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Brain volumes and surface morphology in monozygotic twins.

Because healthy monozygotic twins share an identical genetic complement, they provide a unique opportunity to explore the genetic and environmental determinants of brain development. The purpose of this study was to evaluate the similarities between measures of cerebral and subcortical volumes and surface morphology in monozygotic twins compared with a matched control sample. Combinations of automated and manual methods were used to evaluate total brain volume, gray matter, white matter, ventricles and volumes of the frontal, temporal, parietal and occipital lobes. An artificial neural network algorithm was used to measure the cerebellum, thalamus, caudate and putamen. Measures of surface morphology included an index of gyral and sulcal curvature, surface area and cortical depth. The cerebral volume regions, including the gray matter, white matter and lobar volumes, were highly correlated within monozygotic twin pairs, with nearly all correlation coefficients >0.90. The cerebellum was also highly correlated (r = 0.99). Reasonably high correlations were found for the cortical depth (r = 0.84), caudate (r = 0.84), thalamus (r = 0.75) and putamen (r = 0.75). The surface measures, however, demonstrated the least correlation within twin pairs and thus are more prone to environmental influences. The high to moderate correlations between MZ twins compared with the matched controls highlights the role of heredity in both prenatal and postnatal neurodevelopment.

Adolescent↗

Quantum computation and analysis of Wigner and Husimi functions: toward a quantum image treatment.

We study the efficiency of quantum algorithms which aim at obtaining phase-space distribution functions of quantum systems. Wigner and Husimi functions are considered. Different quantum algorithms are envisioned to build these functions, and compared with the classical computation. Different procedures to extract more efficiently information from the final wave function of these algorithms are studied, including coarse-grained measurements, amplitude amplification, and measure of wavelet-transformed wave function. The algorithms are analyzed and numerically tested on a complex quantum system showing different behavior depending on parameters: namely, the kicked rotator. The results for the Wigner function show in particular that the use of the quantum wavelet transform gives a polynomial gain over classical computation. For the Husimi distribution, the gain is much larger than for the Wigner function and is larger with the help of amplitude amplification and wavelet transforms. We discuss the generalization of these results to the simulation of other quantum systems. We also apply the same set of techniques to the analysis of real images. The results show that the use of the quantum wavelet transform allows one to lower dramatically the number of measurements needed, but at the cost of a large loss of information.

Journal Article↗

Automatic determination of left ventricular ejection fraction from gated blood-pool tomography.

UNLABELLED: The aim of this study was to develop and validate a new algorithm to automatically compute left ventricular ejection fraction (LVEF) from gated blood-pool tomography (GBPT). The results were compared with those of conventional planar radionuclide angiocardiography (PRNA). METHODS: Fifty-three consecutive patients received an injection of 740 MBq (99m)Tc-labeled human serum albumin. PRNA and GBPT were performed consecutively in a random sequence. PRNA served as the reference, and GBPT images were processed using a new edge detection algorithm. The algorithm is fast (<45 s), fully automatic, and works in three-dimensional space. The method includes identification of the valve plane and the septum. The left ventricular cavity at end-diastole is delineated by segmentation using an iterative threshold technique. An optimal threshold is reached when the corresponding isocontour best fits the first derivative of the end-diastolic count distribution in three dimensions. This optimal threshold is then applied to delineate the left ventricular cavity on the other time bins. The data are corrected for the partial-volume effect. Left ventricular volumes are determined using a geometry-based method and are used to calculate the ejection fraction. RESULTS: The success rate of the new algorithm was 94%. LVEFs calculated from GBPT agreed well with those calculated from PRNA (r = 0.78; GBPT = 0.94 PRNA + 6.33). The systematic error was 2.8%, and the random error was 8.8%. Excellent inter- and intraobserver reproducibility was found, with average differences of 1.1% +/- 4.6% and 1.1% +/- 5.0%, respectively, between the two measurements. CONCLUSION: This new algorithm provides a fast, automated, and objective method to calculate LVEF from GBPT.

