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Fluorimetric determinations of nucleic acids using iron, osmium and samarium complexes of 4,7-diphenyl-1,10-phenanthroline.

New sensitive, reliable and reproducible fluorimetric methods for determining microgram amounts of nucleic acids based on their reactions with Fe(II), Os(III) or Sm(III) complexes of 4,7-diphenyl-1,10-phenanthroline are proposed. Two complementary single stranded synthetic DNA sequences based on calf thymus as well as their hybridized double stranded were used. Nucleic acids were found to react instantaneously at room temperature in Tris-Cl buffer pH 7, with the investigated complexes resulting in decreasing their fluorescence emission. Two fluorescence peaks around 388 and 567 nm were obtained for the three complexes using excitation lambda(max) of 280 nm and were used for this investigation. Linear calibration graphs in the range 1-6 microg/ml were obtained. Detection limits of 0.35-0.98 microg/ml were obtained. Using the calibration graphs for the synthetic dsDNA, relative standard deviations of 2.0-5.0% were obtained for analyzing DNA in the extraction products from calf thymus and human blood. Corresponding Recovery% of 80-114 were obtained. Student's t-values at 95% confidence level showed insignificant difference between the real and measured values. Results obtained by these methods were compared with the ethidium bromide method using the F-test and satisfactory results were obtained. The association constants and number of binding sites of synthetic ssDNA and dsDNA with the three complexes were estimated using Rosenthanl graphic method. The interaction mechanism was discussed and an intercalation mechanism was suggested for the binding reaction between nucleic acids and the three complexes.

Animals↗

The evolution of genetic topologies.

This manuscript explores the simultaneous evolution of population genetic parameters and topological features within a population graph through a series of Monte Carlo simulations. I show that node centrality and graph breadth are significantly correlated to population genetic parameters Phi(ST) and M; (rho=-0.95;rho=-0.98, respectively), which are commonly used in quantifying among population genetic structure and isolation by distance. Next, the topological consequences of migration patterns are examined by contrasting N-island and stepping stone models of gene movement. Finally, I show how variation in migration rate influences the rate of formation of specific topological features with particular emphasis to the phase transition that occurs when populations begin to become fixed due to restricted movement of genes among populations. I close by discussing the utility of this method for the analysis of intraspecific genetic variation.

Biological Evolution↗

Visualization of microarray results to assist interpretation.

Whole genome microarrays allow assessment of the profile of genes expressed under particular experimental conditions, including external stimuli such as pH or temperature, and internal changes brought about by deleting or over-expressing a gene. Such experiments produce large data sets, for which sophisticated analysis software is available. What is lacking are tools for analysing data sets from different experiments, in order to test and generate hypotheses about the links between regulatory networks. We describe here a method for presenting results from different experiments as a directed graph constructed using an automated graph drawing program xneato, enhanced by a logic program designed to cluster data and aid in the generation of hypotheses about possible gene interactions. A web-based front-end to the system has been constructed to explore and manipulate the graphical displays produced. Results of microarray experiments on Mycobacterium tuberculosis were used to develop and evaluate the visualization tool and initiate the development of an inference system for gene interactions based on such data. The GeneGraph project can be accessed at: zebrafish.doc.ic.ac.uk

Computer Graphics↗

Complementary identification of multiple flux distributions and multiple metabolic pathways.

Cell robustness and complexity have been recognized as unique features of biological systems. Such robustness and complexity of metabolic-reaction systems can be explored by discovering, or identifying, the multiple flux distributions (MFD) and redundant pathways that lead to a given external state; however, this is exceedingly cumbersome to accomplish. It is, therefore, highly desirable to establish an effective computational method for their identification, which, in turn, gives rise to a novel insight into the cellular function. An effective approach is proposed for complementarily identifying MFD in metabolic flux analysis and multiple metabolic pathways (MMP) in structural pathway analysis. This approach judiciously integrates flux balance analysis (FBA) based on linear programming and the graph-theoretic method for determining reaction pathways. A single metabolic pathway, with the concomitant flux distribution and the overall reaction manifesting itself as the desired phenotype under some environmental conditions, is determined by FBA from the initial candidate sequence of metabolic reactions. Subsequently, the graph-theoretic method recovers all feasible MMP and the corresponding MFD. The approach's efficacy is demonstrated by applying it to the in silico Escherichia coli model under various culture conditions. The resultant MMP and MFD attaining a unique external state reveal the surprising adaptability and robustness of the intricate cellular network as a key to cell survival against environmental or genetic changes. These results indicate that the proposed approach would be useful in facilitating drug discovery.

Algorithms↗

Comprehensive fetal ultrasonographic growth measurements in triplet gestations.

