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PubMed1992

Bias in relative odds estimation owing to imprecise measurement of correlated exposures.

A series of graphs is presented that show the estimated degree of bias in logistic coefficient estimates for two correlated continuous exposures measured with imprecision. These graphs indicate that even when the correlation coefficient between the exposure of interest and a correlated exposure is as low as 0.2, imprecision in the measurement of the latter exposure can result in at least as serious bias in the logistic coefficient estimate for the exposure of interest as measurement imprecision in the exposure of interest itself. The implications for the design and interpretation of epidemiological studies are discussed.

Bias↗

PubMed1994

A geometric approach to the analysis of physiological flow data.

Physiological flow data are common in various medical fields. Examples include urinary, blood and expiratory flows. They are widely used in assessing functions in the urinary, circulatory, or pulmonary systems, respectively. Current statistical methods for analysing these flow data in clinical trials are either univariate analyses, which do not utilize all the information together, or some conventional multivariate methods (such as regression analyses) which yield results that do not render clear medical interpretations. This paper presents a new approach to analysing the flow data, using urinary flow as the primary focus. The basic idea and technical steps are applicable to other flow data as well. The proposed method aims to transform the flow measurements back to the shape of the flow graphs. Since the whole geometric pattern of the flow graph provides more information about the patient's flow condition than any individual flow parameter alone, the method is a meaningful way of combining and analysing the flow data in both statistical and clinical senses. The method is a three-stage procedure. Patients are classified into three classes in the first stage and then ranked in sequence in the second stage, according to the geometry of the shape pattern and some clinical criteria. The classification procedure is shown to be very reliable when compared with the clinician's visual evaluation, and hence can be implemented by computer programming to aid clinical trials involving many patients. The whole ranking score is then readily analysed at the third stage for comparing treatment effects by the analysis of covariance method based on ranks, with the post-treatment score as the response variable and the baseline score as the covariate. An example of a urinary flow data set is provided to illustrate the use of the procedure.

Analysis of Variance↗

PubMed1997

Data note system for capturing laboratory data.

The complexity of genome data limits the usefulness of traditional database management systems. The highly interconnected structure of genome data can be captured in a data representation language based on the mathematical formalism of graphs. We have tailored graphs for describing genome data and have developed a database management system, called the Data Note System, for developing small databases to capture data from genome laboratories. To simplify the use of the Data Note System, a series of tools with graphical user interfaces has been developed. The system is designed to be easy to install and use by novice database developers with a minimal amount of computer expertise. We describe the tools and present examples of their use. The system consists of a storage facility, a schema editing tool to simplify the design of small databases, and three tools for data entry and querying.

Computers↗

PubMed1993

Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm.

A program called PROTEP is described that permits the rapid comparison of pairs of three-dimensional protein structures to identify the patterns of secondary structure elements that they have in common. The representation of the protein structures as labelled graphs, where the secondary structure elements in a protein and the spatial and angular relationships between them correspond to the nodes and edges of a graph, was developed for use with an earlier program, called POSSUM, which identified subgraph isomorphisms in protein structures. PROTEP takes this representation and uses a different and more flexible approach to locating structural patterns in pairs of proteins, using a maximal common subgraph isomorphism algorithm that is based on a clique detection procedure. A range of searches is described to demonstrate that areas of common structural overlap between protein structures taken from the Protein Data Bank can be identified both effectively and efficiently.

Algorithms↗

PubMed2001

Quantitative analysis of nucleic acid three-dimensional structures.