Adult↗

Error propagation as a factor in selection of measurement intervals for the determination of polycyclic aromatic hydrocarbons by second-derivative spectrofluorimetry.

The most suitable wavelength intervals were selected for the determination of 4 polycyclic aromatic hydrocarbons (PAHs; benzo[g,h,i]perylene, dibenzo[a,h]anthracene, pyrene, and triphenylene) in very complex mixtures of 11 PAHs: anthracene, benz[a]anthracene, benzo[a]pyrene, benzo[b]fluoranthene, benzo[g,h,i]perylene, benzo[k]fluoranthene, chrysene, dibenz[a,h]anthracene, phenanthrene, pyrene, and triphenylene. The multiple linear regression algorithm was applied to measurements made in several wavelength intervals previously selected on the basis of sensitivity and minimum number of interfering compounds. Of the different models obtained, those displaying minimum error propagation in the analytical result were selected. By applying the models proposed in this study, we precisely and accurately determined benzo[g,h,i]perylene, dibenz[a,h]anthracene, pyrene, and triphenylene in complex mixtures--a feat that could not be achieved by the use of constant-wavelength spectrofluorimetry in combination with second-derivative techniques.

Algorithms↗

Bone and body composition measurements of small subjects: discrepancies from software for fan-beam dual energy X-ray absorptiometry.

OBJECTIVES: A piglet model was used to determine the variations in measurements from different software algorithms used in the same type of dual energy X ray absorptiometry (DXA) instruments from the same manufacturer. METHODS: Forty-one piglets (6190 +/- 5856g, mean +/- SD) were scanned in duplicate with a fan-beam densitometer (Hologic QDR4500A, Hologic Inc, Bedford, MA) in the infant whole body scan mode. The same scans were analyzed with two software versions: vKH6 (validated with carcass chemical measurement) and v11.2 (commercial software from the same densitometer manufacturer). RESULTS: All analysis values were highly correlated (r = 0.90 to 1.00) and DXA values for total weights were almost identical. However, v11.2 results consistently overestimated bone mineral content (49.3 +/- 23.4%, mean +/- SD), bone area (21.1 +/- 8.2%), bone mineral density (24.1 +/- 22.2%), and fat mass (160.9 +/- 71.7%) but underestimated lean mass (-14.3 +/- 5.5%) when compared to the values from vKH6. Differences between software versions increased with heavier piglets. CONCLUSION: The commercial software for fan-beam DXA measurement of piglets, matched for the size of human infants and young children, has major inaccuracies for bone mineral and body composition that become further exaggerated with increasing weight of the subject.

Absorptiometry, Photon↗

A two-dimensional pencil-beam algorithm for calculation of arc electron dose distributions.

A two-dimensional pencil-beam algorithm is presented for the calculation of arc electron dose distributions in any plane that is perpendicular to the axis of rotation. The dose distributions are calculated by modelling the arced beam as a single broad beam defined by the irradiated surface of the patient. The algorithm is two-dimensional in that the anatomical cross section of the patient and the skin collimators are assumed identical in parallel planes outside the plane of calculation. The broad beam is modelled as a collection of strip beams, each strip beam being characterised by its planar fluence, mean projected angular direction and a root-mean-square spread about the mean direction. Using these parameters, the dose distribution is calculated using pencil-beam theory. Examples of strip-beam parameters and resulting dose distributions for patient geometries are presented. Features of the algorithm, which include (1) incorporation of pencil-beam theory for the calculation of dose in heterogeneous tissue, (2) run times of only about twice that of comparable-sized fixed electron fields and (3) the input requirement of only a single depth dose and four off-axis dose profiles of measured data, make the algorithm practical for clinical use.

Algorithms↗

Minimizing the number of segments in a delivery sequence for intensity-modulated radiation therapy with a multileaf collimator.

