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Effect of chronic exposure to antipsychotic medication on cell numbers in the parietal cortex of macaque monkeys.

Both in vivo and post-mortem investigations have demonstrated smaller volumes of the whole brain and of certain brain regions in individuals with schizophrenia. It is unclear to what degree such smaller volumes are due to the illness or to the effects of antipsychotic medication treatment. Indeed, we recently reported that chronic exposure of macaque monkeys to haloperidol or olanzapine, at doses producing plasma levels in the therapeutic range in schizophrenia subjects, was associated with significantly smaller total brain weight and volume, including an 11.8-15.2% smaller gray matter volume in the left parietal lobe. Consequently, in this study we sought to determine whether these smaller volumes were associated with lower numbers of the gray matter's constituent cellular elements. The use of point counting and Cavalieri's principle on Nissl-stained sections confirmed a 14.6% smaller gray matter volume in the left parietal lobe from antipsychotic-exposed monkeys. Use of the optical fractionator method to estimate the number of each cell type in the gray matter revealed a significant 14.2% lower glial cell number with a concomitant 10.2% higher neuron density. The numbers of neurons and endothelial cells did not differ between groups. Together, the findings of smaller gray matter volume, lower glial cell number, and higher neuron density without a difference in total neuron number in antipsychotic-exposed monkeys parallel the results of post-mortem schizophrenia studies, and raise the possibility that such observations in schizophrenia subjects might be due, at least in part, to antipsychotic medication effects.

Algorithms↗

Three-dimensional structure of acyl carrier protein in solution determined by nuclear magnetic resonance and the combined use of dynamical simulated annealing and distance geometry.

The solution conformation of acyl carrier protein from Escherichia coli (77 residues) has been determined on the basis of 423 interproton-distance restraints and 32 hydrogen-bonding restraints derived from NMR measurements. A total of nine structures were computed using a hybrid approach combining metric matrix distance geometry and dynamic simulated annealing. The polypeptide fold is well defined with an average backbone atomic root-mean-square difference of 0.20 +/- 0.03 nm between the final nine converged structures and the mean structure obtained by averaging their coordinates. The principal structural motif is composed of three helices: 1 (residues 3-12), 2 (residues 37-47) and 4 (residues 65-75) which line a hydrophobic cavity. Helices 2 and 4 are approximately parallel to each other and anti-parallel at an angle of approximately equal to 150 degrees to helix 1. The smaller helix 3 (residues 56-63) is at an angle of approximately equal to 100 degrees to helix 4.

Acyl Carrier Protein↗

Automatic classification of protein sequences into structure/function groups via parallel cascade identification: a feasibility study.

A recent paper introduced the approach of using nonlinear system identification as a means for automatically classifying protein sequences into their structure/function families. The particular technique utilized, known as parallel cascade identification (PCI), could train classifiers on a very limited set of exemplars from the protein families to be distinguished and still achieve impressively good two-way classifications. For the nonlinear system classifiers to have numerical inputs, each amino acid in the protein was mapped into a corresponding hydrophobicity value, and the resulting hydrophobicity profile was used in place of the primary amino acid sequence. While the ensuing classification accuracy was gratifying, the use of (Rose scale) hydrophobicity values had some disadvantages. These included representing multiple amino acids by the same value, weighting some amino acids more heavily than others, and covering a narrow numerical range, resulting in a poor input for system identification. This paper introduces binary and multilevel sequence codes to represent amino acids, for use in protein classification. The new binary and multilevel sequences, which are still able to encode information such as hydrophobicity, polarity, and charge, avoid the above disadvantages and increase classification accuracy. Indeed, over a much larger test set than in the original study, parallel cascade models using numerical profiles constructed with the new codes achieved slightly higher two-way classification rates than did hidden Markov models (HMMs) using the primary amino acid sequences, and combining PCI and HMM approaches increased accuracy.

Algorithms↗

Aortic stiffness is an independent predictor of primary coronary events in hypertensive patients: a longitudinal study.

