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PubMed2004

Using automatically learnt verb selectional preferences for classification of biomedical terms.

In this paper, we present an approach to term classification based on verb selectional patterns (VSPs), where such a pattern is defined as a set of semantic classes that could be used in combination with a given domain-specific verb. VSPs have been automatically learnt based on the information found in a corpus and an ontology in the biomedical domain. Prior to the learning phase, the corpus is terminologically processed: term recognition is performed by both looking up the dictionary of terms listed in the ontology and applying the C/NC-value method for on-the-fly term extraction. Subsequently, domain-specific verbs are automatically identified in the corpus based on the frequency of occurrence and the frequency of their co-occurrence with terms. VSPs are then learnt automatically for these verbs. Two machine learning approaches are presented. The first approach has been implemented as an iterative generalisation procedure based on a partial order relation induced by the domain-specific ontology. The second approach exploits the idea of genetic algorithms. Once the VSPs are acquired, they can be used to classify newly recognised terms co-occurring with domain-specific verbs. Given a term, the most frequently co-occurring domain-specific verb is selected. Its VSP is used to constrain the search space by focusing on potential classes of the given term. A nearest-neighbour approach is then applied to select a class from the constrained space of candidate classes. The most similar candidate class is predicted for the given term. The similarity measure used for this purpose combines contextual, lexical, and syntactic properties of terms.

Abstracting and Indexing↗
PubMed2006

A new general-purpose fully automatic baseline-correction procedure for 1D and 2D NMR data.

A new procedure for automatic baseline correction of NMR data sets is presented. It is based on an improved automatic recognition of signal-free regions that uses a Continuous Wavelet transform derivative calculation, followed by a baseline modelling procedure based on the Whittaker smoother algorithm. The method has been proven to automatically flatten 1D and 2D NMR spectra with large baseline distortions arising from different sources, is tolerant to low signal-to-noise ratio spectra, and to signals of varying widths in a single spectrum. Even though this procedure has so far only been applied to NMR spectra, we believe it to also be applicable to other spectroscopies having relatively narrow peaks (e.g., mass spectrometry), and potentially to those with broad peaks (e.g., near infrared or ultraviolet).

Algorithms↗
PubMed2004

A method for the automatic segmentation of autoradiographic image stacks and spatial normalization of functional cortical activity patterns.

This paper introduces two new methods for the automatic anatomical and functional analysis of neurobiological autoradiographic image stacks, such as 2-fluoro-deoxyglucose (2FDG) images. The difficulty in the evaluation of these "2(1/2)D" datasets is that they do not inherently represent a continuous 3D data volume (as generated by MRI or CT), but consist of a stack of images from single tissue slices, suffering from unavoidable preparation artifacts. In the first part of the paper, a semi-automatic segmentation method is presented which generates a 3D surface model of certain brain structures and which is robust against different cutting directions with respect to the brain coordinate system. The method saves man-hours compared to manual segmentation and the results are highly reproducible. In the second part, a fully automatic method for the extraction, analysis and 3D visualization of functional information is described, which allows not only a more accurate localization of activation sites, but also greatly enhances the comparability of different individuals. Results are shown for 2FDG autoradiographs from rat brains under acoustical stimulation.

Animals↗
PubMed2006

The ABCs of computerized naming: equivalency, reliability, and predictive validity of a computerized rapid automatized naming (RAN) task.

Population-based studies indicate dual routes to disabled reading in adolescence and adulthood: slowed acquisition of single word reading and ADHD (particularly inattention) in early childhood. Impairments in rapid serial naming may be a factor common to both problems. The gold-standard measure of this ability, the Rapid Automatized Naming Task (RAN; [Denckla MB, Rudel R. Rapid automatized naming of pictured objects, colors, letters and numbers by normal children. Cortex 1974;10:186-202]), has traditionally been administered in a paper-pencil format. Recently however, researchers [Neuhaus GF, Carlson CD, Jeng WM, Post Y, Swank PR. The reliability and validity of rapid automatized scoring software ratings for the determination of pause and articulation component durations. Educ Psychol Meas 2001;61:490-504] have begun to use computerized versions of the RAN. Here a slightly modified computerized version of the RAN was created and the equivalency between the computerized RAN and the conventional version was investigated using a university student sample. Naming times on the conventional and computerized RAN were highly correlated, overall, and for each of the four RAN stimulus types (letters, digit, colors, objects). Conventional and computerized RAN times predicted reading rate and reading comprehension scores equally well and both showed very high test-retest reliability. With our university student sample, findings indicate equivalency between the two testing mediums in all areas examined.

