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PubMed2006

Estimating resting motor thresholds in transcranial magnetic stimulation research and practice: a computer simulation evaluation of best methods.

OBJECTIVES: Resting motor threshold is the basic unit of dosing in transcranial magnetic stimulation (TMS) research and practice. There is little consensus on how best to estimate resting motor threshold with TMS, and only a few tools and resources are readily available to TMS researchers. The current study investigates the accuracy and efficiency of 5 different approaches to motor threshold assessment for TMS research and practice applications. METHODS: Computer simulation models are used to test the efficiency and accuracy of 5 different adaptive parameter estimation by sequential testing (PEST) procedures. For each approach, data are presented with respect to the mean number of TMS trials necessary to reach the motor threshold estimate as well as the mean accuracy of the estimates. RESULTS: A simple nonparametric PEST procedure appears to provide the most accurate motor threshold estimates, but takes slightly longer (on average, 3.48 trials) to complete than a popular parametric alternative (maximum likelihood PEST). Recommendations are made for the best starting values for each of the approaches to maximize both efficiency and accuracy. CONCLUSIONS: In light of the computer simulation data provided in this article, the authors review and suggest which techniques might best fit different TMS research and clinical situations. Lastly, a free user-friendly software package is described and made available on the world wide web that allows users to run all of the motor threshold estimation procedures discussed in this article for clinical and research applications.

Computer Simulation↗
PubMed2005

The probability density of the total IBD length over a single autosome in unilineal relationships.

Several authors have studied identity by descent (IBD) by way of a continuous recombination process along a chromosome. Despite its potential uses in, for example, gene mapping or delineation of biological relationships there has been no exact algebraic result given for the probability density function of the IBD proportion in any familial relationship. Other authors have derived algebraic approximations in the case of half-sibs by way of the Poisson clumping heuristic and used computational methods to compute the distribution function of the IBD sharing for unilineal relationships. Here we provide a general numerical method for finding the density of IBD sharing that could be applied to any unilineal relationship and more importantly we derive algebraically an expression for the density for a grandparent-grandchild relationship. Initially we assume that recombination events occur at random along a chromosome, then go on to show how the method could be extended to incorporate a form of genetic interference.

Crossing Over, Genetic↗
PubMed2003

An improved method of computing the wear factor for total hip prostheses involving the variation of relative motion and contact pressure with location on the bearing surface.

A new method of computing the wear factor for total hip prostheses is presented. In the conventional method, only the resultant contact force and the track drawn by the point of its application are considered so that the product of the instantaneous force and sliding increment is integrated over one motion cycle. In the present, improved, method the contact pressure distribution is discretized by a large number of smaller normal forces, and the contribution of each is summed. This is important because the relative motion and contact pressure vary strongly with location, and because the transverse pressure component is substantial. Hence, the present surface integral represents the large contact surface better than the conventional line integral. A prerequisite for the surface integral was the method of computing the relative motion correctly anywhere on the contact surface, developed and published earlier by the present authors. For the pressure discretization, the contact surface was divided into nearly equal-sized surface elements. The contact pressure was modelled with ellipsoidal, paraboloidal and sinusoidal distributions. Two load cases were studied, double-peak and static. When an ellipsoidal contact pressure distribution extending over a hemisphere was discretized by 1000 element forces, the computed wear factor for double-peak load in a biaxial hip wear simulator was 30% lower than in the conventional resultant force case. The present method can be later developed further to involve the temporal variation of size and location of the contact surface.

Computer Simulation↗
PubMed1980

[A computer tomographic method for the determination of tibial torsion (author's transl)].

A computer tomographic method is described for measuring tibial torsion in vivo. The basis of the method depends on transverse scans of the tibia through the knee and ankle joint region by means of which it is possible to establish normal values and abnormal posttraumatic or in congenital torsion. Traumatologists, as well as orthopaedic surgeons, require reproducible measurements, since a detorsion operation may rectify deformities which would lead to degenerative joint changes. A review of previously available methods with torsiometer or conventional radiography shows the limitations of these methods.

Ankle Joint↗
PubMed1990

Pinhole emission computed tomography: method and experimental evaluation.