This paper proposes a sequencing algorithm for intensity-modulated radiation therapy with a multileaf collimator in the static mode. The algorithm aims to minimize the number of segments in a delivery sequence. For a machine with a long verification and recording overhead time (e.g., 15 s per segment), minimizing the number of segments is equivalent to minimizing the delivery time. The proposed new algorithm is based on checking numerous candidates for a segment and selecting the candidate that results in a residual intensity matrix with the least complexity. When there is more than one candidate resulting in the same complexity, the candidate with the largest size is selected. The complexity of an intensity matrix is measured in the new algorithm in terms of the number of segments in the delivery sequence obtained by using a published algorithm. The beam delivery efficiency of the proposed algorithm and the influence of different published algorithms used to calculate the complexity of an intensity matrix were tested with clinical intensity-modulated beams. The results show that no matter which published algorithm is used to calculate the complexity of an intensity matrix, the sequence generated by the algorithm proposed here is always more efficient than that generated by the published algorithm itself. The results also show that the algorithm used to calculate the complexity of an intensity matrix affects the efficiency of beam delivery. The delivery sequences are frequently most efficient when the algorithm of Bortfeld et al. is used to calculate the complexity of an intensity matrix. Because no single variation is most efficient for all beams tested, we suggest implementing multiple variations of our algorithm.

Algorithms↗

Internal tissue displacement measurement based on ultrasonic wave Doppler signal digital detection and its application to fetal movement monitoring.

We have developed a fetal movement monitoring system based on small displacement measurement of internal tissues. When ultrasonic pulses are transmitted to the fetus, the reflected ultrasonic waves which have a Doppler frequency shift due to the fetal movements are detected by using an ultrasonic pulsed Doppler technique. In this paper, we propose a displacement measurement method for internal tissues which is based on the Doppler signal digital detection technique. In the method, the received ultrasonic RF signals are sampled with a sampling frequency of four times higher than the centre frequency of the ultrasonic waves; the Doppler frequency shift signals are derived using digital signal processing. From the detected signals, the internal displacements are estimated using the arc-tangent method. The basic algorithm of the detection method has already been used in the area of blood flow sensing, however, we apply the algorithm to the displacement measurement of internal tissues. The comparison between the proposed method and the conventional method is presented. The fetal movement quantitative monitoring system based on the method which has been constructed is shown.

Algorithms↗

Antibody-antigen interactions measured by surface plasmon resonance: global fitting of numerical integration algorithms.

The interactions between adenylate kinase (AK) and a monoclonal antibody against AK (McAb3D3) were examined by means of optical biosensor technology, and the sensograms were fitted to four models using numerical integration algorithms. The interaction of a solution of McAb3D3 with immobilized AK follows a double exponential function and the data fitted well to an inhomogeneous ligand model. The interaction of a solution AK with immobilized McAb3D3 follows a single exponential function and the data fitted well to a pseudo-first order reaction model. The true association constants of AK binding to McAb3D3 in solution were obtained from competition BIAcore measurements. The difference in results obtained with solid-phase BIAcore and competition BIAcore may be due to rebinding of the dissociated analyte to the immobilized surface. The results obtained with BIAcore are compared to those obtained by ELISA methods. We suggest that the best method for analysis of BIAcore data is direct, global fitting of sensorgrams to numerical integration algorithms corresponding to the different possible models for binding.

Adenylate Kinase↗

[Analysis of nucleotide diversity at the cytochrome b and cytochrome oxidase 1 genes at the population, species, and genus levels].

