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PubMed2007

Automatic procedure for using models of proteins in molecular replacement.

In a crystallography experiment, a crystal is irradiated with X-rays whose diffracted waves are collected and measured. The reconstruction of the structure of the molecule in the crystal requires knowledge of the phase of the diffracted waves, information that is lost in the passage from the three-dimensional structure of the molecule to its diffraction pattern. It can be recovered using experimental methods such as heavy-atom isomorphous replacement and anomalous scattering or by molecular replacement, which relies on the availability of an atomic model of the target structure. This can be the structure of the target protein itself, if a previous structure determination is available, or a computational model or, in some cases, the structure of a homologous protein. It is not straightforward to predict beforehand whether or not a computational model will work in a molecular replacement experiment, although some rules of thumb exist. The consensus is that even minor differences in the quality of the model, which are rather difficult to estimate a priori, can have a significant effect on the outcome of the procedure. We describe here a method for quickly assessing whether a protein structure can be solved by molecular replacement. The procedure consists in submitting the sequence of the target protein to a selected list of freely available structure prediction servers, cluster the resulting models, select the representative structures of each cluster and use them as search models in an automatic phasing procedure. We tested the procedure using the structure factors of newly released proteins of known structure downloaded from the Protein Data Bank as soon as they were made available. Using our automatic procedure we were able to obtain an interpretable electron density map in more than half the cases.

Amino Acids↗

PubMed2005

A new three-dimensional automatic bodymarker system for transvaginal ultrasonography.

OBJECTIVE: To evaluate the accuracy and usefulness of a newly developed three-dimensional automatic bodymarker system for transvaginal ultrasonography. METHODS: A bodymarker system which utilizes an electromagnetic field to specify the probe position was developed. Software was written which enabled the positional information of the probe and the ultrasound image to be simultaneously displayed on a personal computer. The bodymarker was displayed as a three-dimensional graphic model. The differences between the estimated and the actual position--i.e. the error--for both position (x, y and z) and angles (azimuth, elevation and roll) of the probe were measured. The movement of the probe was then evaluated in healthy female volunteers and the comparative time required for ultrasound examination was determined. RESULTS: Both the position and the angles of the probe were accurately shown in the computer display. The errors were 1.0 mm and 0.7 degrees (median) for position and angle, respectively. The system was also shown to work well in healthy female volunteers. Calibration of the new system required only 5.0 seconds, compared with an average of 7.6 seconds for the conventional bodymarker. CONCLUSION: The newly developed three-dimensional automatic transvaginal bodymarker system provides an accurate indication of probe position and its tilting angle. It works well in healthy female volunteers and speeds up the examination time. It may be clinically useful for transvaginal ultrasound examination.

Calibration↗

PubMed1993

Automatic access to lexical semantics in aphasia: evidence from semantic and associative priming.

We report the auditory lexical decision performance of four patients, all of whom are clinically diagnosed as Broca's aphasics. In a task that separates associative from semantic priming, all four patients show significant priming effects and no interaction with type of relatedness. We find no evidence to support some of the current accounts of these patients' linguistic difficulties in terms of an impairment in automatic processing routines. Instead, we argue that automatic access to lexical semantics is intact.

Adult↗

PubMed2001

Automatic lumbar vertebral identification using surface-based registration.

This work proposes the use of surface-based registration to automatically select a particular vertebra of interest during surgery. Manual selection of the correct vertebra can be a challenging task, especially for closed-back, minimally invasive procedures. Our method uses shape variations that exist among lumbar vertebrae to automatically determine the portion of the spinal column surface that correctly matches a set of physical vertebral points. In our experiments, we register vertebral points representing posterior elements of a single vertebra in physical space to spinal column surfaces extracted from computed tomography images of multiple vertebrae. After registering the set of physical points to each vertebral surface that is a potential match, we then compute the standard deviation of the surface error for each registration trial. The registration that corresponds to the lowest standard deviation designates the correct match. We have performed our current experiments on two plastic spine phantoms and two patients.

Computational Biology↗

PubMed2000

The development of automaticity in accessing number magnitude.