Arterial stiffness may predict coronary heart disease beyond classic risk factors. In a longitudinal study, we assessed the predictive value of arterial stiffness on coronary heart disease in patients with essential hypertension and without known clinical cardiovascular disease. Aortic stiffness was determined from carotid-femoral pulse wave velocity at baseline in 1045 hypertensives. The risk assessment of coronary heart disease was made by calculating the Framingham risk score according to the categories of gender, age, blood pressure, cholesterol, diabetes, and smoking. Mean age at entry was 51 years, and mean follow-up was 5.7 years. Coronary events (fatal and nonfatal myocardial infarction, coronary revascularization, and angina pectoris) and all cardiovascular events served as outcome variables in Cox proportional-hazard regression models. Fifty-three coronary events and 97 total cardiovascular events occurred. In univariate analysis, the relative risk of follow-up coronary event or any cardiovascular event increased with increasing level of pulse wave velocity; for 1 SD, ie, 3.5 m/s, relatives risks were 1.42 (95% confidence interval [CI], 1.10 to 1.82; P<0.01) and 1.41 (95% CI, 1.17 to 1.70; P<0.001), respectively. Framingham score significantly predicted the occurrence of coronary and all cardiovascular events in this population (P<0.01 and P<0.0001, respectively). In multivariate analysis, pulse wave velocity remained significantly associated with the occurrence of coronary event after adjustment either of Framingham score (for 3.5 m/s: relative risk, 1.34; 95% CI, 1.01 to 1.79; P=0.039) or classic risk factors (for 3.5 m/s: relative risk, 1.39; 95% CI, 1.08 to 1.79; P=0.01). Parallel results were observed for all cardiovascular events. This study provides the first direct evidence in a longitudinal study that aortic stiffness is an independent predictor of primary coronary events in patients with essential hypertension.

Algorithms↗

Escitalopram (S-citalopram) and its metabolites in vitro: cytochromes mediating biotransformation, inhibitory effects, and comparison to R-citalopram.

Transformation of escitalopram (S-CT), the pharmacologically active S-enantiometer of citalopram, to S-desmethyl-CT (S-DCT), and of S-DCT to S-didesmethyl-CT (S-DDCT), was studied in human liver microsomes and in expressed cytochromes (CYPs). Biotransformation of the R-enantiomer (R-CT) was studied in parallel. S-CT was transformed to S-DCT by CYP2C19 (K(m) = 69 microM), CYP2D6 (K(m) = 29 microM), and CYP3A4 (K(m) = 588 microM). After normalization for hepatic abundance, relative contributions to net intrinsic clearance were 37% for CYP2C19, 28% for CYP2D6, and 35% for CYP3A4. At 10 microM S-CT in liver microsomes, S-DCT formation was reduced to 60% of control by 1 microM ketoconazole, and to 80 to 85% of control by 5 microM quinidine or 25 microM omeprazole. S-DDCT was formed from S-DCT only by CYP2D6; incomplete inhibition by quinidine in liver microsomes indicated participation of a non-CYP pathway. Based on established index reactions, S-CT and S-DCT were negligible inhibitors (IC(50) > 100 microM) of CYP1A2, -2C9, -2C19, -2E1, and -3A, and weakly inhibited CYP2D6 (IC(50) = 70-80 microM). R-CT and its metabolites, studied using the same procedures, had properties very similar to those of the corresponding S-enantiomers. Thus S-CT, biotransformed by three CYP isoforms in parallel, is unlikely to be affected by drug interactions or genetic polymorphisms. S-CT and S-DCT are also unlikely to cause clinically important drug interactions via CYP inhibition.

Algorithms↗

A computer adaptive testing simulation applied to the FIM instrument motor component.