A new computer program to annotate DNA and RNA three-dimensional structures, MC-Annotate, is introduced. The goals of annotation are to efficiently extract and manipulate structural information, to simplify further structural analyses and searches, and to objectively represent structural knowledge. The input of MC-Annotate is a PDB formatted DNA or RNA three-dimensional structure. The output of MC-Annotate is composed of a structural graph that contains the annotations, and a series of HTML documents, one for each nucleotide conformation and base-base interaction present in the input structure. The atomic coordinates of all nucleotides and the homogeneous transformation matrices of all base-base interactions are stored in the structural graph. Symbolic classifications of nucleotide conformations, using sugar puckering modes and nitrogen base orientations around the glycosyl bond, and base-base interactions, using stacking and hydrogen bonding information, are introduced. Peculiarity factors of nucleotide conformations and base-base interactions are defined to indicate their marginalities with all other examples. The peculiarity factors allow us to identify irregular regions and possible stereochemical errors in 3-D structures without interactive visualization. The annotations attached to each nucleotide conformation include its class, its torsion angles, a distribution of the root-mean-square deviations with examples of the same class, the list of examples of the same class, and its peculiarity value. The annotations attached to each base-base interaction include its class, a distribution of distances with examples of the same class, the list of examples of the same class, and its peculiarity value. The distance between two homogeneous transformation matrices is evaluated using a new metric that distinguishes between the rotation and the translation of a transformation matrix in the context of nitrogen bases. MC-Annotate was used to build databases of nucleotide conformations and base-base interactions. It was applied to the ribosomal RNA fragment that binds to protein L11, which annotations revealed peculiar nucleotide conformations and base-base interactions in the regions where the RNA contacts the protein. The question of whether the current database of RNA three-dimensional structures is complete is addressed.

Base Pairing↗

PubMed2001

[1-(13)C] breath test of galactose and fructose for quantitative liver function.

BACKGROUND: Using a rat model of hepatectomy, we investigated whether the severity of hepatopathy could be quantitatively measured from changes in expiratory (13)CO(2) levels after intravenous administration of [1-(13)C]fructose or [1-(13)C]galactose. MATERIALS AND METHODS: Under nembutal anesthesia, 100 mg/kg of [1-(13)C]fructose or [1-(13)C]galactose was administered to rats via the femoral vein, and expiratory (13)CO(2) levels were measured for 120 min. Then, 30, 70, or 90% hepatectomy was performed. In the control group, simple laparotomy was performed. A breath test was conducted 20 min after laparotomy. We examined the correlation of a single point (13)CO(2) level (SP) every 5 min until 30 min, and at 45 and 60 min with liver wt/body wt (LW/BW) (%). RESULTS: In the control group and all groups undergoing hepatectomy, the [1-(13)C]fructose breath test graph reached a plateau level at about 25 min. In the control group, the [1-(13)C]galactose breath test graph reached a plateau level, but in all groups undergoing hepatectomy a plateau level was not reached during measurement. The correlation coefficient between SP(5) after [1-(13)C]fructose administration and LW/BW was the highest, 0.656 (P = 0.0017). The correlation coefficient between SP(25) after [1-(13)C]galactose administration and LW/BW was the highest, 0.923 (P < 0.0001). CONCLUSION: In the breath test with intravenously administered [1-(13)C]fructose, hepatopathy could not be quantitatively evaluated accurately. However, hepatopathy could be quantitatively evaluated accurately by measuring SP(25) in the breath test with intravenously administered [1-(13)C]galactose over a short period.

Animals↗

PubMed1997

Multifactorial comparative study of spatial point pattern analysis methods.

A way of studying cooperative behaviour of biological entities (proteins, cells, etc.) is by using topographical analysis: the quantification of the spatial patterns formed by the entities considered as points. Five methods of topographical analysis were compared in terms of discriminant power, stability of parameters, methodological bias and algorithms. We tested five methods (nearest neighbour distribution, radial distribution, Voronoï paving, quadrat count, minimal spanning tree graph) which generated nine parameters on four simulated models (random point process, hardcore model and two cluster models) and on experimental cellular models. The method which offers the best discrimination power and stability seems to be the minimal spanning tree graph edge length distribution.

Animals↗

PubMed2000

Structural group analysis of functional activation maps.

