SEARCH · PubMed Health

Results for “Graph”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 343 records · Page 19Linked to original sources

PubMed1996

Regret graphs, diagnostic uncertainty and Youden's Index.

Regret is the difference in outcome between the action we took and the best action we could, in retrospect, have taken. 'Tent graphs', representing decision problems under uncertainty in terms of expected regret, offer an instructive geometric supplement to standard formulae, allow instant calculations, and suggest, as we shall illustrate, novel algebraic properties. For instance, the problem of finding the pre-test probability range in which it is worthwhile doing a diagnostic test becomes trivial, even when test costs depend on the unknown disease status; we take the opportunity to explore the (non-trivial) algebraic properties of this problem. The graphs also provide a simple way to illustrate and read off the expected value of information and expected value of perfect information. This property is used to derive a clinical interpretation of Youden's Index (sensitivity + specificity - 1), namely, it is the maximum proportional reduction in expected regret achieved by the test. Finally, we examine the relationship between Youden's Index and the area under an ROC curve.

Aged↗

PubMed1998

A statistical method for quantitative evaluation of the progression of chronic diseases: the mean score graph (MSG).

We present a quantitative method of evaluation of the clinical course of chronic disease with long-term progressive deterioration. The method takes into account information on all patients, whatever their duration of follow-up. We present the 'mean score graph' as a descriptive device which is an extension of a survival graph. The description of progression of idiopathic torsion dystonia, comparing progression in males and females, is used as an example of the application. A test for group comparison is described.

Age of Onset↗

PubMed1999

Reasoning about data with directed graphs.

This paper constructs graphical models for two important analysis problems to demonstrate how graphs can clearly represent complex relationships. A powerful property of graphical models called d-separation describes the statistical associations in a given graphical model. This allows the effects of unmeasured variables to be predicted, and suggests conditional analyses which can distinguish conjectured models. If an assumption called quasi-linearity is made, further conclusions can be drawn based on the structure of the graph and d-separation. Making the quasi-linearity assumption explicit also contributes to our understanding of which aspects of our causal intuition are based on linearity assumptions. The examples that we consider are the scientific interpretation of interventions and the evaluation of the validity of candidate surrogate endpoints for clinical trials. Intervention studies can be plagued by non-compliance with assigned treatment and ambiguity in interpreting results when treatment assignment manipulates multiple factors. We show graphically the conclusions that can be drawn under various assumptions. The topic of surrogate endpoints is addressed in causal terms and modelled graphically.

Bayes Theorem↗

PubMed1999

Characterization and comparison of Escherichia coli transfer RNAs by graph theory based on secondary structure.

We have developed a model to characterize the tRNA structures of Escherichia coli using graph theory. First of all, tRNAs were represented as graphs, whose vertices correspond to nucleotides and the edges to phosphodiester and hydrogen bond linkages. Vertices and edges were weighted using the results of a preliminary quantum study of the nucleotides and the possible coupling between pair bases using the semiempirical method AM1. For each vertex, we defined a nucleotide valence that measures the capability of forming hydrogen bonds. Edges were differentiated by using bond orders. We have proposed weighted structural descriptors-closely related to molecular Randic connectivity and Balaban distance indices-as a distinctive characteristic of each structure. Molecules were characterized by a set of weighted structural descriptors and classified by a clustering method and discriminant function analysis. Two main groups of tRNAs that correspond to the biosynthetic amino acid pathways, in agreement with Wong's coevolution theory of the genetic code, were obtained.

Escherichia coli↗

PubMed1999

The ancestral graph and gene genealogy under frequency-dependent selection.

Minority-advantage frequency-dependent selection has been proposed as the cause for the high level of observed polymorphism in some self/nonself-recognition systems. We present a mathematically rigorous derivation of the ancestral graph for a sample of genes that evolved according to a haploid infinite-alleles model of minority-advantage frequency-dependent selection. In the case of sufficiently weak selection, the gene genealogy can be extracted from the ancestral graph. We demonstrate that the gene genealogy under this model is identical to that obtained for a diploid model with heterozygote advantage. The case of strong selection is exemplified by a one-locus haploid self-incompatibility system; in this context, we investigate the number of alleles that can be maintained in a spatial versus a non-spatial habitat. Finally, we compare gametophytic self-incompatibility to the haploid self-incompatibility model.

Gene Frequency↗

PubMed1991

A graph-theoretic approach to modeling metabolic pathways.

The metabolic pathways of medazepam, oxazepam, and diazepam were modeled using graph-theoretic transforms which are incorporable into computer-assisted metabolic analysis programs. The information, represented in the form of a graph-theoretic transform kit, which was obtained from these pathways was then used to predict the metabolites of other benzodiazepine compounds. The transform kits gave statistically significant predictions with respect to a statistical method for evaluating the performance of the transform kits.

Anti-Anxiety Agents↗

PubMed1980

The discrimination between different blood-CSF barrier dysfunctions and inflammatory reactions of the CNS by a recent evaluation graph for the protein profile of cerebrospinal fluid.