A method for pinhole emission computed tomography (ECT) using the image-processing capabilities of a gamma camera system is described and evaluated. The tomographic imaging capability of the method was assessed by studies of phantoms and its practical use by the distribution of inhaled 99Tc(m)-labelled aerosol particles in rabbits. The phantom studies demonstrate the tomographic properties in central and non-central planes. A reconstructed resolution of 4.4 mm (FWHM) and an overall homogeneity of +/-10% was obtained for a radius of rotation of the pinhole of about 8 cm. Pinhole ECT showed the distribution of inhales particles to be considerably different in two rabbits, subjected to different modes of mechanical ventilation. In planar images, on the other hand, it was difficult to appreciate the difference.

Animals↗
PubMed2006

Assembly of transmembrane helices of simple polytopic membrane proteins from sequence conservation patterns.

The transmembrane (TM) domains of most membrane proteins consist of helix bundles. The seemingly simple task of TM helix bundle assembly has turned out to be extremely difficult. This is true even for simple TM helix bundle proteins, i.e., those that have the simple form of compact TM helix bundles. Herein, we present a computational method that is capable of generating native-like structural models for simple TM helix bundle proteins having modest numbers of TM helices based on sequence conservation patterns. Thus, the only requirement for our method is the presence of more than 30 homologous sequences for an accurate extraction of sequence conservation patterns. The prediction method first computes a number of representative well-packed conformations for each pair of contacting TM helices, and then a library of tertiary folds is generated by overlaying overlapping TM helices of the representative conformations. This library is scored using sequence conservation patterns, and a subsequent clustering analysis yields five final models. Assuming that neighboring TM helices in the sequence contact each other (but not that TM helices A and G contact each other), the method produced structural models of Calpha atom root-mean-square deviation (CA RMSD) of 3-5 A from corresponding crystal structures for bacteriorhodopsin, halorhodopsin, sensory rhodopsin II, and rhodopsin. In blind predictions, this type of contact knowledge is not available. Mimicking this, predictions were made for the rotor of the V-type Na(+)-adenosine triphosphatase without such knowledge. The CA RMSD between the best model and its crystal structure is only 3.4 A, and its contact accuracy reaches 55%. Furthermore, the model correctly identifies the binding pocket for sodium ion. These results demonstrate that the method can be readily applied to ab initio structure prediction of simple TM helix bundle proteins having modest numbers of TM helices.

Bacteriorhodopsins↗
PubMed1986

Mantle dentine in man--a quantitative microradiographic study.

50 microradiographs taken in a standardized manner of midsagittal ground sections of teeth of individuals aged 18 to 56 years were densitometrically evaluated along a track passing through enamel, dentine and an aluminium stepwedge. Semi-quantitative analysis of mineral density uniformly showed an irregular platform representing circumpulpal dentine and a peripheral down slope in the region of the amelodentinal junction, representing mantle dentine. The width of this less mineralized peripheral zone measured on densitometric recordings averaged 150 microns (+/- 50). Quantitative analysis of the two dentinal regions permitted the calculation of the mineral content in terms of volume percentage using both a graphic method and an electronic computer method. The sections were also examined by polarized light microscopy which clearly visualized the presence of peripheral mantle dentine. The mean mineral density of circumpulpal dentine was 46% according to both the graphic and the computer methods; mantle dentine yielded means close to 42% according by both methods. The 4% difference in density between circumpulpal dentine and mantle dentine proved to be statistically significant; there was no significant difference between the means obtained graphically and those obtained electronically. The need for further investigation of this region of the amelodentinal junction was stressed.

Adolescent↗
PubMed2002

New criteria for estimating baroreflex sensitivity using the transfer function method.

Computer simulations were carried out to appraise three new criteria for the estimation of baroreflex sensitivity (BRS) using the transfer function method. The major goal was to identify a computation procedure able to overcome the intrinsic limitations of the classical coherence criterion. Four representative shapes of the gain function and three different average gains (2, 5 and 8 ms(mmHg)(-1) in the low-frequency (LF) band (0.04-0.15Hz) were considered. The signal-to-noise ratio was made to vary so that the peak coherence in the LF band changed from 0.15 to 0.9. All simulation parameters were derived from previous observations in healthy subjects and heart disease patients. The error of the estimated gain function was obtained from its confidence interval. BRS was computed as average gain in the LF band: (a) including in the average only those points having error < or = threshold (criterion 1, C1); (b) calculating the mean error in the band and accepting BRS measurements only when this error was < or = threshold (criterion 2, C2); (c) including in the average all points, regardless of the error (criterion 3, C3). The three criteria were compared in terms of measurability (percentage of measured BRS) and accuracy (bias and SD of BRS). Using C1 and C2, measurability dropped to 10% when the peak coherence in the LF band decreased, respectively, to 0.18-0.41 and to 0.26-0.53, depending on the shape and strength of the gain. In this condition (lower bound of measurability), worst bias and SD (average gain: 8 ms(mmHg)(-1)) were, respectively, 0.8 ms(mmHg)(-1) and 3.3ms(mmHg)(-1) (C1), and 0.1 ms(mmHg)(-1) and 1.0 ms(mmHg)(-1) (C2). C3, by definition, always ensured 100% measurability and showed bias and SD comparable with, or even lower than, C1 and C2, within the common range of measurable BRS. In the extreme condition of 0.15 coherence, bias and SD were, respectively, 1.7 ms(mmHg)(-1) and 2.3ms(mmHg)(-1) (average gain: 8ms(mmHg)(-1)). Hence, error checking (C1 and C2) dramatically reduced measurability and did not improve accuracy of BRS measurements compared with performing no error check (C3). In conditions of low signal-to-noise ratio and/or impaired baroreflex gain, leading to markedly reduced coherence, the simple average of the gain function in the LF band allows BRS to be estimated with accuracy adequate for clinical purposes.