Adult↗
PubMedDate not supplied

Image segmentation for automatic particle identification in electron micrographs based on hidden Markov random field models and expectation maximization.

Three-dimensional reconstruction of large macromolecules like viruses at resolutions below 10 A requires a large set of projection images. Several automatic and semi-automatic particle detection algorithms have been developed along the years. Here we present a general technique designed to automatically identify the projection images of particles. The method is based on Markov random field modelling of the projected images and involves a pre-processing of electron micrographs followed by image segmentation and post-processing. The image is modelled as a coupling of two fields--a Markovian and a non-Markovian. The Markovian field represents the segmented image. The micrograph is the non-Markovian field. The image segmentation step involves an estimation of coupling parameters and the maximum á posteriori estimate of the realization of the Markovian field i.e, segmented image. Unlike most current methods, no bootstrapping with an initial selection of particles is required.

Algorithms↗
PubMed2004

A graphical user interface for automatic image registration software designed for radiotherapy treatment planning.

Medical imaging forms a vital component of radiotherapy treatment planning and its evaluation. The integration of the useful data obtained from multiple imaging modalities for radiotherapy planning is achieved by image registration softwares. In radiotherapy planning systems, normally the computed tomography (CT) slices are kept as a standard upon which other modality images (magnetic resonance imaging [MRI], single photon emission computed tomography [SPECT], positron emission tomography [PET], etc.) are aligned--automatically or interactively. Following validation of successful registration, they are resampled and reformatted, as per the requirements. This paper defines the minimum requirements of automatic image registration software for 3-dimensional (3D) radiotherapy planning and describes the implementation of a suitable graphical user interface developed in Visual Basic (version 5). The automatic image registration (AIR) routines freely available from Dr. Roger P. Woods, UCLA, (USA) were used in this software. This software could be easily implemented and was easy to use for image processing suitable for radiotherapy planning systems.

Algorithms↗
PubMed2005

Confhusius: a robust and fully automatic calibration method for 3D freehand ultrasound.

This paper describes a new robust and fully automatic method for calibration of three-dimensional (3D) freehand ultrasound called Confhusius (CalibratiON for FreeHand UltraSound Imaging USage). 3D Freehand ultrasound consists in mounting a position sensor on a standard probe. The echographic B-scans can be localized in 3D and compounded into a volume. However, especially for quantitative use, this process dramatically requires a calibration procedure that determines its accuracy and usefulness. Calibration aims at determining the transformation (translations, rotations, scaling) between the coordinates system of the echographic images and the coordinate system of the localization system. To calibrate, we acquire images of a phantom whose 3D geometrical properties are known. We propose a robust and fully automatic calibration method based on the Hough transform and robust estimators. Experiments have been done with synthetic and real sequences, and this calibration method is shown to be easy to perform, accurate, automatic and fast enough for clinical use.

Calibration↗
PubMed2004

Neural correlates of auditory sensory memory and automatic change detection.

An auditory event-related potential component, the mismatch negativity (MMN), reflects automatic change detection and its prerequisite, sensory memory. This study examined the neural correlates of automatic change detection using BOLD fMRI and two rates of presentation previously shown to induce either a large or no MMN. A boxcar block design was employed in two functional scans, each performed twice. A block consisting of 1000-Hz standards (S) alternated with one consisting of 1000-Hz standards and 2000-Hz infrequent deviants (S + D). Presentation rate was either 150 or 2400 ms. Fourteen participants were instructed to ignore all auditory stimulation and concentrate on a film (no audio) by reading subtitles. Data analysis used SPM99 and random effects approach. Cluster statistics (P < 0.05, corrected) were employed at a height threshold of P < 0.001. At the short ISI, there was a significant BOLD response in the right superior temporal gyrus (STG), the left insula, and the left STG (including parts of primary auditory cortex). There were no suprathreshold clusters at the long rate, with S + D blocks inducing no greater activity than S blocks. These results support the hypothesis that the automatic detection of auditory change occurs in the STG bilaterally and relies on the maintenance of sensory memory traces.

Adult↗
PubMed2005

Automatic analysis of cerebral asymmetry: an exploratory study of the relationship between brain torque and planum temporale asymmetry.