A graph for the evaluation of the CSF-protein profile is presented as a basic program for the clinical-neurochemical laboratory. The graph has the following advantages: Simultaneous information on the functional state of the blood-CSF barrier and the inflammatory response of the CNS; maximal sensitivity for the determination of a pathological local IgG production in CNS--with the possibility of calculating the IgG fraction in CSF originating from the CNS; minimal number of protein assays necessary (albumin and IgG in serum and CSF); suitable for the demonstration of the course of the disease in a single patient as well as for demonstration of a group of cases for statistical purposes. Complementary chemical investigations and the correspondence with the clinical diagnosis are discussed for a number of typical cases. Two different types of blood-CSF barrier dysfunctions are discriminated by a proportional and a dis-proportionate increase of the CSF/serum protein concentration gradients.

Albumins↗

PubMed1979

A graph theoretic approach to the development of minimal phylogenetic trees.

The problem of determining the minimal phylogenetic tree is discussed in relation to graph theory. It is shown that this problem is an example of the Steiner problem in graphs which is to connect a set of points by a minimal length network where new points can be added. There is no reported method of solving realistically-sized Steiner problems in reasonable computing time. A heuristic method of approaching the phylogenetic problem is presented, together with a worked example with 7 mammalian cytochrome c sequences. It is shown in this case that the method develops a phylogenetic tree that has the smallest possible number of amino acid replacements. The potential and limitations of the method are discussed. It is stressed that objective methods must be used for comparing different trees. In particular it should be determined how close a given tree is to a mathematically determined lower bound. A theorem is proved which is used to establish a lower bound on the lenghtof any tree and if a tree is found with a length equal to the lower bound, then no shorter tree can exist.

Mathematics↗

PubMed2001

Frontotemporal dementia: evidence for impairment of ascending serotoninergic but not noradrenergic innervation. Immunocytochemical and quantitative study using a graph method.

A graph method was employed to analyze the spatial neuronal patterns of nuclear grays of the pontine tegmentum with ascending aminergic projections to the forebrain in 12 cases of frontotemporal dementia (FTD). The nuclear grays examined were the nucleus centralis superior (NCS), a part of the nucleus raphae dorsalis (NRD), and the locus coeruleus (LC). The results were compared with 30 cases of Alzheimer's disease (AD) and 35 non-demented controls. In addition to the graph evaluations, neuronal cytoplasmic inclusion bodies were stained by silver impregnation and ubiquitin (Ub) and tau immunohistochemistry. The FTD cases showed a significant, 40%, decline in number of neurons in the NCS and NRD, while the LC was spared. The magnitude of neuronal loss matched that of AD where, by contrast, the LC was also severely changed. Amyloid deposition and Alzheimer neurofibrillary tangles occurred in the aminergic nuclei almost exclusively in AD and, to a minor extent, in some aged controls. No cytoplasmic inclusion bodies were found in the aminergic nuclei of the FTD cases. However, 6 cases had Ub-positive but tau-negative neuronal inclusions in the hippocampal dentate fascia and in layer 2 of the prefrontal isocortex, and 3 showed clinical and histological signs of motor neuron disease. Our results suggest that the serotoninergic raphe nuclei with ascending projections to the forebrain, but not the LC, become directly or indirectly involved in frontotemporal dementia both with and without motor neuron disease.

Adult↗

PubMed1986

Computerized scoring and graphing of the Farnsworth-Munsell 100-hue color vision test.

The Farnsworth-Munsell 100-hue test is a sensitive and accurate test of color discrimination. A major disadvantage of the test is the laborious and time-consuming calculation needed to score the results and plot them on a chart for interpretation. We present a computer program, written in Microsoft's BASIC language, that performs the calculation and reports both the individual color cap error scores (from which the graph is plotted) and the total error score. If used with an IBM personal computer (or compatible) capable of graphics, the program plots a graph in a modified polar coordinate format that can be printed on a dot-matrix printer.

Color Perception↗

PubMed1978

Bond graph models for plant biosystems.

Computable dynamic models for plant biosystems permit the study of effects of environmental variables on plant growth and productivity. Using bond graphs, a comprehensive phenomenological model of a plant biosystem may be developed and used in computer simulations. Elements of a model studied in this papaer include a gas diffusion network between the atmosphere and leaf cytoplasm, intracellular chemistry, and the translocation networks of the phloem. Bond graphs are shown to provide a conceptual basis for the development of biological subsystem and system models and lead to computable representations.

Atmosphere↗

PubMed1991

Structural analysis of neural circuits using the theory of directed graphs.

A new approach to analysis of structural properties of biological neural circuits is proposed based on their representation in the form of abstract structures called directed graphs. To exemplify this methodology, structural properties of a biological neural network and randomly wired circuits (RC) were compared. The analyzed biological circuit (BC) represented a sample of 39 neural nuclei which are responsible for the control of the cardiovascular function in higher vertebrates. Initially, direct connections of both circuits were stored in a square matrix format. Then, standard algorithms derived from the theory of directed graphs were applied to analyze the pathways of the circuits according to their length (in number of synapses), degree of connectedness, and structural strength. Thus, the BC was characterized by the presence of short, reciprocal, and unidirectional pathways which presented a high degree of heterogeneity in their strengths. This heterogeneity was mainly due to the existence of a small cluster of reciprocally connected neural nuclei in the circuit that have access, through short pathways, to most of the network. On the other hand, RCs were characterized by the presence of long and mainly reciprocal pathways which showed lower and absolute homogeneous strengths. Through this study the proposed methodology was demonstrated to be a simple and efficient way to store, analyze, and compare basic neuroanatomical information.