Baroreflex↗
PubMed1998

Bone age in 116 untreated patients with Turner's syndrome rated by a computer-assisted method (CASAS).

Bone age maturation in 116 untreated patients with Turner's syndrome was evaluated in a cross-sectional and longitudinal analysis. A total of 265 radiographs were rated using the TW2-RUS method on the computer-assisted skeletal age score (CASAS) system. Bone age was found to be retarded from the chronological age of 3 to 6y. Between the ages of 7 and 12 y bone age almost equalled chronological age and progressed normally at a rate of 1 y y(-1). Bone maturation slowed down thereafter and epiphyseal closure was not reached before the age of 17 y. Reference data are presented on bone age and a bone age maturation curve for untreated patients with Turner's syndrome to be used in clinical practice. In the assessment of bone age and bone age velocity in Turner's syndrome the CASAS system produced reliable and valid results. The absolute difference between repeated bone age ratings was 0.26 "y" (median) with a range of 0.00-0.56 "y". Future studies evaluating the effect of growth-promoting treatment in Turner's syndrome should use a computerized method for the determination of bone age.

Adolescent↗
PubMed1999

A two-step computer-assisted method for deriving steady-state rate equations.

A number of computer-assisted methods have been described for the derivation of enzyme-catalyzed steady-state rate equations [K. R. Runyan and R. B. Gunn (1989) Methods Enzymol. 171, 164-190; R. Varon, F. Garcia-Seville, M. Garvia-Moreno, F. Garcia-Canovas, R. Peyro, and R. G. Duggleby (1997) Comput. Appl. Biosci. 13, 159-167]; however, the required programs are either not readily available or require special software. We present here a two-step computer-assisted procedure for deriving steady-state rate equations using the widely available program Mathematica. In the first step, the differential equations for a particular kinetic mechanism that describe changes in enzyme concentration as a function of time are set equal to zero and entered into Mathematica in matrix form. In the second step, a single command allows for the computation of the distribution equations for the free enzyme and each enzyme-ligand complex.

Computer Simulation↗
PubMed1993

Variables affecting the accuracy of stereotactic localization using computerized tomography.

Stereotactic localization using computerized tomography (CT) is increasingly employed to guide neurosurgical procedures in crucial areas of the brain such as the brain stem. This technique allows the surgeon to resect a lesion in its entirety while sparing critical areas of the brain. Thus, the parameters used for scanning should be selected for maximum accuracy. While the small pixel size of CT scanners suggests a high degree of precision in localization, there have been few systematic studies of this accuracy. The authors have studied the amount of error in localization created by variables such as CT scan thickness, interscan spacing, size of lesion, and method of computation when using the Brown-Roberts-Wells (BRW) stereotactic system. Over 1000 CT scans were made of a phantom composed of spheres of differing diameter and location. The CT slice thickness was varied from 1.5 to 5.0 mm, and interscan spacing was varied from 0.5 to 3.0 mm. The coordinates of the center of the spheres were calculated independently using the laptop computer supplied with the unit and also by a stereotactic computer which automatically calculates the center of the fiducials. The actual BRW coordinates of the sphere center were obtained using the phantom base and were then compared to the computer-calculated coordinates to determine error in localization. Variables with a significant effect on error included the scan thickness, interscan spacing, and sphere size. The mean error decreased 23% as the scan thickness decreased from 5.0 to 1.5 mm and 45% as the interscan spacing decreased from 3.0 to 0.5 mm. Mean error was greatest for the smallest sphere sizes. The two computational methods did not differ in error. This study suggests that, for critical areas of the brain or for small lesions, a scan thickness of 1.5 mm and interscan spacing of 0.5 mm should be employed.