Leftward occipital and rightward frontal lobe asymmetry (brain torque) and leftward planum temporale asymmetry have been consistently reported in postmortem and in vivo neuroimaging studies of the human brain. Here automatic image analysis techniques are applied to quantify global and local asymmetries, and investigate the relationship between brain torque and planum temporale asymmetries on T1-weighted magnetic resonance (MR) images of 30 right-handed young healthy subjects (15 male, 15 female). Previously described automatic cerebral hemisphere extraction and 3D interhemispheric reflection-based methods for studying brain asymmetry are applied with a new technique, LowD (Low Dimension), which enables automatic quantification of brain torque. LowD integrates extracted left and right cerebral hemispheres in columns orthogonal to the midsagittal plane (2D column maps), and subsequently integrates slices along the brain's anterior-posterior axis (1D slice profiles). A torque index defined as the magnitude of occipital and frontal lobe asymmetry is computed allowing exploratory investigation of relationships between this global asymmetry and local asymmetries found in the planum temporale. LowD detected significant torque in the 30 subjects with occipital and frontal components found to be highly correlated (P<0.02). Significant leftward planum temporale asymmetry was detected (P<0.05), and the torque index correlated with planum temporale asymmetry (P<0.001). However, torque and total brain volume were not correlated. Therefore, although components of cerebral asymmetry may be related, their magnitude is not influenced by total hemisphere volume. LowD provides increased sensitivity for detection and quantification of brain torque on an individual subject basis, and future studies will apply these techniques to investigate the relationship between cerebral asymmetry and functional laterality.

Adult↗
PubMed2005

The effect of group size on health and growth rate of Swedish dairy calves housed in pens with automatic milk-feeders.

Group pens equipped with automatic milk-feeding systems are increasingly being used for young dairy calves in Sweden. The system is, however, associated with an increased risk of clinical respiratory-tract disease and a reduced growth rate. In an experimental study we compared the health and growth rate of two different group sizes of calves (6-9 versus 12-18) kept in pens with automatic milk-feeders. The experiment was performed from September 2002 to February 2004, in nine commercial dairy farms in south-west Sweden. Each farm was equipped with two pens with automatic milk-feeders and no possibility of direct contact between calves from different pens. The calves were housed individually until 3-35 (median, 12) days of age, and then were allocated to one of the two group pens by random-number lists. Altogether 892 calves were studied: 297 in the small- and 595 in the large-sized groups. The calves' heart girths were measured at birth and at 56 days of age. Blood samples for analysis of serum haptoglobin concentration (S-Hp) were collected once for each calf, at four to eight weeks of age. Diseases were recorded by the farmers and by a veterinarian, who visited the farms every third week and physically examined all the calves. The effects of group size on the risks of diarrhoea, clinical respiratory-tract disease and increased respiratory sounds, and on the growth rate and S-Hp were evaluated using multiple logistic- and linear-regression models with herd as fixed effect. Age at transfer to group pen, breed, immunoglobulin concentration of colostrum received, parity of the dam and presence of diarrhoea before transfer to the group pen, season, sex, year, and, in the analysis of growth rate, birth heart girth were extra explanatory variables. Calves in pens for 12-18 calves had a higher incidence of respiratory illness (OR: 1.4) and grew 0.022 cm/day less than calves housed in groups of 6-9 animals (equivalent to approximately 40 g/day). We detected no differences between calves kept in the small-sized versus the large-sized groups in terms of risk of diarrhoea or mean S-Hp. We concluded that housing calves in groups of under 10 calves is preferable from a health and growth perspective.

Animal Husbandry↗
PubMed2006

Amygdala reactivity predicts automatic negative evaluations for facial emotions.

The amygdala is a key structure in a limbic circuit involved in the rapid and unconscious processing of facial emotions. In the present study, the role of the amygdala in automatic, involuntary appraisal processes, which are believed to be a crucial component of emotion processing, was investigated in 23 healthy subjects. Amygdala activity was recorded in response to masked displays of angry, sad, and happy facial expressions using functional magnetic resonance imaging (fMRI). In a subsequent experiment, the subjects performed a masked affective priming task that characterizes automatic emotion processing by investigating the biasing effect of subliminally presented emotional faces on evaluative ratings to subsequently presented neutral stimuli. In the affective priming task, significant valence-congruent evaluation manipulation was observed. Subjects rated neutral targets more positively if they were primed by happy faces. Significant correlations were found between amygdala responses to masked negative facial expressions and negative evaluation shifts elicited by the corresponding emotion quality in the affective priming task. Spontaneous amygdala reactivity to facial emotions appears to be a determinant of automatic negative evaluative response tendencies. This finding might shed some light on how amygdala hyperresponsivity contributes to negative cognitive biases commonly observed in affective disorders.

Adult↗
PubMed2004

Preliminary in-hospital experience with a fully automatic external cardioverter-defibrillator.