OBJECTIVE: Our purpose was to create tables and graphs of ultrasonographically derived fetal growth parameters in longitudinally studied triplet gestations from a single center. STUDY DESIGN: All triplet pregnancies managed by our division from 1987 through 1998 were identified. All had first-trimester dating sonograms and complete obstetric sonograms obtained by means of 3.5- or 5.0-MHz curvilinear transducers with freeze-freeze capability and on-screen calipers. Sonograms to assess fetal growth were obtained every 2 to 4 weeks, from 16 to 18 weeks' gestation until delivery. Fetal parameters obtained with each sonogram included biparietal diameter; head circumference; bicerebellar diameter; abdominal circumference; femur, humerus, tibia, and fibula lengths; estimated fetal weight; and head circumference/abdominal circumference ratio. Regression analysis was performed with JMP and Cricket Graph software packages, and lines of best fit with 95% confidence intervals were generated. RESULTS: A total of 443 ultrasonographic examinations were performed for 33 triplet pregnancies (99 fetuses). Each had between 3 and 6 sonograms obtained, all between 16 and 35 weeks' gestation. Scatterplots of each of the fetal growth parameters against gestational age were created with regression lines of best fit and 95% confidence intervals. All growth parameters were dependent on gestational age. CONCLUSION: A comprehensive set of fetal growth measurements in triplets from the United States is now available and can be used to assess longitudinal fetal growth.

Birth Weight↗

A comparison of three methods of identifying reliable and clinically significant client changes: commentary on Hageman and Arrindell.

Objectives of this commentary are to (1) note major similarities and differences of three methods of identifying reliable and clinically significant client changes, (2) demonstrate how graphs can be used to identify reliable and clinically significant client changes with each method, (3) describe uses and interpretations of overlaid graphs, (4) draw attention to an alternative to the Hageman and Arrindell method of estimating true score changes, and (5) caution users of the three methods against interpreting reliable and/or clinically significant changes which occur in psychotherapy as evidence of therapy 'efficacy' or 'effectiveness'.

Data Interpretation, Statistical↗

LINUCS: linear notation for unique description of carbohydrate sequences.

The use of proteomics databases has become indispensable for daily work of molecular biologists, but this situation has not yet been achieved for carbohydrate applications. One obvious reason is that existing data collections are only rarely annotated and no cross-linking to other resources exists. The existence of a generally accepted linear, canonical description for carbohydrates which can be readily processed by computers will enable efficient automatic cross-linking of distributed carbohydrate data collections by serving as a unique and unambiguous database access key. Various possibilities to derive a canonical notation are discussed. They can be divided into attempts that require structure description alone and alternatives that profit from the fact that a preferred graph direction (non-reducing to reducing end) exists within the structure. To open a fruitful discussion among glycoscientists a possible solution is presented where the reducing monosaccharide unit is selected as graph root and linkage information is used to define the priority of the various branches. A Web interface (http://www.dkfz.de/spec/linucs/) has been created that directly converts the commonly used extended representation of complex carbohydrates into the preferred canonical description or into its inverted form.

Algorithms↗

Numerical approach to plug-flow activated sludge reactor kinetics.

In this study, general relationships applicable to a wide variety of microbial-mediated treatment processes are developed using a number of continuous-flow stirred tank reactors-in-series. Simultaneous equations resulting from mass balance on substrate and biomass are solved numerically taking the longitudinal biomass gradient into account. A relationship between substrate and biomass concentrations is developed as a function of hydraulic residence time. Monod kinetics and mathematical models of reactors-in-series are used to represent the actual conditions resulting from varying degrees of axial dispersion and wastewater quality. Dimensionless quantities are used to reduce the number of parameters to be taken into account. Computer techniques are applied to express the results generally. By means of the numerical approach, the variation of the ratio between the hydraulic residence time of a given reactor and that of an equivalent plug-flow tank with the same inlet and outlet conditions is investigated. Results are expressed in the form of graphs to characterize the plug-flow activated sludge systems and to provide a basis of design. Experimental data reported in the literature are also evaluated to demonstrate the cases where the existing classical solution to the problem differs from the actual results obtained from the computer program and the design graphs given.

Algorithms↗

THEMPO: a knowledge-based system for therapy planning in pediatric oncology.

This article describes the knowledge-based system THEMPO (Therapy Management in Pediatric Oncology), which supports protocol-directed therapy planning and configuration in pediatric oncology. THEMPO provides a semantic network controlled by graph grammars to cover the different types of knowledge relevant in the domain, and offers a suite of acquisition tools for knowledge base authoring. Medical problem solvers, operating on the oncological network, reason about adequate therapeutic and diagnostic timetables for a patient. Furthermore, a corresponding patient record, also based on semantic networks and graph grammars, has been implemented to represent the course of therapy of an oncological patient.