OBJECTIVE: To determine whether computer adaptive testing (CAT) can be used to decrease the number of FIM trade mark instrument motor component items administered in assessing persons with spinal cord injury (SCI). DESIGN: For a CAT simulation, a 3-step algorithm was used to select 6 FIM items for each individual; items were selected according to the subject's motor ability as estimated by 2 initial items. Separate estimates of motor ability for admission, discharge, and follow-up data (plus combined time points) derived from 6 items were compared statistically with estimates derived from 14 items (walking and wheelchair mobility were split). SETTING: Records from the Spinal Cord Injury Model Systems (SCIMS). PARTICIPANTS: Patients served by the SCIMS, for whom complete motor FIM information was available for rehabilitation admission (N=5,969), discharge (N=5,964), or follow-up at a first or later anniversary (N=5,176). INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: Similarity of mean, standard deviation, skewness, kurtosis, and Rasch reliability and separation of persons and items based on 6 and 13 items; intraclass correlation coefficient (ICC) for parallel estimates. RESULTS: Calibrations for FIM items and FIM steps differed for the 3 time points, but showed sufficient agreement (ICC, >.90) that combined calibration was feasible. Means and other distribution characteristics differed minimally between the 6- and 13-item estimates. The person and item separations and reliabilities were somewhat lower and the mean measurement errors somewhat higher for the 6-item estimates, but only marginally so. ICCs between 6- and 13-item estimates were .95 or higher. CONCLUSION: CAT can be used to reduce data collection time; the level of precision of estimates is minimally less than that provided by traditional assessment approaches.

Algorithms↗

Orientation in the cuttlefish Sepia officinalis: response versus place learning.

Several studies have demonstrated that mammals, birds and fish use comparable spatial learning strategies. Unfortunately, except in insects, few studies have investigated spatial learning mechanisms in invertebrates. Our study aimed to identify the strategies used by cuttlefish (Sepia officinalis) to solve a spatial task commonly used with vertebrates. A new spatial learning procedure using a T-maze was designed. In this maze, the cuttlefish learned how to enter a dark and sandy compartment. A preliminary test confirmed that individual cuttlefish showed an untrained side-turning preference (preference for turning right or left) in the T-maze. This preference could be reliably detected in a single probe trial. In the following two experiments, each individual was trained to enter the compartment opposite to its side-turning preference. In Experiment 1, distal visual cues were provided around the maze. In Experiment 2, the T-maze was surrounded by curtains and two proximal visual cues were provided above the apparatus. In both experiments, after acquisition, strategies used by cuttlefish to orient in the T-maze were tested by creating a conflict between the formerly rewarded algorithmic behaviour (turn, response learning) and the visual cues identifying the goal (place learning). Most cuttlefish relied on response learning in Experiment 1; the two strategies were used equally often in Experiment 2. In these experiments, the salience of cues provided during the experiment determined whether cuttlefish used response or place learning to solve this spatial task. Our study demonstrates for the first time the presence of multiple spatial strategies in cuttlefish that appear to closely parallel those described in vertebrates.

Animals↗

The Twente Photoacoustic Mammoscope: system overview and performance.

We present PAM, the Photoacoustic Mammoscope developed at the University of Twente, intended for initial retrospective clinical studies on subjects with breast tumours. A parallel plate geometry has been adopted and the breast will be gently compressed between a glass plate and a flat ultrasound detector matrix. Pulsed light (5 ns) from an Nd:YAG laser will impinge the breast through the glass plate in regions of interest; an appropriate number of the 590 elements of the detector matrix will be activated in succession to record photoacoustic signals. Three-dimensional image reconstruction employs a delay-and-sum beamforming algorithm. We discuss various instrumental aspects and the proposed imaging protocol. Performance studies of the ultrasound detector are presented in terms of sensitivity, frequency response and resolution. Details of the patient-instrument interface are provided. Finally some imaging results on well-characterized breast tissue phantoms with embedded tumour simulating inserts are shown.

Acoustics↗

Information technology applications in biomedical functional imaging.

In parallel with rapid advances in computer technology, biomedical functional imaging is having an ever-increasing impact on healthcare. Functional imaging allows us to see dynamic processes quantitatively in the living human body. However, as we need to deal with four-dimensional time-varying images, space requirements and computational complexity are extremely high. This makes information management, processing, and communication difficult. Using the minimum amount of data to represent the required information, developing fast algorithms to process the data, organizing the data in such a way as to facilitate information management, and extracting the maximum amount of useful information from the recorded data have become important research tasks in biomedical information technology. For the last ten years, the Biomedical and Multimedia Information Technology (BMIT) Group and, recently, the Center for Multimedia Signal Processing have conducted systematic studies on these topics. Some of the results relating to functional imaging data acquisition, compression, storage, management, processing, modeling, and simulation are briefly reported in this paper.