BACKGROUND: Ventricular fibrillation (VF) and ventricular tachycardia (VT) are frequently present as initial rhythms during in-hospital cardiac arrest. Although ample evidence exists to support the need for rapid defibrillation, the response to in-hospital cardiac arrest remains without major advances in recent years. The delay between the arrhythmic event and intervention is still a challenge for clinical practice. OBJECTIVE: To analyze the performance and safety of in-hospital use of a programmable, fully automatic external cardioverter-defibrillator (AECD). METHODS: We conducted a prospective study at the Emergency Department of a university hospital. A total of 55 patients considered to be at risk of sustained VT/VF were included. Patients underwent monitoring of their cardiac rhythm by the AECD. Upon detection of a ventricular tachyarrhythmia, the AECD was programmed to automatically deliver shock therapy. RESULTS: We recorded 19 episodes of VT/VF in 3 patients. The median time between the beginning of the arrhythmia and the first defibrillation was 33.4 s (21-65 s). One episode of spontaneous reversion of VT was documented 20 s after its origin and shock therapy was aborted. The defibrillation success was 94.4% (17/18) for the first shock and 100% (1/1) for the second shock. No case of inappropriate shock discharge was registered during the study period. CONCLUSION: The AECD has the feasibility to combine long-term monitoring with automatic defibrillation safely and effectively. It presents the possibility of providing rapid identification of, and response to, in-hospital ventricular tachyarrhythmias.

Defibrillators↗
PubMed2004

CPR courses and semi-automatic defibrillators--life saving in cardiac arrest?

OBJECTIVES: The aim was to assess the knowledge of life-supporting first-aid in both cardiac arrest survivors and relatives, and their willingness to have a semi-automatic external defibrillator in their homes and use it in an emergency. MATERIAL AND METHODS: Cardiac arrest survivors, their families, friends, neighbours and co-workers were interviewed by medical students using prepared questionnaires. Their knowledge and self-assessment of life-supporting first-aid, their willingness to have a semi-automatic defibrillator in their homes and their willingness to use it in an emergency before and after a course in cardiopulmonary resuscitation (CPR) with a semi-automatic external defibrillator was evaluated. Courses were taught by medical students who had received special training in basic and advanced life support. RESULTS: Both patients and relatives, after a course of 2-3 h, were no longer afraid of making mistakes by providing life-supporting first-aid. The automated external defibrillator (AED) was generally accepted and considered easy to handle. CONCLUSION: We consider equipping high-risk patients and their families with AEDs as a viable method of increasing their survival in case of a recurring cardiac arrest. This, of course, should be corroborated by further studies.

Cardiopulmonary Resuscitation↗
PubMed2004

A general automatic method for the analysis of NREM sleep microstructure.

OBJECTIVE: To define a unified method for the automatic recognition and quantitative description of EEG phasic events of sleep microstructure occurring during NREM sleep, particularly arousals, phase A subtypes of cyclic alternating pattern and spindles. METHODS: The NREM sleep EEG of 10 normal young subjects was examined in order to recognize formal phasic events of sleep microstructure. The following 'formal' events (i.e. events defined exclusively on the basis of automatic analysis criteria) were classified: arousals, A1-phases (A-phases not including arousals) and A2- and A3-phases (A-phases including arousals). Spindle bursts, corresponding to visually recognized spindles, were also formally defined. The identification of these events was carried out following a three-step procedure: (1) computation of band-related descriptors derived from the EEG signal, (2) introduction of suitable thresholds and (3) application of simple logical principles, i.e. an exclusion principle and an overlapping principle. RESULTS: Formal A-phases, arousals and spindle bursts showed spectral characteristics which were consistent with visual inspection. The value of the parameter Correctness for the recognition of the A-phases was 83.5%. In particular, the different physiological distribution of the A-phases in Stage 2 preceding slow wave sleep with respect to Stage 2 preceding REM sleep was confirmed. CONCLUSIONS: The proposed method provides a unified quantitative approach to the study of sleep microstructure. Visually defined events can be reliably identified by means of automatic recognition.

Adult↗
PubMed2004

Strategies for reliable automatic onset time picking of acoustic emissions and of ultrasound signals in concrete.