Animals↗

PubMed1983

A graph-theoretical analysis of metabolic regulation.

A graph theoretical method is proposed for modeling metabolic networks including enzymic cascades and synergistic binding of ligands to enzymes. Formal operations on the graph of a given network leads to the identification of feedback metabolites and the enzymes which regulate the feedback. These systemic properties are thus isolated from the purely local regulation of individual enzymes. The method was applied to a model of glycogen metabolism. At low cyclic AMP and insulin levels feedback control of the system is predicted to be largely with the glycogen branching and debranching enzymes, which set the amount of glycogen in the metabolically available outer branches.

Cyclic AMP↗

PubMed1984

A graph theory model of the glomerular capillary network and its development.

Graph theory methods were used to analyze the topology of the renal glomerular capillary network using data both from a serial reconstruction of a rat glomerulus and from the literature. The graphs obtained were tested for planarity, and all but one were found to be nonplanar. This result indicated that the development of the glomerular capillary network must include a nonplanar growth process, and new growth models were proposed. In addition, the statistical properties of capillary branching patterns were analyzed, and a node degree distribution function estimate was obtained.

Animals↗

PubMedDate not supplied

A study of chemical systems using signal flow graph theory: application to Neptune.

Photochemistry of giant planets and their satellites is characterized by numerous reactions involving many chemical species. In the present paper, chemical systems are modeled by signal flow graphs. Such a technique evaluates the transmission of any input into the system (solar flux, electrons...) and gives access to the identification of the most important mechanisms in the chemical system. For a given chemical system, we first evaluate rate coefficients. Then, in order to obtain concentrations of each compound, we integrate the set of continuity equations by Gear's method. Gear's method is chosen rather than another classical method because it is recommended for a system of stiff equations due to the existence of greatly differing time constants. Finally, the technique of signal flow graphs is used. This method is applied to the production of hydrocarbons in the atmospheres of giant planets. In particular, the production of C2H6 in the atmosphere of Neptune from the photodissociation of CH4 is investigated. Different paths of dissociation of CH4 are possible from L alpha radiations. A chemical system containing 14 species and 30 reactions including these different paths of dissociation is integrated. The main mechanism of production of C2H6 is identified and evaluated for each model of dissociation. The importance of various reaction paths as a function of time is discussed.

Atmosphere↗

PubMed1989

The automation of routine calculations and graphing for alkaline filter elution analysis on a computer-controlled liquid scintillation analyzer.

The data calculations and graphing functions for the widely used alkaline filter elution technique have been completely automated. This saves considerable time and increases both efficiency and accuracy by eliminating human error. The automation was accomplished utilizing Lotus 1-2-3 and Lotus Graphwriter II on a Packard Tri-Carb 1900CA liquid scintillation analyzer containing a built-in pico-XTE computer. A batch file is used to control the overall execution of the process. It copies the data stored by the 1900CA into the Lotus subdirectory and invokes Lotus 1-2-3. A Lotus macro automatically imports the data file, performs the calculations, and prints the results. Graphwriter II is then invoked by the batch file and the charts are composed and graphed. Finally, the instrument operating software for the 1900CA is reentered and sample analysis can be resumed for any unanalyzed samples.

Alkalies↗

PubMed1984

Sample size graphs for "proving the null hypothesis".

Sample size graphs are given for clinical trials designed to test whether an experimental therapy is as effective as a standard therapy. We assume a dichotomous outcome variable and a one-sided test of the hypothesis that the probability of success with standard therapy is greater than the probability of success with experimental therapy by at least some specified amount delta. Graphs are given for significance level alpha = 0.01, 0.025, 0.05; type II error beta = 0.10, 0.20; and delta = 0.10, 0.20.

Clinical Trials as Topic↗

PubMed1992

Automated site-directed drug design: a method for the generation of general three-dimensional molecular graphs.

A new algorithm for creating diverse, irregular and physically reasonable three-dimensional linear atomic chains is described. The linear chains of atoms, or molecular graphs, are generated by solving a series of trigonometric equations within geometric constraints for a given set of atom types. The nature and number of the chains that are produced can be controlled by changing the palette of atom types, so that a chemist user could generate template suggestions that are synthetically relevant to a drug design project. Testing has shown that the method is sufficiently robust to be used in a general context. The molecular graphs could serve as useful structural templates for joining up regions in an active site where a ligand might interact strongly with the receptor. This paper is concerned with the description and proof of the methodology. The approach will form part of a larger structural tool kit for helping chemists to design novel ligands for a specified site.

Algorithms↗