Algorithms↗

Generalized Haar DWT and transformations between decision trees and neural networks.

The core contribution of this paper is a three-fold improvement of the Haar discrete wavelet transform (DWT). It is modified to efficiently transform a multiclass- (rather than numerical-) valued function over a multidimensional (rather than low dimensional) domain, or transform a multiclass-valued decision tree into another useful representation. We prove that this multidimensional, multiclass DWT uses dynamic programming to minimize (within its framework) the number of nontrivial wavelet coefficients needed to summarize a training set or decision tree. It is a spatially localized algorithm that takes linear time in the number of training samples, after a sort. Convergence of the DWT to benchmark training sets seems to degrade with rising dimension in this test of high dimensional wavelets, which have been seen as difficult to implement. This multiclass multidimensional DWT has tightly coupled applications from learning "dyadic" decision trees directly from training data, rebalancing or converting preexisting decision trees to fixed depth boolean or threshold neural networks (in effect parallelizing the evaluation of the trees), or learning rule/exception sets represented as a new form of tree called an "E-tree", which could greatly help interpretation/visualization of a dataset.

Journal Article↗

Dynamic variable selection in SNP genotype autocalling from APEX microarray data.

BACKGROUND: Single nucleotide polymorphisms (SNPs) are DNA sequence variations, occurring when a single nucleotide--adenine (A), thymine (T), cytosine (C) or guanine (G)--is altered. Arguably, SNPs account for more than 90% of human genetic variation. Our laboratory has developed a highly redundant SNP genotyping assay consisting of multiple probes with signals from multiple channels for a single SNP, based on arrayed primer extension (APEX). This mini-sequencing method is a powerful combination of a highly parallel microarray with distinctive Sanger-based dideoxy terminator sequencing chemistry. Using this microarray platform, our current genotype calling system (known as SNP Chart) is capable of calling single SNP genotypes by manual inspection of the APEX data, which is time-consuming and exposed to user subjectivity bias. RESULTS: Using a set of 32 Coriell DNA samples plus three negative PCR controls as a training data set, we have developed a fully-automated genotyping algorithm based on simple linear discriminant analysis (LDA) using dynamic variable selection. The algorithm combines separate analyses based on the multiple probe sets to give a final posterior probability for each candidate genotype. We have tested our algorithm on a completely independent data set of 270 DNA samples, with validated genotypes, from patients admitted to the intensive care unit (ICU) of St. Paul's Hospital (plus one negative PCR control sample). Our method achieves a concordance rate of 98.9% with a 99.6% call rate for a set of 96 SNPs. By adjusting the threshold value for the final posterior probability of the called genotype, the call rate reduces to 94.9% with a higher concordance rate of 99.6%. We also reversed the two independent data sets in their training and testing roles, achieving a concordance rate up to 99.8%. CONCLUSION: The strength of this APEX chemistry-based platform is its unique redundancy having multiple probes for a single SNP. Our model-based genotype calling algorithm captures the redundancy in the system considering all the underlying probe features of a particular SNP, automatically down-weighting any 'bad data' corresponding to image artifacts on the microarray slide or failure of a specific chemistry. In this regard, our method is able to automatically select the probes which work well and reduce the effect of other so-called bad performing probes in a sample-specific manner, for any number of SNPs.

Algorithms↗

A physician-based architecture for the construction and use of statistical models.

Physicians need specially tailored computer tools to take advantage of published research results. We present a knowledge-based computer framework--the physician-based (PB) architecture--for constructing such tools, and we use the problem of physicians' interpretation of two-arm parallel randomized clinical trials (TAPRCT) as a working example. Statistical models are represented by influence diagrams. The interpretation of influence-diagram elements are mapped into users' language in a domain-specific, physician-based user interface, called a patient-flow diagram. Statistical-model transformations that maintain the semantic relationships of the model and that embody clinical-epidemiological knowledge are encoded in a mediating structure called the cohort-state diagram. The algorithm that coordinates the interactions among the knowledge representations uses modular actions called construction steps. This architecture has been implemented in a Bayesian system, called THOMAS, that supports physician decision making in light of TAPRCT data. This support entails assessing clinical significance, prior beliefs, and methodological concerns. We suggest that the PB architecture applies to a wide range of statistical tools and users.