Brain↗
PubMed1979

General method for computer measurement of complex chromatograms.

Usual computerized methods for measuring peak areas and associated computations on chromatograms require relatively highly reproducible retnetion times. They are prone to mis-identification of substances in chromatography of physiological fluids. The method described was developed for amino acid analyses of physiological mouse tissues. It tolerates noisy output, drifting baselines, variable retention times and unidentified peaks.

Amino Acids↗
PubMed1984

[Alternative use of the simulator method and computer tomography in planning radiotherapy for non-metastasizing prostatic cancer].

Simulator method and computed tomography use different pictures for measurements of the tumor volume for therapy planning: X-ray pictures taken from two different directions can only show the indirect volume of the tumor, while CT pictures give information of the real size of the tumor. For estimation of the value of the two methods therapy planning was performed by the simulator method in 34 patients with carcinoma of the prostate (T1-T3) and the results were added to CT pictures. Comparison of the two methods resulted in equivalent consequences. Therefore economic aspects should be taken into account for selection of a special method of radiation therapy planning.

Humans↗
PubMed1995

Pole-tracking algorithms for the extraction of time-variant heart rate variability spectral parameters.

Various algorithms of autoregressive (AR) recursive identification make it possible to evaluate power spectral distribution in correspondence with each sample of a time series, and time-variant spectral parameters can be calculated through the evaluation of the pole positions in the complex z-plane. In traditional analysis, the poles are obtained by zeroing the denominator of the model transfer function, expressed as a function of the AR coefficients. In this paper, two algorithms for the direct updating and tracking of movements of poles of an AR time-variant model on the basis of the innovation given to the coefficients are presented and investigated. The introduced algorithms are based upon 1) the classical linearization method and 2) a recursive method to compute the roots of a polynomial, respectively. In the present paper, applications in the field of heart rate variability (HRV) signal analysis are presented and efficient tools are proposed for quantitative extraction of spectral parameters (power and frequency of the low-frequency (LF) and high-frequency (HF) components) for the monitoring of the action of the autonomic nervous system in transient patho-physiological events. These computational methods seem to be very attractive for HRV applications, as they inherit the peculiarity of recursive time-variant identification, and provide a more immediate comprehension of the spectral process characteristics when expressed in terms of poles and AR spectral components.

Algorithms↗
PubMed1990

A method for computing the derivative of noisy time-activity curves and its application to radioisotope dynamic analysis.

A method for computing the slope or the derivative of time-activity curves containing statistical fluctuations is described. The algorithm presented employs digital differentiation as a digital filter. In designing an effective differentiating filter the Chebyshev-type min-max method and Remez exchange algorithm are used to minimise the weighted Chebyshev error. The validity of this method has been investigated using computer-based Monte Carlo simulation. Renogram curve analysis is presented as an example of an application of this method to radioisotope dynamic analysis. The ratio of the bilateral slopes of the renogram's second segments estimated using this method correlated well with the renal plasma flow ratio (r = 0.97, n = 16). The functional images of the slope of the renogram's second segments have been constructed and ascertained to be clinically useful. This method is considered to provide a powerful tool for extraction of quantitative information both in research and in routine nuclear medicine clinical work, and may be useful in various other fields.

Algorithms↗
PubMed2000

The 630-kb lung cancer homozygous deletion region on human chromosome 3p21.3: identification and evaluation of the resident candidate tumor suppressor genes. The International Lung Cancer Chromosome 3p21.3 Tumor Suppressor Gene Consortium.