Algorithms of nucleotide diversity measures and other measures of genetic divergence at the molecular level are analyzed. Based on a database of p-distances, we have compared genetic divergence of populations (1) and taxa of different rank, such as sibling species (2), species within a genus (3), and species from different genera within a family (4). Based on the theory and algorithms of distance calculation from the primary DNA sequences, as well as the actual distances estimated from literature, it is recommended to use in analysis of experimental data a specific model selected from the eight available ones. The empirical data for more than 24,000 vertebrate and invertebrate species demonstrate that the data series are realistic and interpretable when p-distance or its various estimates are used. This testifies to the applicability of p-distance for most interspecies and intraspecies comparisons of genetic divergence up to the family level by two genes compared. Data on p-distances revealed various and increasing levels of genetic divergence of the sequences of genes Cyt-b and Co-1 in four groups compared. Mean unweighted scores of distances for the four groups were as follows: Cyt-b (1) 1.55 +/- 0.56, (2) 5.52 +/- 1.34, (3) 10.69 +/- 1.34, (4) 18.51 +/- 2.09 and Co-1 (1) 0.55 +/- 0.19, (2) 4.91 +/- 0.83, (3) 9.66 +/- 0.72, (4) 14.69 +/- 1.02. Differences in divergence between the genes themselves at the four levels were also found, although the total mean distances for the two genes did not show statistically significant differences. This conforms to the ample evidence showing different and nonuniform evolution rates of these and other genes and their various regions. The results of the analysis of the nucleotide and allozyme divergence within species and higher taxa of animals, first, are in a good agreement with these results, including data on protein gene markers, and, second, this evidence suggests that in animals, phyletic evolution is likely to prevail at the molecular level, while speciation mainly corresponds to the type D1 geographic model). The prevalence of the D1 speciation mode does not mean that the other modes are absent. There are at least seven various modes of speciation. Recognition of speciation modes is a task that seems to require construction of a quantitative genetic model (theory) of speciation. Although, in view of a vast diversity of the possible causes of reproductive isolating barriers (RIBs) and speciation initiation, as well as the "empirical nature" of the formalized approach, proposed in the present work, some newly arising questions may be left without an answer. Their solution probably lied in increasing the number of descriptors and members of equations, proposed in this study, on the basis of DNA markers and other genomic characteristics.

Animals↗

Qualitative and quantitative evaluation of six algorithms for correcting intensity nonuniformity effects.

The desire to correct intensity nonuniformity in magnetic resonance images has led to the proliferation of nonuniformity-correction (NUC) algorithms with different theoretical underpinnings. In order to provide end users with a rational basis for selecting a given algorithm for a specific neuroscientific application, we evaluated the performance of six NUC algorithms. We used simulated and real MRI data volumes, including six repeat scans of the same subject, in order to rank the accuracy, precision, and stability of the nonuniformity corrections. We also compared algorithms using data volumes from different subjects and different (1.5T and 3.0T) MRI scanners in order to relate differences in algorithmic performance to intersubject variability and/or differences in scanner performance. In phantom studies, the correlation of the extracted with the applied nonuniformity was highest in the transaxial (left-to-right) direction and lowest in the axial (top-to-bottom) direction. Two of the six algorithms demonstrated a high degree of stability, as measured by the iterative application of the algorithm to its corrected output. While none of the algorithms performed ideally under all circumstances, locally adaptive methods generally outperformed nonadaptive methods.

Algorithms↗

QT-RR relationship in healthy subjects exhibits substantial intersubject variability and high intrasubject stability.

Recently, it was demonstrated that the QT-RR relationship pattern varies significantly among healthy individuals. We compared the intra- and interindividual variations of the QT-RR relationship. Twenty-four-hour 12-lead digital electrocardiograms (ECGs; SEER MC, GE Marquette; 10-s ECG recorded every 30 s) were obtained at baseline and after 24 h, 1 wk, and 1 mo in 75 healthy subjects (42 women, 33 men, age 27.9 +/- 9.6 vs. 26.8 +/- 7.5 yr, P = not significant). QT interval was measured automatically in each ECG by six different algorithms, and the mean of the six measurements was analyzed. In each recording of each individual, QT-RR relationship was assessed by 10 different regression models including linear (QT = beta + alpha x RR) and parabolic (QT = beta x RR(alpha)) models. Standard deviations (SDs) of regression parameters alpha and beta of consecutive recordings of each individual were compared with SD of the individual means. Intrasubject stability and interindividual variability were further tested by ANOVA. With all models, intraindividual SDs of the regression parameters were highly significantly smaller than SD of individual means (P < 10(-5)-10(-9)). The intrasubject stability was further confirmed by ANOVA (P < 10(-19)-10(-30)). The QT-RR relationship exhibits substantial intersubject variability as well as a high intrasubject stability. This has practical implications for a precise estimation of the heart rate-corrected QT interval in which optimized subject-specific rate correction formulas should be used.