Algorithms↗

Optimal inference explains dimension-specific contractions of spatial perception.

It is known that people misperceive scenes they see during rapid eye movements called saccades. It has been suggested that some of these misperceptions could be an artifact of neurophysiological processes related to the internal remapping of spatial coordinates during saccades. Alternatively, we have recently suggested, based on a computational model, that transsaccadic misperceptions result from optimal inference. As one of the properties of the model, sudden object displacements that occur in sync with a saccade should be perceived as contracted in a non-linear fashion. To explore this model property, here we use computer simulations and psychophysical methods first to test how robust the model is to close-to-optimal approximations and second to test two model predictions: (a) contracted transsaccadic perception should be dimension-specific with more contraction for jumps parallel to the saccade than orthogonal to it, and (b) contraction should rise as a function of visuomotor noise. Our results are consistent with these predictions. They support the idea that human transsaccadic integration is governed by close-to-optimal inference.

Adult↗

The influence of air cavities on interface doses for photon beams.

PURPOSE: As the quantification of dose in homogeneous media is now better understood, it is necessary to further quantify effects from heterogeneous media. The most extreme case is related to air cavities. Although dose corrections at large distances beyond a cavity are accountable by attenuation differences, perturbations at air-tissue interfaces are complex to measure or calculate. These measurements helps understand the physical processes that govern these perturbations. METHODS AND MATERIALS: A thin window parallel-plate chamber and a special diode were used for measurements with various air cavity geometries (layer, channel, cubic cavity, triangle) in x-ray beams of 4 and 15 MV. RESULTS: Underdosing effects occur at both the distal and proximal air cavity interfaces. The magnitude depends on geometry, energy, and field sizes. As the cavity thickness increases, the central axis dose at the distal interface decreases. Increasing field size remedied the underdosing, as did the introduction of lateral walls. Following a 2.0 cm wide air channel for a 4 MV, 4 x 4 cm2 field there was an 11% underdose at the distal interface, while a 2.0 cm cubic cavity yielded only a 3% loss. Measurements at the proximal interface showed losses of 5% to 8%. For a 4 MV parallel opposed beam irradiation the losses at the interfaces were 10% for a channel cavity (in comparison with the homogeneous case) and 1% for a cube. The losses were slightly larger for the 15 MV beam. Underdosage at the lateral interface was 4% and 8% for the 4 MV and 15 MV beams, respectively. CONCLUSION: Although reports suggest better clinical results using lower photon energies with the presence of air cavities, there is no reliable dose calculation algorithm to predict interface doses accurately. The measurements reported here can be used to guide the development of new calculation models under nonequilibrium conditions. This situation is of clinical concern when lesions such as larynx carcinoma beyond air cavities are irradiated.

Absorption↗

Some remarks on the calculation of the pore size distribution function of activated carbons.

Different authors investigated the effects of geometric and energetic heterogeneities on adsorption and on carbon characterization methods. In most theoretical studies carbon structure is modeled as parallel infinite graphite walls that form ideal slit-shaped pores of the fixed widths. In the literature there is the lack of systematic studies showing the influence of pore structural and Lennard-Jones (LJ) potential parameters on the pore-size distribution functions. Moreover, the parameters characterizing the properties of the adsorbed phase and the heterogeneity of the adsorbent surface should be taken into account. The Nguyen and Do method with proposed by us ASA algorithm, were utilized for the assessment of the porosity from the series of almost few thousands numerically generated local adsorption isotherms. The values of the mentioned-above parameters are varied over the wide range (ca. +/-20%) of the reference ones. Different types of the theoretical and experimental adsorption isotherms (nitrogen at 77 K) were taken into account as the global ones. They were related to the mechanism of the primary, secondary or mixed micropore filling. The variations in some above-mentioned parameters have significant effects only for PSDs (and for average pore widths) corresponding to the primary micropore filling mechanism. On the other hand, for the process of the secondary micropore filling, the influence of these parameters (without the BET coefficient for adsorption on a "flat" surface, c(s,B)) is rather insignificant. Nevertheless the differences between local and global adsorption isotherms (in the whole range of relative pressures) the absence of micropores having pore half width equal to ca. 1 nm on PSDs was observed for studied adsorbate-adsorbent systems with exceptions of the strictly microporous adsorbents and/or the low values of c(s,B). Comparison of the experimental data with the generated theoretical isosteric enthalpy of adsorption indicates that the phenomenal uptake observed from experiment can be explained in terms of the reasonable solid-fluid interaction parameters. Therefore, we varied the heterogeneity of the adsorbent surface via the strength and the range of the solid-fluid potential and the parameter c(s,B) in order to reproduce the experimental data of enthalpy of adsorption. Note that similar procedure was applied by Wang and Johnson to reproduce some hydrogen adsorption data measured for carbon nanofibres. The analysis of the obtained results shows that the selection of the values of the parameters of the intermolecular interactions and the quantities characterizing the properties of the adsorbed phase and the heterogeneity of the adsorbent walls for molecular simulations should be made with care and the influence of possible errors should be considered.

