboratories, and under the effect of cocaine or amphetamine. "Darting" was defined as having higher acceleration during progression segments while moving less during stops. D2 mice darted significantly more than B6 mice in each laboratory, despite being significantly less active. These differences were maintained following cocaine administration (up to 20mg/kg) and only slightly altered by amphetamine (up to 5mg/kg) despite a several fold increase in activity. The replicability of darting behavior was confirmed in additional experiments distinct from those used for its design. The strategy leading to the darting measure may be used to develop additional discriminative and replicable endpoints of open-field behavior.

Amphetamine↗
PubMed1997

Cognitive evaluation: how to assess the usability of information technology in healthcare.

As the adoption of information technology has increased, so too has the demands that these systems become more adapted to the physicians and nurses environments, to make access and management of information easier. The developers of information systems in Healthcare must use quality management techniques to ensure that their product will satisfy given requirements. This underlines the importance of the preliminary phase where Users Requirements are elicited. Some methodologies, such as KAVAS (E.M.S. Van Gennip, F. Grémy, Med. Inform. 18, 1993, 179) chose to use a continuous assessment protocol as a key strategy for quality management. At each stage of the conception and development of a prototype, the assessment checks that it conforms to the expectation of the users' requirements. The methodology of evaluation is then seen as a dynamic process which is able to improve the design and development of a dedicated system. The purpose of this paper is to demonstrate the necessity to include a cognitive evaluation phase in the process of evaluation by: (1) evaluating the integration (usability) of the I.T. in the activity of the users; and (2) understanding the motives underlying their management of information. This will help the necessary integration of information management in the workload of the healthcare professionals and the compatibility of the prototypes with the daily activity of the users.

Cognition↗