This study traces developmental changes in automatic and intentional processing of Arabic numerals using a numerical-Stroop paradigm. In Study 1, university students compared the numerical or physical size of Arabic numerals varying along both dimensions. In Study 2, first graders (mean age = 6 years 6 months), third graders (mean age = 8 years 4 months), and fifth graders (mean age = 10 years 3 months) were tested to examine developmental changes in numerical and physical comparisons. In the numerical comparison task, a size congruity effect was found at all ages (i.e., relative to a neutral control, congruent physical sizes facilitated, and incongruent sizes interfered with, the numerical comparison). The pattern of facilitation and interference, however, was modulated by age. In the physical comparison task, the incongruity between physical and numerical size affected only older children and adults. These findings strongly suggest that the automatization in number processing is achieved gradually as numerical skills progress.

Adult↗

PubMed1994

Rational automatic search method for stable docking models of protein and ligand.

An efficient automatic method has been developed for docking a ligand molecule to a protein molecule. The method can construct energetically favorable docking models, considering specific interactions between the two molecules and conformational flexibility in the ligand. In the first stage of docking, likely binding modes are searched and estimated effectively in terms of hydrogen bonds, together with conformations in part of the ligand structure that includes hydrogen bonding groups. After that part is placed in the protein cavity and is optimized, conformations in the remaining part are also examined systematically. Finally, several stable docking models are obtained after optimization of the position, orientation and conformation of the whole ligand molecule. In all the screening processes, the total potential energy including intra- and intermolecular interaction energy, consisting of van der Waals, electrostatic and hydrogen bonding energies, is used as the index. The characteristics of our docking method are high accuracy of the results, fully automatic generation of models and short computational time. The efficiency of the method was confirmed by four docking trials using two enzyme systems. In two attempts to dock methotrexate to dihydrofolate reductase and 2'-GMP to ribonuclease T1, the exact structures of complexes in crystals were reproduced as the most stable docking models, without any assumptions concerning the binding modes and ligand conformations. The most stable docking models of dihydrofolate and trimethoprim, respectively, to dihydrofolate reductase were also in good agreement with those suggested by experiment. In all test cases, it was shown that our method can accurately predict the correct docking structures, discriminating the correct model from incorrect ones. The efficiency of our method was further tested from the viewpoint of ability to predict the relative stability of the docking structures of two triazine derivatives to dihydrofolate reductase. Our docking method provides a useful tool for rational drug design and investigations of biochemical reaction mechanisms.

Algorithms↗

PubMed2001

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons.

Orthologs are genes in different species that originate from a single gene in the last common ancestor of these species. Such genes have often retained identical biological roles in the present-day organisms. It is hence important to identify orthologs for transferring functional information between genes in different organisms with a high degree of reliability. For example, orthologs of human proteins are often functionally characterized in model organisms. Unfortunately, orthology analysis between human and e.g. invertebrates is often complex because of large numbers of paralogs within protein families. Paralogs that predate the species split, which we call out-paralogs, can easily be confused with true orthologs. Paralogs that arose after the species split, which we call in-paralogs, however, are bona fide orthologs by definition. Orthologs and in-paralogs are typically detected with phylogenetic methods, but these are slow and difficult to automate. Automatic clustering methods based on two-way best genome-wide matches on the other hand, have so far not separated in-paralogs from out-paralogs effectively. We present a fully automatic method for finding orthologs and in-paralogs from two species. Ortholog clusters are seeded with a two-way best pairwise match, after which an algorithm for adding in-paralogs is applied. The method bypasses multiple alignments and phylogenetic trees, which can be slow and error-prone steps in classical ortholog detection. Still, it robustly detects complex orthologous relationships and assigns confidence values for both orthologs and in-paralogs. The program, called INPARANOID, was tested on all completely sequenced eukaryotic genomes. To assess the quality of INPARANOID results, ortholog clusters were generated from a dataset of worm and mammalian transmembrane proteins, and were compared to clusters derived by manual tree-based ortholog detection methods. This study led to the identification with a high degree of confidence of over a dozen novel worm-mammalian ortholog assignments that were previously undetected because of shortcomings of phylogenetic methods.A WWW server that allows searching for orthologs between human and several fully sequenced genomes is installed at http://www.cgb.ki.se/inparanoid/. This is the first comprehensive resource with orthologs of all fully sequenced eukaryotic genomes. Programs and tables of orthology assignments are available from the same location.

