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Applications for microarrays in renal biology and medicine.

Groundbreaking recent developments, such as the near completion of human and mouse genome sequencing efforts and the emergence of robust microarray (gene chip) technologies, enabling comprehensive analysis of transcriptomes, provide new opportunities of unprecedented scale for researchers of kidney biology and disease. Combined with advanced computational and mathematical approaches for microarray data analysis, microarray applications promise to revolutionize our understanding of molecular mechanisms of kidney development and renal pathogenesis. New knowledge in this field will facilitate new approaches for molecular diagnostics, drug discovery, and eventually "personalized" renal medicine. In this review, we outline current and future research applications of microarray and computational approaches in renal biology and disease. We describe basic steps in microarray data analysis and introduce advanced computational approaches to optimize data mining of vast microarray datasets.

Genomics↗

A review of the numerical analysis of blood flow in arterial bifurcations.

Arterial bifurcation flow has been of special interest for some years because of its important role in the formation of atherosclerotic plaques and thrombi. To investigate the flow phenomena analytically, four major factors need to be accommodated--the three-dimensionality of a general bifurcation, the pulsatile nature of the laminar flow, the distensibility of the arterial wall and the non-Newtonian character of the blood. In this review, both engineering and medical aspects of each factor are carefully surveyed. It is demonstrated that the latest generation of computational fluid dynamics codes can treat this problem area and that it is both feasible and desirable to investigate the effects of each independent factor.

Arteries↗

Detection of overall space-time clustering in a non-uniformly distributed population. DiMe Study Group.

We developed a test statistic based on an approach of Whittemore et al. (1987) to detect space-time clustering for non-infectious diseases. We extended the spatial test of Whittemore et al. by deriving conditional probabilities for Poisson distributed random variables. To combine spatial and time distances we defined a distance matrix D, where dij is the distance between the ith and jth cell in a three-dimensional space-time grid. Spatial and temporal components are controlled by a weight. By altering the weight, both marginal tests and the intermediate test can be reached. Allowing a continuum from a pure spatial to a pure temporal test, the best result will be gained by trying different weights, because the occurrence of a disease might show some temporal and some spatial tendency to cluster. We examined the behaviour of the test statistic by simulating different distributions for cases and the population. The test was applied to the incidence data of insulin-dependent diabetes mellitus in Finland. This test could be used in the analysis of data which are localized according to map co-ordinates, by addresses or postcodes. This information is important when using the Geographical Information System (GIS) technology to compute the pairwise distances needed for the proposed test.

Child↗

Estimates of permeability and irreducible water saturation by means of a new robust computation of fractional power average relaxation times.

In a suite of water-saturated sandstones, we have recently demonstrated that irreducible water saturation can be well estimated using relaxation time only, in the form of any of several "averages" giving more emphasis to short times than does the geometric mean time. The best estimate of permeability came from fits giving more emphasis to slightly longer times. In this paper we present estimates of irreducible water saturation and permeability using approximations (here called Robusta approximation) to the fractional power average relaxation time (Tp)1/p. The advantage of this approximation is that it does not involve previous computation of exponential components; therefore, it does not depend on the choice of the inversion method, and it permits a very fast computation. The Robusta approximation gives some of the best correlations using p = -0.55 for irreducible water saturation and p = +0.18 for permeability.

Fractals↗

The statistical significance of nucleotide position-weight matrix matches.

MOTIVATION: To improve the detection of nucleotide sequence signals (e.g. promoter elements) by position-weight matrices (PWM) using the concept of statistically significant matches. RESULTS: The Mksite program was originally developed for analyzing protein sequences. We report NMksite, a new version adapted to the processing of nucleotide sequences. NMksite creates PWM from nucleotide sequence block alignments or occurrence tables using three weight computation schemes. An original feature of NMksite is the numerical computation of the statistical significance of PWM matches. The utility of this concept is demonstrated in the context of the prediction of splice sites and promoter regions.

Base Sequence↗

A simple program to create exact person-time data in cohort analyses.

BACKGROUND: Before disease rates can be calculated a tabulation of the length of follow-up for each person in the cohort has to be made. In complicated analyses such tabulations are often stratified by many characteristics, some which show no change with time, such as gender or year of birth, and some which do change with time, such as age or cumulative exposure. Available computer programs often restrict the way these tables can be made, particularly when handling time-dependent variables. METHODS: This paper presents a simple computer program which calculates the length of follow-up for each person in a study. RESULTS: Person-time data can be tabulated by a large number of variables using this method. This program is extremely flexible in the way that time-dependent variables can be created, can categorize observations by any unit of person-time, and will run on a range of platforms including a personal computer. CONCLUSIONS: This method should simplify the task of creating person-time data for analyses of disease rates in epidemiological studies.

Cohort Studies↗

Dynamics of biological systems: role of systems biology in medical research.

