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At least 829 records · Page 46Linked to original sources
PubMed2001

Mining DNA microarray data using a novel approach based on graph theory.

The recent demonstration that biochemical pathways from diverse organisms are arranged in scale-free, rather than random, systems [Jeong et al., Nature 407 (2000) 651-654], emphasizes the importance of developing methods for the identification of biochemical nexuses--the nodes within biochemical pathways that serve as the major input/output hubs, and therefore represent potentially important targets for modulation. Here we describe a bioinformatics approach that identifies candidate nexuses for biochemical pathways without requiring functional gene annotation; we also provide proof-of-principle experiments to support this technique. This approach, called Nexxus, may lead to the identification of new signal transduction pathways and targets for drug design.

Apoptosis↗
PubMed1983

Basal body temperature graph and the luteal phase defect.

Basal body temperature (BBT) charts from three menstrual cycles of 20 normal women and 20 women with biopsy-proven luteal phase defect (LPD) were reviewed. Mean luteal phase length in the normal women was 13.4 days, and that of the women with LPD was 11.8 days (P less than 0.05). Six (30%) of the LPD patients had luteal phases of less than 11 days according to BBT, and five of these patients had severely out-of-phase endometrial biopsies. None of the normal patients had luteal phases of less than 11 days. There was no significant difference in the mean rate of postovulatory BBT rise between the two groups. It is suggested that the slope of postovulatory temperature shift is not helpful in the diagnosis of LPD but that evidence of a luteal phase of less than 11 days on BBT does indicate a high likelihood of LPD.

Body Temperature↗
PubMed1985

The prediction of ovulation: a comparison of the basal body temperature graph, cervical mucus score, and real-time pelvic ultrasonography.

Ninety-five menstrual cycles were studied in 20 women undergoing donor artificial insemination (AID). In 49 cycles basal body temperature (BBT) changes were charted daily and both daily cervical mucus scoring (modified Insler score) and daily realtime ultrasonography (USS) were performed from day 11 to ovulation. AID was performed only on the day of follicular rupture. A control group, not subjected to USS, were inseminated two to three times per cycle over 46 cycles in the periovulatory period. The Insler score was found to be a reliable indicator of follicular development and rupture. The BBT was found to be less reliable than the Insler score or USS. While USS may be used to confirm follicular development, the Insler score is reliable and less costly.

Body Temperature↗
PubMed1999

Modeling chromatographic parameters by a novel graph theoretical sub-structural approach.

A novel approach to the study of quantitative relationships between chromatographic parameters and the chemical structure is introduced. It is based on the computation of the spectral moments of the topological bond matrix by using different weights as diagonal entries of this matrix. The main advantage of the present approach is that the quantitative contributions of the structural fragments of molecules to the chromatographic parameters studied can be obtained explicitly. By using this approach we study two data sets: one composed of 156 alkanes and the other of 81 oxygen-containing organic molecules. In both cases excellent quantitative structure-chromatographic retention relationships were obtained. The contributions of the different fragments to the chromatographic retention were generated obtaining tables of additive contributions to the properties studied. The physicochemical interpretation of the results on the basis of the retention mechanisms is also analyzed in light of this new approach.

Chromatography↗
PubMed1983

Inhibition of enzyme-catalysed reactions by excess substrate. A theoretical and Monte Carlo study of turning points in v(S) graphs.

Some difficulties associated with observing and defining substrate inhibition curves are discussed. Then a new method for measuring the steepness of substrate inhibition curves is derived and a parameter, lambda, is defined to measure the steepness of descent from a maximum or steepness of ascent from a minimum in v(S) plots. A mathematical theorem is presented to show how the magnitude of lambda is limited by the degree of the rate equation. Conditions for satisfactory Monte Carlo simulations of enzyme mechanisms are explored and the constraints necessary to generate v(S) curves with profiles in physiological ranges of substrate concentrations are investigated using 16 enzyme mechanisms. The probability of detecting substrate inhibition is estimated. It is shown that there exists a lower limit to the substrate concentration at which maxima can occur in v(S) plots but no upper limit and also that enzyme mechanisms can approach but never achieve the maximum steepness of descent possible for arbitrary rational functions with non-negative coefficients.

Enzyme Inhibitors↗
PubMed1986

A systematic method for the compilation of the King & Altman graphs of a steady-state enzyme model suitable for manual or computer use.

The schematic way of computing the King & Altman (1956) patterns for complex enzyme models is rather tedious. In this paper, a systematic method for the compilation of these patterns is proposed. This method ensures the generation of all the King & Altman patterns including those containing cycles. The importance of such patterns for an automatic recognition of the cyclic pathways of a given model is emphasized. The suggested algorithm is suitable for manual or computer processing.

Algorithms↗
PubMed2001

Involving the male partner for interpreting the basal body temperature graph.

OBJECTIVE: To determine if the male cohabiting partner of a woman may serve as a control for exogenous influences on basal body temperature (BBT). METHODS: Twelve couples from the Atlanta area were enrolled for a total of 41 couple-cycles. Couples recorded their oral temperatures daily and used urinary test kits for luteinizing hormone to estimate the day of ovulation. The covariability between the pre-ovulatory temperature of the women and their partners was assessed. The gaps in the couples' temperatures (female temperature minus male temperature) were compared in the pre- and postovulatory phases. RESULTS: Considerable covariability was found between temperatures of partners in the pre-ovulatory phase (covariance parameter = 0.49; P <.001). The pre- and postovulatory temperature gaps for all couples were significantly different in size (P <.001). For all couple-cycles, the size of the mean postovulatory temperature gap was at least 0.3-degree Fahrenheit greater than the mean pre-ovulatory temperature gap. CONCLUSION: Recording the BBT of women's partners may improve interpretation and accuracy of the BBT method. An increase in the size of a couple's temperature gap accompanies the transition from the pre- to the postovulatory phase. By this method, a given couple could determine their unique temperature gap indicating this transition.

Adult↗
PubMed2002

Improved QSPR analysis of standard entropy of acyclic and aromatic compounds using optimized correlation weights of linear graph invariants.

Entropy is calculated for a representative set of acyclic and aromatic compounds within the realm of QSAR/QSPR theory. Flexible topological molecular indices are chosen as independent variables in the fitting equations. The comparison with results derived from quantum mechanical calculations shows that the present approach gives better predictions. Some possible future extensions are pointed out.

Journal Article↗
PubMed2000

Graphing the death of Escherichia coli.

The graphical presentation of measurements of the progress over time of bacterial death or inactivation is discussed. Specifically, the Weibull distribution may be a useful generalisation of the exponential distribution. Data from experiments on the non-thermal death of Escherichia coli reported by Shadbolt et al. [Int. J. Food Microbiol. 49 (1999) 129] are reexamined to support this claim.

Escherichia coli↗
PubMed1997

Graphs in sequence spaces: a review of statistical geometry.

Statistical geometry is a method of comparative sequence analysis of genes. Based on the concept of the sequence space of nucleic acids it computes the geometries of sequence sets, mainly quartets, by combining both the vertical and horizontal information content of the sequences. The geometries can be used to deduce, for example, the degree of tree-likeness of the data set without any a priori assumption of an evolution model. Furthermore, statistical geometry allows to detect varying positional substitution rates in sequences. Applications of the method to tRNA sequences have provided an assessment for the age of the genetic code. Furthermore, applications of statistical geometry to homeoboxes as well as different virus families have helped to assign reliable kinship relationships. In addition, a lower bound for the age of the common ancestor of the human and simian immunodeficiency viruses has been established.

DNA, Viral↗