Determining the onset of transient signals like seismograms, acoustic emissions or ultrasound signals is very time consuming if the onset is picked manually. Therefore, different approaches exist, especially in seismology. The concepts of the most popular approaches are summarized. An own approach adapted to ultrasound signals and acoustic emissions, based on the Akaike Information Criterion (AIC), is presented. The AIC-picker is compared to an automatic onset detection algorithm based on the Hinkley criterion and also adapted to acoustic emissions. Manual picks performed by an analyst are used as reference values. Both automatic onset detection algorithms are applied to ultrasound signals which are used to monitor the setting and hardening of concrete. They are also applied to acoustic emissions recorded during a pull-out test. The AIC-picker produces sufficient reliable results for ultrasound signals where the deviation from the manual picks varies between 2% and 4%. Concerning acoustic emissions, only 10% of the events result in a mislocation vector greater than 5mm. It can be shown that our AIC-picker is a reliable tool for automatic onset detection for ultrasound signals and acoustic emissions of varying signal to noise ratio.

Journal Article↗
PubMed2006

Automatic timing of aortic valve closure in apical tissue Doppler images.

Ultrasound color tissue Doppler imaging (TDI) can be used to estimate velocities of moving left ventricular cardiac tissue. Aortic valve closure (AVC) can be observed as a notch in apical TDI velocity/time curves occurring after ejection, but before early relaxation. This work sought to evaluate automatic and automated algorithms using TDI for timing AVC. Mitral valve position and the time point of early relaxation were extracted and used to accomplish the task. To test the algorithms, phonocardiogram of the second heart sound was recorded simultaneously with TDI and used as a reference method. The algorithms were tested on apical views of 16 healthy subjects. In 98% of the cardiac cycles, the automatic algorithm estimated the time point of AVC within 25 ms of the reference. Automatic detection of AVC might save manual effort and provide a marker separating ejection and diastole for further automated analysis.

Adolescent↗
PubMed1997

Automatic measurement of corrected QT interval in Holter recordings: comparison of its dynamic behavior in patients after myocardial infarction with and without life-threatening arrhythmias.

This study was designed to determine the value of automatic corrected QT-interval measurement in Holter tapes in patients after myocardial infarction as a marker of life-threatening ventricular arrhythmias. We compared the corrected QT interval, automatically measured in 24-hour Holter recordings, in two groups of patients after myocardial infarction: group I was composed of 14 patients admitted consecutively to our hospital for documented sustained ventricular tachycardia or out-of-hospital cardiac arrest. Group II consisted of 28 patients with previous myocardial infarction with characteristics similar to those of group I, but without malignant ventricular arrhythmias in the follow-up. The global mean 24-hour corrected QT interval was longer in group I (425 +/- 20 msec) than in those patients after myocardial infarction without arrhythmias (group II) (405 +/- 17 msec; p < 0.01). Furthermore, a significant proportion of patients of group I (seven of 14) exhibited more peaks of corrected QT longer than 500 msec compared with patients of group II (two of 28; p < 0.005). A circadian rhythm of corrected QT peaks was observed in group I, having a significantly higher incidence from 11 PM to 11 AM (p < 0.05). We conclude that automatic corrected QT-interval measurement on Holter electrocardiogram is now available and feasible. Our results suggest that this is a marker for risk assessment of life-threatening ventricular arrhythmias. Large-scale trials are needed to confirm these results and to determine the predictive value of this technique for risk stratification.

Algorithms↗
PubMed1984

The treatment of malignant ventricular arrhythmias with combined endocardial resection and implantation of the automatic defibrillator: preliminary report.

Fourteen patients with refractory ventricular tachyarrhythmias were treated with combined endocardial resection and implantation of the automatic defibrillator. There were 11 men and 3 women with a mean age of 53 years (range, 41 to 58 years). All patients had coronary artery disease; the mean ejection fraction was 26%, and the mean number of cardiac arrests was 2.6. Programmed electrical stimulation induced sustained ventricular tachycardia in 13 patients and nonsustained ventricular tachycardia in 1. Operative endocardial mapping in the 13 patients with sustained ventricular tachycardia demonstrated a septal focus of early activation in 9 patients and a nonseptal site in 4. Following resection, sustained ventricular tachycardia could not be reinduced. There was 1 operative death. Programmed electrical stimulation performed one month after operation induced ventricular tachycardia in 5 patients, but tachycardia could not be induced in the other 8 survivors. The longest follow-up was 32 months; the average was 17 months. There were 2 late deaths. One patient died of myocardial infarction and 1 of pulmonary edema following a routine cholecystectomy. In another patient, late ventricular tachycardia developed but was automatically terminated by the implanted defibrillator. These results suggest that endocardial resection combined with implantation of the automatic defibrillator may offer the greatest protection yet available to patients with malignant ventricular tachyarrhythmias.

Adult↗