Algorithms↗

PubMed2000

The NMR spectra of samples dissolved in liquid-crystalline phases: automatic analysis with the aid of multiple quantum spectra--the case of flexible molecules.

Homonuclear N(S) = 0 and heteronuclear N(S) not equal 0 multiple quantum spectra, involving changes in the magnetic number m(I) by (N(I)-1), (N(I) - 2), and (N(I)-3), with N(I) and N(S) the number of interacting nuclei of magnetogyric ratio gamma(I) and gamma(S), are used for the automatic analysis of (1)H NMR spectra of flexible molecules dissolved in liquid-crystalline phases. The automatic procedure has been applied to study molecules of general formula Ph-CH(2)-X starting from a parameter set having all the spectral parameters set to zero. The results of such an analysis are then used as starting parameters for analysis of the single quantum spectrum. The method was first tested when X = Br and X = H in order to compare strategies differing for the types of parameters used and was then applied to the analysis of 3-phenylprop-1-yne.

Magnetic Resonance Spectroscopy↗

PubMed2002

Automatic tuned MRI RF coil for multinuclear imaging of small animals at 3T.

We have developed an MRI RF coil whose tuning can be adjusted automatically between 120 and 128 MHz for sequential spectroscopic imaging of hydrogen and fluorine nuclei at field strength 3 T. Variable capacitance (varactor) diodes were placed on each rung of an eight-leg low-pass birdcage coil to change the tuning frequency of the coil. The diode junction capacitance can be controlled by the amount of applied reverse bias voltage. Impedance matching was also done automatically by another pair of varactor diodes to obtain the maximum SNR at each frequency. The same bias voltage was applied to the tuning varactors on all rungs to avoid perturbations in the coil. A network analyzer was used to monitor matching and tuning of the coil. A Pentium PC controlled the analyzer through the GPIB bus. A code written in LABVIEW was used to communicate with the network analyzer and adjust the bias voltages of the varactors via D/A converters. Serially programmed D/A converter devices were used to apply the bias voltages to the varactors. Isolation amplifiers were used together with RF choke inductors to provide isolation between the RF coil and the DC bias lines. We acquired proton and fluorine images sequentially from a multicompartment phantom using the designed coil. Good matching and tuning were obtained at both resonance frequencies. The tuning and matching of the coil were changed from one resonance frequency to the other within 60 s.

Animals↗

PubMed2001

Automatic discovery of sub-molecular sequence domains in multi-aligned sequences: a dynamic programming algorithm for multiple alignment segmentation.

Automatic identification of sub-structures in multi-aligned sequences is of great importance for effective and objective structural/functional domain annotation, phylogenetic treeing and other molecular analyses. We present a segmentation algorithm that optimally partitions a given multi-alignment into a set of potentially biologically significant blocks, or segments. This algorithm applies dynamic programming and progressive optimization to the statistical profile of a multi-alignment in order to optimally demarcate relatively homogenous sub-regions. Using this algorithm, a large multi-alignment of eukaryotic 16S rRNA was analyzed. Three types of sequence patterns were identified automatically and efficiently: shared conserved domain; shared variable motif; and rare signature sequence. Results were consistent with the patterns identified through independent phylogenetic and structural approaches. This algorithm facilitates the automation of sequence-based molecular structural and evolutionary analyses through statistical modeling and high performance computation.

Algorithms↗

PubMed2001

Automatic segmentation of the ventricular system from MR images of the human brain.