We present here a new method for cerebral activation detection over a group of subjects. This method is performed using individual activation maps of any sort. It aims at processing a group analysis while preserving individual information and at overcoming as far as possible limitations of the spatial normalization used to compare different subjects. We designed it such that it provides the individual occurrence of the activations detected at a group level. The localization can then be performed on the individual anatomy of each subject. The analysis starts with a hierarchical multiscale object-based description of each individual map. These descriptions are then compared, rather than comparing the images directly. The analysis is thus performed at an object level instead of voxel by voxel. It is made using a comparison graph, on which a labeling process is performed. The label field on the graph is modeled by a Markov random field, which allows us to introduce high-level rules of interrogation of the data. The process has been evaluated on simulated data and real data from a PET protocol.

Brain↗

PubMed2000

Effects of some antibiotics on enzyme activity of glucose-6-phosphate dehydrogenase from human erythrocytes.

Inhibitory effects of some antibiotics on glucose-6-phosphate dehydrogenase from the erythrocytes of human have been investigated. For this purpose, at the beginning, erythrocyte glucose-6-phosphate dehydrogenase was purified 13.654 times in a yield of 28% by using ammonium sulphate precipitation and 2',5'-ADP Sepharose 4B affinity gel. Temperature of +4 degrees C was maintained during the purification process. Enzyme activity was determined with the Beutler method by using a spectrophotometer at 340 nm. This method was utilized for all kinetic studies. Sodium ceftizoxime, sodium ampicillin, sodium cefuroxime, sodium cefazolin, sodium cefoperazone, streptomycin sulphate, gentamicin sulphate, and netilmicin sulphate were used as antibiotics. All the antibiotics indicated the inhibitory effects on the enzyme. K(i) constants for glucose-6-phosphate dehydrogenase were found by means of Lineweaver-Burk graphs. While sodium cefoperazone, gentamicin sulphate, and netilmicin sulphate showed competitive inhibition, the others displayed non-competitive inhibition. In addition, I(50) values of the antibiotics were determined by plotting activity percent vs [I]. In addition, in vivo studies were done for sodium sefuroxime in Sprague-Dawley type rats. It was found that G6PD in erythrocyte was more inhibited by the drug in 2.5 h.

Adult↗

PubMed2000

Most recent common ancestor probability distributions in gene genealogies under selection.

A computational study is made of the conditional probability distribution for the allelic type of the most recent common ancestor in genealogies of samples of n genes drawn from a population under selection, given the initial sample configuration. Comparisons with the corresponding unconditional cases are presented. Such unconditional distributions differ from samples drawn from the unique stationary distribution of population allelic frequencies, known as Wright's formula, and are quantified. Biallelic haploid and diploid models are considered. A simplified structure for the ancestral selection graph of S. M. Krone and C. Neuhauser (1997, Theor. Popul. Biol. 51, 210-237) is enhanced further, reducing the effective branching rate in the graph. This improves efficiency of such a nonneutral analogue of the coalescent for use with computational likelihood-inference techniques.

Algorithms↗

PubMed1991

Integration of pecking, filter feeding and drinking mechanisms in waterfowl.

This paper is one of several contributions in a series, illustrating the application of a specific deductive methodology to explain diversity of form. The methodology facilitates the explanation of feeding morphologies in various ducks as a transformation of the mallard's feeding design maximized for specific proportions of performance that are contributed by pecking and filter feeding mechanisms. The earlier described anatomy and formal analyses of the three mechanisms in the mallard served as the initial conditions used in simulation models. Four elements of the feeding system were chosen that play a major role in all three mechanisms. For each element, the main parameter was selected: storage capacity of the rostral mouth cavity, transport capacity of the rostral mouth tube, storage capacity of the caudal mouth cavity and transport capacity of the caudal mouth tube. The boundary conditions for the simulation were determined from internal organismic constraints. The total food uptake of the mallard was regarded as the function to be maximized. This 'object' function is the summation of the food uptake by one second of pecking and one second of filter feeding. The drinking mechanism was shown not to interfere, since that mechanism operates sufficiently whenever the pumping mechanism works properly. The 'object' function, made up by the pecking and filter feeding performances was graphed. From these graphs a morphospace was developed: the region within which modifications of the mouth design are feasible. This procedure allowed examination of the general hypothesis that different modifications of one design for a complex multi-role system are explainable from differences in proportions of the functional performance contributed by each of the roles. Two predictions were evaluated more specifically: 1) If filter feeding performance must increase for a specific change in total food uptake, the volume of the rostral mouth cavity must increase; this requires widening and lengthening of the rostral maxillar portion and also a phase shift in jaw and lingual motion patterns, increasing the stroke volume. 2) If pecking performance must increase, the transport capacity of the rostral mouth tube must increase; this requires shortening of the maxillar mid portion. These two predictions regarding change in mouth morphology were borne out by shovelers and tufted ducks, respectively.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed1995