Adolescent↗

Measurement of gas holes and mechanical openness in cheese by image analysis.

A method to measure the amount of the surface area of cheese slices occupied by gas holes was developed to reflect the relative gas production among different cheeses. A digital camera mounted on a copy stand with lighting was used to make digital images of each slice of cheese. A commercial digital image analysis software program was used and an algorithm was written to measure the area of the image of the cheese slice occupied by holes. The image was cropped and scanned to determine which color channel produced the best image contrast. The MATLAB program allowed the user to eliminate mechanical openness or false holes and then to scan the image to produce a percent distribution of pixels in the image as a function of pixel intensity. The user then determined a threshold value to differentiate pixels that were in holes from those representing areas with no holes. The percentage of the total surface area occupied by holes was calculated. The coefficient of variation of the method ranged from 2.43% with gas holes of about 1% of the surface of the cheese slice to a coefficient of variation of 0.92% with gas holes of about 6.8% of the surface area of the cheese slice. Examples of applications of this method are given for Emmental, Ragusano, and Cheddar cheeses. The method can be used as a tool in research studies to correlate the amount of gas production with manufacturing conditions or as a quality control tool in cheese manufacturing.

Cheese↗

Quantitative high D-dimer value is predictive of pulmonary embolism occurrence independently of clinical score in a well-defined low risk factor population.

We performed a prospective study to assess whether positive quantitative D-dimer (DD) levels could be integrated for a selected population in a defined strategy to accurately diagnose pulmonary embolism (PE). For this purpose, 1528 in- or outpatients with clinically suspected PE were investigated according to our prescription rules. Clinical probability was defined as low, intermediate or high. Patients in whom DD levels were measured met criteria defined by our previously described decision-making algorithm: in- and outpatients, < 80 years, without surgery in the previous 30 days or active cancer. Nine hundred and twenty-three patients (60.4%) had quantitative DD measurement using automated latex DD assay (STA-Liatest D-Di). According to our decision-making algorithm, DD measurement was applied to 70.5% of out-, and 55.7% of inpatients, and PE diagnosis was ruled out in 49.5% of the 923 patients. This allowed us to confirm prospectively that our specific rules greatly improve the DD testing efficiency. PE was diagnosed in 115 (12.5%) patients. For a 0.5 mg L(-1) cut-off, the test sensitivity was 97.4%, but its specificity was only 56.7%. However, PE prevalence increased gradually with DD levels. The true observed PE prevalence, according to the quantitative assessment of DD levels, differed from that predicted with pretest clinical probability only. Moreover, in this well-defined patient group, a quantitative DD level > 2 mg L(-1) was predictive of PE occurrence independently of the clinical score (odds ratio 6.9, 95% confidence interval 3.7, 12.8). As part of a defined strategy, knowledge of positive DD quantitative value, together with the clinical probability score, improves the PE predictive model. A clinical validation of these results in a follow-up study would now be necessary before considering the implementation of this strategy into clinical practice.

Adolescent↗

Monte Carlo calculations for absolute dosimetry to determine machine outputs for proton therapy fields.

The prescribed dose in radiation therapy has to be converted into machine monitor units for patient treatment. This is done routinely for each spread-out Bragg peak (SOBP) field either by calibration measurements, by using analytical algorithms or by relying on empirical data. At the Northeast Proton Therapy Center, a monitor unit corresponds to a fixed amount of charge collected in a segmented transmission ionization chamber inside the treatment head. The goal of this work was to use a detailed Monte Carlo model of the treatment head to calculate the dose delivered to the patient as a function of ionization chamber reading, i.e. to yield absolute dose in patients in terms of machine monitor units. The results show excellent agreement with measurements. For 50 SOBP fields considered in this study, the mean absolute difference between the experimental and the calculated value is 1.5%, where approximately 50% of the fields agree within 1%. This is within the uncertainties of the data. The Monte Carlo method has advantages over analytical algorithms because it takes into account scattered and secondary radiation, does not rely on empirical parameters, and provides a tool to study the influence of parts of the treatment head on the ionization chamber reading. Compared to experimental methods the Monte Carlo method has the advantage of being able to verify the dose in the patient geometry.