An algorithm was developed that automatically segments the lateral and third ventricles from T1-weighted 3-D-FFE MR images of the human brain. The algorithm is based upon region-growing and mathematical morphology operators and starts from a coarse binary total brain segmentation, which is obtained from the 3-D-FFE image. Anatomical knowledge of the ventricular system has been incorporated into the method in order to find all constituting parts of the system, even if they are disconnected, and to avoid inclusion of nonventricle cerebrospinal fluid (CSF) regions. A test of the method on a synthetic MR brain image produced a segmentation overlap of 0.98 between the simulated ventricles ("model") and those defined by the algorithm. Further tests were performed on a large data set of 227 1.5 T MR brain images. The algorithm yielded useful results for 98% of the images. The automatic segmentations had intra-class correlation coefficients of 0.996 for the lateral ventricles and 0.86 for the third ventricle, with manually edited segmentations. Comparison of ventricular volumes of schizophrenia patients compared with those of healthy control subjects showed results in agreement with the literature.

Algorithms↗

PubMed2002

A robust method for extraction and automatic segmentation of brain images.

A new protocol is introduced for brain extraction and automatic tissue segmentation of MR images. For the brain extraction algorithm, proton density and T2-weighted images are used to generate a brain mask encompassing the full intracranial cavity. Segmentation of brain tissues into gray matter (GM), white matter (WM), and cerebral spinal fluid (CSF) is accomplished on a T1-weighted image after applying the brain mask. The fully automatic segmentation algorithm is histogram-based and uses the Expectation Maximization algorithm to model a four-Gaussian mixture for both global and local histograms. The means of the local Gaussians for GM, WM, and CSF are used to set local thresholds for tissue classification. Reproducibility of the extraction procedure was excellent, with average variation in intracranial capacity (TIC) of 0.13 and 0.66% TIC in 12 healthy normal and 33 Alzheimer brains, respectively. Repeatability of the segmentation algorithm, tested on healthy normal images, indicated scan-rescan differences in global tissue volumes of less than 0.30% TIC. Reproducibility at the regional level was established by comparing segmentation results within the 12 major Talairach subdivisions. Accuracy of the algorithm was tested on a digital brain phantom, and errors were less than 1% of the phantom volume. Maximal Type I and Type II classification errors were low, ranging between 2.2 and 4.3% of phantom volume. The algorithm was also insensitive to variation in parameter initialization values. The protocol is robust, fast, and its success in segmenting normal as well as diseased brains makes it an attractive clinical application.

Adult↗

PubMed2005

Automatic 3D segmentation of intravascular ultrasound images using region and contour information.

Intravascular ultrasound (IVUS) produces images of arteries that show the lumen in addition to the layered structure of the vessel wall. A new automatic 3D IVUS fast-marching segmentation model is presented. The method is based on a combination of region and contour information, namely the gray level probability density functions (PDFs) of the vessel structures and the image gradient. Accurate results were obtained on in-vivo and simulated data with average point to point distances between detected vessel wall boundaries and validation contours below 0.105 mm. Moreover, Hausdorff distances (that represent the worst point to point variations) resulted in values below 0.344 mm, which demonstrate the potential of combining region and contour information in a fast-marching scheme for 3D automatic IVUS image processing.

Algorithms↗

PubMed2005

Automatic segmentation of the articular cartilage in knee MRI using a hierarchical multi-class classification scheme.

Osteoarthritis is characterized by the degeneration of the articular cartilage in joints. We have developed a fully automatic method for segmenting the articular cartilage in knee MR scans based on supervised learning. A binary approximate kNN classifier first roughly separates cartilage from background voxels, then a three-class classifier assigns one of three classes to each voxel that is classified as cartilage by the binary classifier. The resulting sensitivity and specificity are 90.0% and 99.8% respectively for the medial cartilage compartments. We show that an accurate automatic cartilage segmentation is achievable using a low-field MR scanner.

Algorithms↗

PubMed2005

Shape modeling using automatic landmarking.

This paper describes a novel approach to automatically recover accurate correspondence over various shapes. In order to detect the features points with the capability in capturing the characteristics of an individual shape, we propose to calculate the skeletal representation for the shape curve through the medial axis transform. Employing this shape descriptor, mathematical landmarks are automatically identified based on the local feature size function, which embodies the geometric and topological information of the boundary. Before matching the resulting landmarks, shape correspondence is first approached by matching he major components of the shape curves using skeleton features. This helps in keeping the consecutive order and reducing the search space during the matching process. Point matching is then performed within each pair of corresponding components by solving a consecutive assignment problem. The effectiveness of this approach is demonstrated through experimental results on several different training sets of biomedical object shapes.