Cellular systems are networks of interacting components that change with time in response to external and internal events. Studying the dynamic behavior of these networks is the basis for an understanding of cellular functions and disease mechanisms. Quantitative time-series data leading to meaningful models can improve our knowledge of human physiology in health and disease, and aid the search for earlier diagnoses, better therapies and a healthier life. The advent of systems biology is about to take the leap into clinical research and medical applications. This review emphasizes the importance of a dynamic view and understanding of cell function. We discuss the potential for computer-aided mathematical modeling of biological systems in medical research with examples from some of the major therapeutic areas: cancer, cardiovascular, diabetic and neurodegenerative medicine.

Animals↗

[Optimizing performance documentation in gynecology--assistance from the internet].

The documentation of operations in the field of gynecology and obstetrics is regulated by social laws in Germany. Only by optimal encoding of diagnoses and procedures an efficient cashing with the health insurance's can be achieved. This requires profound knowledge of the invoice modalities and usually support by computer systems. The Internet offers in this respect some assistance, which in the following is pointed out and evaluated critically.

Documentation↗

[Extent of agreement in case of complete identity].

Two diagnostic procedures with binary outcomes are usually compared by Cohen's kappa coefficient of agreement. If the results of the two procedures are completely identical on a sample and so kappa equals to 1, the precision of the estimate can not be computed with the usual formulae and statistical softwares. A formula for variance which is valid in this particular case is presented together with a real example.

Analysis of Variance↗

Inhibition-based rhythms: experimental and mathematical observations on network dynamics.

An increasingly large body of data exists which demonstrates that oscillations of frequency 12-80 Hz are a consequence of, or are inextricably linked to, the behaviour of inhibitory interneurons in the central nervous system. This frequency range covers the EEG bands beta 1 (12-20 Hz), beta 2 (20-30 Hz) and gamma (30-80 Hz). The pharmacological profile of both spontaneous and sensory-evoked EEG potentials reveals a very strong influence on these rhythms by drugs which have direct effects on GABA(A) receptor-mediated synaptic transmission (general anaesthetics, sedative/hypnotics) or indirect effects on inhibitory neuronal function (opiates, ketamine). In addition, a number of experimental models of, in particular, gamma-frequency oscillations, have revealed both common denominators for oscillation generation and function, and subtle differences in network dynamics between the different frequency ranges. Powerful computer and mathematical modelling techniques based around both clinical and experimental observations have recently provided invaluable insight into the behaviour of large networks of interconnected neurons. In particular, the mechanistic profile of oscillations generated as an emergent property of such networks, and the mathematical derivation of this complex phenomenon have much to contribute to our understanding of how and why neurons oscillate. This review will provide the reader with a brief outline of the basic properties of inhibition-based oscillations in the CNS by combining research from laboratory models, large-scale neuronal network simulations, and mathematical analysis.

Electroencephalography↗

A computer program in compiled BASIC for the IBM personal computer to calculate the mean platelet survival time with the multiple-hit and weighted mean methods.

We developed an easy-to-operate computer program for the IBM personal computer to calculate, display and store in a database platelet kinetic data determined by analysis of the rate of clearance of radiolabeled blood platelets from the circulation. This was done by curve fitting using the weighted mean method and multiple-hit model. These models are complementary and calculating the mean platelet survival time with both is recommended. Improvement of the weighted mean method was investigated. The optimized weighting and fitting the exponential function with the Marquardt non-linear least squares method improved the weighted mean method. The weighted mean and multiple-hit models fit the survival curve data equally well. The calculation of the mean platelet survival time with the weighted mean method was very fast. The duration of calculation with the multiple-hit model could take up to 2 minutes. Calculation of the mean platelet survival time using both models has the advantage that conditions when calculation of the mean platelet survival time would be invalid, can be detected. The computer program will promote the valid comparison of results obtained at different institutions.

Blood Platelets↗

Parallel computation of ECG fields.

A parallel implementation of a finite difference model for computing the electric field of cardiac sources is presented. On a relatively inexpensive SIMD parallel computer, a full-forward solution is obtained in minutes, using accurate thoracic detail including anisotropy if required. Because the computation is based on a volume grid with constant size voxels, it readily accepts anatomical data from classified magnetic resonance imaging scans. By using a variation of the colored successive over-relaxation iteration, our finite difference model takes full advantage of the performance of massively parallel computers. Evaluations of the accuracy and performance of the model show the practicality of using specific anatomical models to recover the electrocardiographic field distributions for individual subjects. A relatively modest parallel machine is capable of assembling and computing a specific direct inverse solution from body surface potentials within an hour of measurement, assuming the magnetic resonance imaging classification has been previously completed.

Electrocardiography↗

The remarkable influence of steroid A/B-ring junction on the Wittig olefination reaction of the 11-oxo group: towards the synthesis of 5 alpha- and 5 beta-oriented delta 3-isomers of desogestrel.

The 5 alpha- and 5 beta-oriented delta 3-double bond isomers 8, 9 of the widely used progestin desogestrel (7) were synthesized. Wittig olefination reaction of the 5 alpha-intermediate 12 showed a dramatically reduced reaction rate compared with the olefination of the 5 beta-intermediate 13. Computational studies suggest that different energies of the intermediary 1,2-oxaphosphetanes may, at least partially, have been the reason for this phenomenon.