Journal Article↗

Karyometry of pseudostratified, metaplastic and dysplastic nasal epithelium by morphometry and stereology. 1. A general model for automated image analysis of epithelia.

Nuclear enlargement, usually due to the existence of abnormally high DNA (ploidy) values, is one of the alterations most often encountered in pathological epithelia, especially in cancerous and precancerous states. Direct DNA measurements on microscopic sections are impossible, and karyometric studies must take the difficult stereologic problem of spheroid sectioning into account. A mathematical model is proposed to describe an aggregate of separate parallel anisotropic prolate spheroids of variable size and eccentricity. This model appears suitable for the study of epithelial nuclei. After a tentative estimation of the biopsy angle, the application of the model to nuclear profile measurements produces the stereologic data of the mean spheroid nucleus: major and minor axes (and their ratio), volume, surface area (and the V/S ratio), and numerical density. Considerable time may be saved by the use of an image analyser with a specific algorithm. Most of the steps are entirely automated, but the user retains the interactive choice of the nuclei to be studied, for instance by separating the different epithelial layers. The profile data are computer-filed and several programs can yield the stereologic estimations and plots of nuclear profile areas. Poolings of cases of similar histologic staging and nearly the same sectioning angle can be used for the profile area plots. The model has been applied to pseudostratified and altered nasal mucosa of nickel workers. The stereologic estimates, mainly the nuclear volume, correlate well with histologic gradings. The nuclear profile area plots are considered useful for an assessment of the nuclear polyploidism. The complete model should be applicable to many other types of functionally or pathologically altered epithelia, particularly for cancer and precancer screenings, when the use of sectioned material is a prerequisite.

Electronic Data Processing↗

A new method of multiplanar emission tomography using a seven pinhole collimator and an Anger scintillation camera.

A new method of multiplanar emission tomography is described; it uses a wide-field Anger scintillation camera (37.5 cm crystal diameter) and a seven-pinhole collimator. The pinholes (5.5 mm) acquire data simultaneously from the emissing source and project the data onto seven independent regions of the camera crystal. Multiple planes are reconstructed from the initial seven-view data acquisition through the use of a computerized addition-multiplication algorithm and variation of the superposition relationships among the projected views. These planes are then altered iteratively by a least-error criterion following ray-sum comparison with the original views. Planar resolution (full-width-half-maximum) is 1.0 cm and depth resolution is 1.5 cm. In 42 patients with angiographically demonstrated coronary-artery disease, studies of myocardial Tl-201 perfusion, under exercise, have shown improved detection sensitivity in comparison with scintigraphy using parallel-hole collimation.

Coronary Disease↗

Distributed parallel processing for multidimensional maximum entropy reconstruction.

We have developed a two-dimensional maximum entropy spectrum reconstruction program designed to run in parallel on workstation clusters. Test reconstructions of planes extracted from a three-dimensional NMR data set indicate that the parallel speedup is nearly equal to the number of processors provided that the individual processors have comparable performance and that there are at least as many planes as processors. The program also works well in a typical laboratory setting consisting of heterogeneous workstations.

Algorithms↗