Algorithms↗

PubMed1987

Application of automatic image analysis for morphometric studies of peroxisomes stained cytochemically for catalase. II. Light-microscopic application.

The feasibility of the application of a television-based image analyzer, the Texture Analysis System (TAS, Leitz Wetzlar, FRG) in conjunction with a light microscope for morphometric studies of hepatic peroxisomes has been investigated. Rat liver peroxisomes were stained with the alkaline-DAB method for localization of catalase and semithin (0.25 and 1 micron) sections of plastic-embedded material were examined under an oil immersion objective. The TAS detected the peroxisomal profiles selectively and determined their morphometric parameters automatically. The same parameters were obtained also by morphometric analysis of electron micrographs from the same material. The volume density of peroxisomes determined by TAS in semithin sections of normal liver, after correction for section thickness, is quite close to the corresponding value obtained by morphometry of electron micrographs. The difference is approximately 20%. In animals treated with the hypolipidemic drug bezafibrate, which causes proliferation of peroxisomes, TAS detected readily the increase in volume density of peroxisomes in semithin sections. In comparison with electron microscopy, however, the light-microscopic approach seems to underestimate the proliferation. The lower resolution of the light microscope and overlapping of neighbouring particles in relatively thick sections used for light-microscopic analysis may account for the differences. The present study has demonstrated the usefulness of automatic image analysis in conjunction with selective cytochemical staining of peroxisomes for morphometry of this organelle in rat liver. The light-microscopic approach is not only faster but is also extremely economical by obviating the use of an electron microscope.

Animals↗

PubMed1994

The importance of somatosensory information in triggering and scaling automatic postural responses in humans.

To clarify the role of somatosensory information from the lower limbs of humans in triggering and scaling the magnitude of automatic postural responses, patients with diabetic peripheral neuropathy and age-matched normal controls were exposed to posterior horizontal translations of their support surface. Translation velocity and amplitude were varied to test the patients' ability to scale their postural responses to the magnitude of the translation. Postural response timing was quantified by measuring the onset latencies of three shank, thigh, and trunk muscles and response magnitude was quantified by measuring torque at the support surface. Neuropathy patients showed the same distal-to-proximal muscle activation pattern as normal subjects, but the electromyogram (EMG) onsets in patients were delayed by 20-30 ms at all segments, suggesting an important role for somatosensory information from the lower limb in triggering centrally organized postural synergies. Patients showed an impaired ability to scale torque magnitude to both the velocity and amplitude of surface translations, suggesting that somatosensory information from the legs may be utilized for both direct sensory feedback and use of prior experience in scaling the magnitude of automatic postural responses.

Aged↗

PubMed1985

Characterization and automatic identification of ECG conduction abnormalities using segmental multiharmonic Fourier analysis of gated blood-pool scintigrams.

This study of biventricular segmental timing sequences compared patterns of the first-harmonic phase with those of multiharmonic Fourier-analysis-derived parameters to determine their suitability for the classification of patients using an automatic pattern recognition scheme. The study involved nine patients with normal ECGs, six with left bundle branch block, 4 with right bundle branch block, and 6 with right-ventricular pacemakers; all patients had normal left-ventricular function. The segmental sequence described by the time of end systole was similar to that described by the first-harmonic phase, with a lower correlation using the time of maximum filling rate, and a rather poor correlation of the time of maximum ejection rate with the other parameters. Thus, despite theoretical difficulties, timing patterns described by phase best agreed with those of the time of end systole. Intersegmental timing differences were used as criteria for discriminating between groups by means of a sequential logic tree. Using either phase, time of end systole or time of maximum ejection rate, all patients were correctly classified into the four ECG categories. More intersegmental timing differences were useful as criteria for phase (57) than for the time of end systole (45) or the time of maximum ejection rate (30). The first-harmonic phase was more efficient than the time of end systole for separating patient groups. Sequential biventricular timing disorders can be objectively classified using either first-harmonic or multiharmonic Fourier analysis, and their patterns can be automatically recognized and used for classification.

Bundle-Branch Block↗