Antineoplastic Combined Chemotherapy Protocols↗

Flow-injection spectrophotometric determination of certain cephalosporins based on the formation of dyes.

A flow-injection spectrophotometric method is described for the determination of cefadroxil (I) and cefotaxime (II). The method is based on the hydrolysis of the cephalosporin with sodium hydroxide whereby the sulfide ion is produced. The latter is allowed to react with N,N-diethyl-p-phenylenediamine sulfate (N,N-DPPD) and Fe (III), and the blue color produced is measured at 670 nm (method A). Linear calibration graphs are obtained in the range 36.34-109.2 and 95.48-477.4 microgml(-1) for I and II, respectively. The experimental limits of detection (three times the noise signal) are 0.036 and 0.048 microgml(-1) for I and II, respectively. The total flow-rate is 5.3 ml min(-1) for both drugs. Alternately, the sulfide ion produced is allowed to react with p-phenylenediamine dihydrochloride (PPDD) and Fe (III), and the violet color produced is measured at 597 nm (method B). Linear calibration graphs are obtained in the range 0.5-400 and 0.5-450 microg ml(-1) for I and II, respectively. The limits of detection are 0.4 and 0.2 microg ml(-1) for I and II, respectively. The total flow-rate is 3 ml min(-1) for both drugs. The methods have been successfully applied to the analysis of some pharmaceutical formulations, particularly of the injection and capsule types. The relative standard deviation (RSD) (n = 10) at the 50 and 100 microg ml(-1) levels of I and II were 0.83-0.77 and 0.9-0.8% with N,N-DPPD and PPDD as reagents, respectively. Recoveries were quantitative; the results obtained agreed with those obtained by other reported methods.

Cefadroxil↗

Maternal serum human chorionic gonadotropin concentrations and fetal sex prediction.

The feasibility of using maternal serum human chorionic gonadotropin (hCG) concentrations for prenatal sex prediction was examined. hCG was mesured in 822 serum samples from 560 women with uncomplicated pregnancies. Significantly higher hCG concentrations were found in the serum of women bearing female fetuses than in the serum of women bearing male fetuses during the third trimester, especially during the 10th lunar month. The data were utilized to construct probability graphs for fetal sex prediction based upon a single maternal serum hCG determination during the third trimester and during the 10th lunar month. However, the utility of these graphs is limited by the small proportion of pregnant women with serum hCG concentrations that were high or low enough to allow a prediction with high probability.

Chorionic Gonadotropin↗

Pregnancy-specific parameters in early pregnancies after in vitro fertilization: prediction of the course of pregnancy.

The plasma concentrations of the beta subunit of human chorionic gonadotropin (beta-hCG), pregnancy-specific glycoprotein, and progesterone were measured in 37 pregnancies after in vitro fertilization. Twenty-one pregnancies ended with delivery, 9 as clinical abortions, and 7 as biochemical abortions. To predict the pregnancy outcome as early as possible, we designed a prediction graph by calculating a "cutoff line" using discriminant analysis and prediction bands up to 95% probability. This prediction graph can help in the estimation of the probability of pregnancy outcome with satisfactory reliability by determination of beta-hCG only.

Abortion, Spontaneous↗

Liquid chromatography of demoxepam and phenothiazines using a post-column photochemical reactor and fluorescence detection.

Upon irradiation with short-wavelength UV light the tranquillizer demoxepam is converted into a highly fluorescent product. This reaction serves as a sensitive and selective means of detection of low levels of demoxepam in e.g., serum after separation by means of reversed-phase high-performance liquid chromatography. The effect of mobile phase composition and time of irradiation on the intensity of the fluorescence signal has been studied. A residence time of about 2 min in the post-column photochemical reactor is optimal, band broadening being efficiently suppressed (delta t ca. 1 sec) by means of air segmentation. Linear calibration graphs are obtained over a three-orders of magnitude concentration range; the detection limit for demoxepam is about 100 pg. Further work has demonstrated that detection limits of between 40 and 100 pg can also be obtained for the photoproducts of the phenothiazines fenergan, largactil, levopromazine and nedaltran. The calibration graphs show good linearity and the analysis of spiked serum samples was successful.

Anti-Anxiety Agents↗

Determination of sildenafil citrate and its main metabolite by sample stacking with polarity switching using micellar electrokinetic chromatography.