Alkenes↗

Development of molecular hydrogen-bonding potentials (MHBPs) and their application to structure-permeation relations.

Hydrogen bonds are major forces of recognition in biochemistry and molecular pharmacology; they are an essential component of intermolecular interactions and determine to a significant extent the 3D-structure of bio-macromolecules. To explore three-dimensional H-bonding properties, a new tool called Molecular Hydrogen-Bonding Potentials (MHBPs) was created. The development of this tool is based on a stepwise procedure similar to the one used successfully to generate the Molecular Lipophilicity Potential (MLP). First, a H-bonding fragmental system was developed starting from published solvatochromic parameters. An atomic H-bonding donor fragmental value (alpha) is associated to each hydrogen atom in a polar moiety. Similarly, an atomic H-bonding acceptor fragmental value (beta) is associated to each polar atom. A distance function and an angle function were defined to take into account variations of the MHBPs in space. The fragmental system and the geometric functions were then combined to generate the MHBPs. These are calculated at each point of an adequate molecular surface or on a three-dimensional grid. The MHBPs were compared with GRID interactions energies and correlated with success to oral drug absorption data. Available examples demonstrate that the MHBPs are a promising computational tool in drug design. Their combination with CoMFA and VolSurf is being studied.

Algorithms↗

Sample size for comparing linear growth curves.

Assuming a linear growth curve model under a suitable link function, we compute the sample size for comparing two treatment groups when the repeated measurements marginally follow exponential family distributions. From the treatment profiles of the chosen link function, we compute the common intercept beta0 and the regression slopes beta1 and beta2 to define delta = beta1 - beta2, the difference to be detected, under a specified alternative hypothesis. The dispersion matrices of the generalized estimating equations estimators are obtained under the null and alternative hypotheses using a suitable working correlation matrix. We compute the sample size assuming that delta is asymptotically normal. Details are worked out for repeated measures designs with binary and count data along with numerical examples.

Female↗

Longitudinal studies with continuous responses.

The analysis of serial measurements obtained in longitudinal studies plays an increasingly prominent role in applied research. The last few years have seen the development of many new techniques for carrying out analyses, including computer software. These methods can be used in a variety of standard problems, including repeated measures and cross-over designs, as well as growth curve analyses. We review these new methods, their application, and available computer packages. Data from a longitudinal study of lung function is used to illustrate the methods.

Adolescent↗

High-resolution electron microscopy of glycoproteins: the crystalline cell wall of Lobomonas.

Lobomonas piriformis is a member of an order of green algae (Volvocales) that have crystalline glycoprotein cell walls. As part of a program of investigation of these glycoproteins and their architecture we have studied the cell wall of Lobomonas by a variety of chemical, electron-microscopical and image-analysis techniques. Lobomonas and Vitreochlamys incisa show a very similar structure in their cell walls and represent I of the 4 classes into which all the structures of the wall of these algae that we have so far examined fall. The 2 classes that we have previously studied in detail, represented by Chlamydomonas reinhardii and chlorogonium elongatum, have a crystalline component of the wall that is a more or less smooth continuous surface overlying an amorphous inner wall layer. Although Lobomonas also has this 2-layer structure, the crystalline layer consists of distinct plates, each of which is built around a single, very coherent crystal lattice. The polar nature of the architecture of the cell wall is shown by sectioning and by examination of the cell-wall surface by metal-shadowing of carbon replicas, both of intact cells and of isolated cell-wall plates. There are great similarities in chemical composition between the glycoproteins of the cell wall of C. reinhardii and those of Lobomonas. Both has a large content of hydroxyproline in their amino acid composition and a sugar/hydroxyproline ratio of about 6.0, and both contain sugar sulphates. Lobomonas however has a large glucose content, whereas Chlamydamonas has almost none. Electron micrographs of walls stained with methylamine tungstate and shadowed specimens show that the Lobomonas crystal structure is entirely different from that of C. Reinhardii, and that there is a distinctly different structure in the centre of the plates from that at their edges, although the transition between the 2 areas occurs with no distortion of the crystal lattice. Computer image analysis has been used to calculate reconstructed images of the 2 areas, and by using minimal-dose techniques has yielded 2-dimensional maps of the negatively stained structure at a resolution of I.8 nm. The 2-sided plane group of both areas of the crystal is P2, and the centre area contains 2 distinct structural units, both centered on dyad axes, together with other more complex features. In the edge structure, one of the structural units appears unchanged, but the other unit has a considerably different appearance. The most likely interpretation of this is as a conformational or positional change in one of the subunits. However, because the underlying lattice is so accurately maintained across this transition, it seems probable that the basic structural arrangement that defines the lattice is common to the 2 areas. Some of the computational and mathematical techniques used in the image analysis have not been previously published and are described in detail and compared with published techniques in an Appendix.

Cell Wall↗