The atom assignment problem in automated de novo drug design. 4. Tests for site-directed fragment placement based on molecular complementarity.

Three previous papers in this series have outlined an optimization method for atom assignment in drug design using fragment placement. In this paper the procedure is rigorously tested on a selection of five ligand-protein co-crystals. The algorithm is presented with the molecular graph of the ligand, and the electrostatic/hydrophobic potential of the site, with the aim of creating a placement on the molecular graph which is as electrostatically complementary or hydrophobically similar to the site as possible. Various designer options were tested, including, where appropriate, hydrogen bonding and a restricted number of halogens. In most cases, the placement obtained was at least as good as the native ligand, if not significantly better.

4-Hydroxybenzoate-3-Monooxygenase↗

PubMed1996

Similarity and complementarity of molecular shapes: applicability of a topological analysis approach.

Developments based on a topological analysis approach of electron density maps are presented and applied to two different fields: the interpretation of electron density maps of proteins and the description of shape complementarity between a cyclodextrin host and a guest molecule. A global representation of the electron density distribution, through the location, identification and linkage of its critical points (points where the gradient of the density vanishes, i.e., peaks and passes), is generated using the program ORCRIT. On one hand, the interpretation of protein electron density maps is based on similarity evaluations between graphs of critical points and known structures. So far, the method has been applied to 3 A resolution maps for the recognition of secondary structure motifs using a procedure relevant to expert systems in artificial intelligence. Satisfying matches between critical point graphs and their corresponding protein structure depict the ability of the topological analysis to catch the essential secondary structural features in electron density maps. On the other hand, mapping the accessible volume of a host molecule is achieved by representing the peaks as ellipsoids with axes related to local curvature of the electron density function. Related energies of the interacting species can also be estimated. A qualitative comparison is made between the results generated by the topological analysis and energy values obtained by conventional molecular mechanics calculations. A positive comparison and a close complementarity between cyclodextrin and ligands shows that the topological analysis method gives a good representation of the electron density function.

Computer Simulation↗

PubMed1993

SPROUT: a program for structure generation.

SPROUT is a new computer program for constrained structure generation that is designed to generate molecules for a range of applications in molecular recognition. It uses artificial intelligence techniques to moderate the combinatorial explosion that is inherent in structure generation. The program is presented here for the design of enzyme inhibitors. Structure generation is divided into two phases: (i) primary structure generation to produce molecular graphs to fit the steric constraints; and (ii) secondary structure generation which is the process of introducing appropriate functionality to the graphs to produce molecules that satisfy the secondary constraints, e.g., electrostatics and hydrophobicity. Primary structure generation has been tested on two enzyme receptor sites; the p-amidino-phenyl-pyruvate binding site of trypsin and the acetyl pepstatin binding site of HIV-1 protease. The program successfully generates structures that resemble known substrates and, more importantly, the predictive power of the program has been demonstrated by its ability to suggest novel structures.

Artificial Intelligence↗

PubMed1995

Computer-assisted assignment of peptides with non-standard amino acids.