We used overlapping and nested homozygous deletions, contig building, genomic sequencing, and physical and transcript mapping to further define a approximately 630-kb lung cancer homozygous deletion region harboring one or more tumor suppressor genes (TSGs) on chromosome 3p21.3. This location was identified through somatic genetic mapping in tumors, cancer cell lines, and premalignant lesions of the lung and breast, including the discovery of several homozygous deletions. The combination of molecular manual methods and computational predictions permitted us to detect, isolate, characterize, and annotate a set of 25 genes that likely constitute the complete set of protein-coding genes residing in this approximately 630-kb sequence. A subset of 19 of these genes was found within the deleted overlap region of approximately 370-kb. This region was further subdivided by a nesting 200-kb breast cancer homozygous deletion into two gene sets: 8 genes lying in the proximal approximately 120-kb segment and 11 genes lying in the distal approximately 250-kb segment. These 19 genes were analyzed extensively by computational methods and were tested by manual methods for loss of expression and mutations in lung cancers to identify candidate TSGs from within this group. Four genes showed loss-of-expression or reduced mRNA levels in non-small cell lung cancer (CACNA2D2/alpha2delta-2, SEMA3B [formerly SEMA(V), BLU, and HYAL1] or small cell lung cancer (SEMA3B, BLU, and HYAL1) cell lines. We found six of the genes to have two or more amino acid sequence-altering mutations including BLU, NPRL2/Gene21, FUS1, HYAL1, FUS2, and SEMA3B. However, none of the 19 genes tested for mutation showed a frequent (>10%) mutation rate in lung cancer samples. This led us to exclude several of the genes in the region as classical tumor suppressors for sporadic lung cancer. On the other hand, the putative lung cancer TSG in this location may either be inactivated by tumor-acquired promoter hypermethylation or belong to the novel class of haploinsufficient genes that predispose to cancer in a hemizygous (+/-) state but do not show a second mutation in the remaining wild-type allele in the tumor. We discuss the data in the context of novel and classic cancer gene models as applied to lung carcinogenesis. Further functional testing of the critical genes by gene transfer and gene disruption strategies should permit the identification of the putative lung cancer TSG(s), LUCA, Analysis of the approximately 630-kb sequence also provides an opportunity to probe and understand the genomic structure, evolution, and functional organization of this relatively gene-rich region.

Carcinoma, Non-Small-Cell Lung↗
PubMedDate not supplied

Finite element method evaluation: articulations and diagonals in an 8-pin type 1B external skeletal fixator.

OBJECTIVE: To determine the mechanical properties of articulations and diagonals in an 8-pin type 1b external skeletal fixator (ESF). STUDY DESIGN: Finite element method-computer simulation. METHODS: The control type 1b ESF was supplemented with different articulations and diagonals. The parameters of frame angle, articulation diameter, and pin- or connector-based fastening were altered. The configurations were loaded for axial compression, torsion, and craniocaudal and mediolateral bending as single loads and as a combination. Three-dimensional linear and rotational gap strain and Von Mises stress maxima were determined. RESULTS: For 90 degrees , 60 degrees , and 30 degrees frame angles and 0.48-cm-diameter articulations and diagonals, the best configurations, based on lower gap strain combined with decreased or minimally increased stress maxima for the combined load, were single or double diagonals or four horizontal articulations. Combining double diagonals with double wide horizontal articulations further lowered gap strain. For a 90 degrees frame angle and 0.32-cm-diameter articulations and diagonals, the superior configurations, showing the lowest gap strain combined with decreased or minimally increased stress maxima for the combined load, were double diagonals, four horizontal, or wide double horizontal articulations. The 0.48-cm articulations and diagonals provided lower or similar gap strain than 0.32-cm articulations and diagonals. The connector-to-connector version of these superior configurations provided slightly lower or similar gap strain and stress maxima than the pin-to-pin version. Only pin-to-pin-fastened double diagonals provided better stress maxima than the corresponding connector-to-connector version. CONCLUSIONS: Supplementing a type 1b ESF with double diagonals and wide double articulations results in the greatest increase in stability at the fracture gap for complex fractures or in the initial phase of bone healing.

Animals↗
PubMedDate not supplied

Machine learning approaches for prediction of linear B-cell epitopes on proteins.

Identification and characterization of antigenic determinants on proteins has received considerable attention utilizing both, experimental as well as computational methods. For computational routines mostly structural as well as physicochemical parameters have been utilized for predicting the antigenic propensity of protein sites. However, the performance of computational routines has been low when compared to experimental alternatives. Here we describe the construction of machine learning based classifiers to enhance the prediction quality for identifying linear B-cell epitopes on proteins. Our approach combines several parameters previously associated with antigenicity, and includes novel parameters based on frequencies of amino acids and amino acid neighborhood propensities. We utilized machine learning algorithms for deriving antigenicity classification functions assigning antigenic propensities to each amino acid of a given protein sequence. We compared the prediction quality of the novel classifiers with respect to established routines for epitope scoring, and tested prediction accuracy on experimental data available for HIV proteins. The major finding is that machine learning classifiers clearly outperform the reference classification systems on the HIV epitope validation set.

Algorithms↗