Algorithms↗

Analysis of forced expired volume signals using multi-exponential functions.

Patients with pulmonary disease are often unable to complete forced expiration manoeuvres. The aim of the study is to evaluate whether forced vital capacity (FVC), the volume exhaled at the end of completed forced expiration, can be estimated by extrapolating volume-time curves obtained from uncompleted manoeuvres. The suitability of mono-, bi-, and tri-exponential functions to characterise complete volume-time curves from 50 subjects is investigated. Mono-exponential modelling is insufficient, whereas bi-exponential fitting yields an adequate description for 47 data sets. Tri-exponential models lead to overfitting in all but three cases (normalised sum of least squares: 50.2 +/- 34.5 for mono-, 2.76 +/- 4.11 for bi-, 2.74 +/- 4.19 for tri-exponential modelling; condition number of the correlation matrix: 1.0025 +/- 0.0004 for mono-, 1.08 +/- 0.08 for bi-, 34.7 +/- 100.1 for tri-exponential fitting (mean +/- SD)). Thus, FVC is estimated by the extrapolation of 27 uncompleted spirograms using bi- or tri-exponential models, depending on their accordance with measured data and on the identifiability of their parameters. This algorithm yields unbiased estimates (difference from measured inspiratory vital capacity: 0.01 +/- 0.21 L). This method can be used for investigation of the lung function of subjects who cannot complete the forced expiration manoeuvre.

Adolescent↗

Amplitude distribution of calcium sparks in confocal images: theory and studies with an automatic detection method.

Determination of the calcium spark amplitude distribution is of critical importance for understanding the nature of elementary calcium release events in striated muscle. In the present study we show, on general theoretical grounds, that calcium sparks, as observed in confocal line scan images, should have a nonmodal, monotonic decreasing amplitude distribution, regardless of whether the underlying events are stereotyped. To test this prediction we developed, implemented, and verified an automated computer algorithm for objective detection and measurement of calcium sparks in raw image data. When the sensitivity and reliability of the algorithm were set appropriately, we observed highly left-skewed or monotonic decreasing amplitude distributions in skeletal muscle cells and cardiomyocytes, confirming the theoretical predictions. The previously reported modal or Gaussian distributions of sparks detected by eye must therefore be the result of subjective detection bias against small amplitude events. In addition, we discuss possible situations when a modal distribution might be observed.

Algorithms↗

Oblique needle segmentation and tracking for 3D TRUS guided prostate brachytherapy.

An algorithm was developed in order to segment and track brachytherapy needles inserted along oblique trajectories. Three-dimensional (3D) transrectal ultrasound (TRUS) images of the rigid rod simulating the needle inserted into the tissue-mimicking agar and chicken breast phantoms were obtained to test the accuracy of the algorithm under ideal conditions. Because the robot possesses high positioning and angulation accuracies, we used the robot as a "gold standard," and compared the results of algorithm segmentation to the values measured by the robot. Our testing results showed that the accuracy of the needle segmentation algorithm depends on the needle insertion distance into the 3D TRUS image and the angulations with respect to the TRUS transducer, e.g., at a 10 degrees insertion anglulation in agar phantoms, the error of the algorithm in determining the needle tip position was less than 1 mm when the insertion distance was greater than 15 mm. Near real-time needle tracking was achieved by scanning a small volume containing the needle. Our tests also showed that, the segmentation time was less than 60 ms, and the scanning time was less than 1.2 s, when the insertion distance into the 3D TRUS image was less than 55 mm. In our needle tracking tests in chicken breast phantoms, the errors in determining the needle orientation were less than 2 degrees in robot yaw and 0.7 degrees in robot pitch orientations, for up to 20 degrees needle insertion angles with the TRUS transducer in the horizontal plane when the needle insertion distance was greater than 15 mm.

Agar↗