A comprehensive peptide assignment program and its application to a cyclic peptide, cyclosporin A, are presented in this paper. A group of graph theoretical algorithms using fuzzy logic are discussed with the aid of examples from cyclosporin A. The algorithms deal with heavily overlapped peaks, recover disjointed and distorted spin coupling networks, and include strategies for sequence-specific assignment. A procedure to extend the Protein Knowledge Base for automatically assigning non-standard amino acid residues is also presented. The program is capable of completely automated assignment for small peptides (approximately 20 residues). For such molecules, it is insensitive to whether the peptide chain is cyclic or acyclic, and to whether amide protons are present or absent. For larger peptides/proteins, more user interaction is required and the sequence-specific assignment step usually must proceed through fragments smaller than the full length to avoid problems due to occurrence of a combinatorial explosion. The program can be applied as a rigorous tool to check manual assignments. The fuzzy graph theoretical concepts built in the program are illustrated with 2D proton spectra of a peptide, but may be extended to higher-dimensional spectra, other biopolymers, natural products and other organic structures.

Algorithms↗

PubMed1983

Karyometric investigation on circadian rhythmic changes in the periportal and perivenous zones of the acinus of the rat liver.

In untreated adult male albino rats changes in nuclear volume within the periportal and the perivenous zones of the liver acinus were measured during a full day and night cycle. Only the perivenous zone displayed circadian rhythmic changes as expressed in the sinus-like course of the nuclear volume-distribution graph (polynomial) with a maximum between 16.00 h and 18.00 h and a minimum at 8.00 h. In all groups studied zonal heterogeneity of the means of nuclear volume and the percent-distribution graphs of nuclear volume classes were retained during the full cycle. Within each zone, however, distribution curves of nuclear volume classes were homogeneous indicating an equally directed trend in time-dependent changes in nuclear volume.

Animals↗

PubMed1996

Determination of trunk motion patterns associated with permanent or transient stenosis of the lumbar spine.

Dynamometric devices used to assess back function are becoming increasingly used in research as well as in clinical practice. These devices provide values for a variety of movement variables such as torque, displacement, and velocity, but they also enable the study of movement patterns. The purpose of this study was to determine the movement patterns of patients presenting with specific spinal pathologies. Thirteen patients with spinal stenosis and 14 patients with degenerative changes and a borderline spinal canal diameter, as well as a control group of 30 symptom-free subjects, were studied. An isoinertial trunk-testing dynamometric device was used. Sagittal velocity and position were measured against a resistance set to 50% of the subject's maximum isometric torque. A phase plane analysis (velocity against position) was performed for each subject. An ensemble averaging technique was used to average the repetitions of every subject and a normalization technique was employed to draw an average graph for each group. This graph showed distinct patterns of movement for the three groups. The differences appeared mostly during the extension phase of movement, as confirmed by statistical analysis. The spinal stenosis group showed lower velocities than the controls during the entire extension phase (P < 0.05), while the borderline spinal canal group demonstrated a significant decrease in velocity at the end of the extension phase (P < 0.01). These findings can be related to the increase in disk bulge and decrease in the diameter of the spinal canal during extension. This study shows the relation between some spinal pathologies and movement patterns. This type of functional assessment may be a valuable tool for assessing the relation between anatomical lesions and function and for determining the responsibility of findings such as bulging disk and/or facet syndrome in causing a patient's complaints.

Adult↗

PubMed1994

Are heart rate responses reproducible in the tilt-table test?

Measurement of blood pressure and heart rate in active orthostasis has proven to be effective in the diagnosis of autonomic regulatory dysfunctions. The following study was carried out in order to clarify to what extent reproducible heart rate reactions also occur in passive orthostasis. 61 people with normal results in five standardized tests were examined. All 61 test persons had individually differing courses of heart rate. After an initial increase of frequency an almost straight line results from a superimposed projection of the graphs. In 20 of these cases the tilt-table test was repeated in order to detect intra-individual regularities. Even when the test was repeated, no reproducible intraindividual heart rate reactions occurred. And here as well, projection of the graphs produced an almost straight line. We could not find any quotient, such as the 30/15 ratio in active orthostasis, during our tests with the tilt-table.

Adult↗