Micellar electrokinetic capillary chromatography (MEKC) coupled with sample stacking and polarity switching was investigated for the determination of Viagra (sildenafil citrate, SC) and its metabolite (UK-103,320, UK) in human serum in the concentration range of clinical interest. Human serum samples spiked with SC and UK were eluted with methanol from a C18 cartridge, the extract was evaporated and regenerated in a solution that contained 1 mM phosphate buffer (pH 12.3) and 20% methanol. The MEKC separation was performed using an injection time of 275 s, a polarity switching time of 93 s, a phosphate buffer, (pH 12.3, 15 mM) containing 25 mM sodium dodecyl sulfate as separation electrolyte and a fused-silica capillary. The analysis takes about 6 min and gives satisfactory inter-day precision with respect to migration times and linear responses over the 80-900 ng/ml concentration range investigated for SC and UK. Intra-day RSDs (n=4 graphs) for the slopes of the calibration graphs were 4.86% for SC and 3.50% for UK. Inter-day RSDs for the slopes were 4.37% for SC and 5.39% for UK. Detection limits (S/N=3) were about 17 ng/ml for both compounds in human serum. A 1-ml volume of blood serum was necessary to do this determination.

Calibration↗

Molar enthalpy and molar volume of methylene and benzene homologues in reversed-phase liquid chromatography.

In this study, thermodynamic properties are measured for methylene and benzene homologues in reversed-phase liquid chromatography using octadecylsilica stationary phases and methanol mobile phase. The change in molar enthalpy (delta H degree) is determined from graphs of the logarithm of the capacity factor versus the inverse temperature (15 to 60 degrees C), whereas the change in molar volume (delta V degrees) is determined from graphs of the logarithm of the capacity factor versus pressure (830 to 5000 p.s.i.). For octadecylsilica phases with low bonding density (2.7 mumol m-2), delta H degree and delta V degree are small and are relatively unaffected by temperature and pressure. These thermodynamic parameters are linearly related to the homologue number for the methylene homologues, but not for the benzene homologues. For the ethylene group, delta delta H degree and delta delta V degree are in the order of -0.41 kcal mol-1 and -1.0 cm3 mol-1, respectively, at 30 degrees C. As the bonding density increases (5.4 mumol m-2), the molar volume and molar enthalpy decrease in a significant and nonlinear manner with the homologue number. Moreover, these thermodynamic parameters are markedly affected by temperature and pressure. For the ethylene group, delta delta H degree and delta delta V degree are in the order of -3.65 kcal mol-1 and -14.1 cm3 mol-1, respectively, at 30 degrees C. The theoretical and practical implications of these measurements are discussed with respect to the retention mechanism in reversed-phase liquid chromatography.

Benzene↗

Parameter evaluation of the inverse power-law spectrum of heart rate. A quantitative approach for ECG arrhythmia analysis.

A preliminary study was performed to ensure reliable R-wave detection and fiducial mark location. A generalized phase-sampling model for spectral estimation was then used, based on an interest in beat-to-beat variations. Heart rate spectrum characteristics of 32 presumed-normal subjects and 44 records from the MIT-BIH electrocardiographic database (Massachusetts Institute of Technology, Cambridge, MA) were analyzed and three parameters were calculated: regression line slope, intercept, and cross correlation between the spectral data and the regression lines. Evaluation of these inverse power-law spectrum parameters provides a potential quantitative approach for characterizing erratic fluctuations of heart rate and is possibly used to distinguish between healthy and abnormal subjects. From the 44 recordings in the MIT-BIH database, a V-shaped curve was found in a plot of the regression line slope versus cross correlation. The results for both unmedicated and medicated patients with normal sinus rhythm cluster in the top left region of the graph. Also, 29 of the presumed-normal subjects cluster in the same region. Patients with premature ventricular contraction beats cluster in the top right region of the V-shaped curve. The rest of the recordings from the variety of arrhythmia cases in the database have low slopes and cross correlations, so they cluster near the apex of the V-shaped curve. Three volunteers who each had more than 32 atrial premature contraction and premature ventricular contraction beats also fall in this region of the graph. The results from 10 young volunteers from the United States and 15 volunteers from seven other countries cluster into different regions.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

Electromyography of the rectum and colon in Hirschsprung's disease.

The electromyographic activity of the large bowel was studied in patients suffering from aganglionic megacolon and in comparable normal infants and children, using of an intraluminal electrode. Graphs obtained in control children showed a basic electrical rhythm of 4-6 waves/min with bursts of high frequency spikes, 3-4/sec, superimposed on the top of the slow waves. The recordings in Hirschprung's disease showed an irregular basic electrical rhythm with waves of variable duration and no high frequency potentials, as long as the electrode was positioned in the aganglionic zone. As soon as the electrode was introduced further up into the normally innervated colon the graph became identical to that seen in the normal bowel. Intraluminal electromyography of the rectum and colon seems to be a suitable procedure to diagnose aganglionosis of the rectum and the extent of the lesion.

Child↗

A simple objective system for early recognition of overwhelming neonatal respiratory distress.

The early recognition of severe respiratory distress in the newborn allows for optimal care. The prompt identification of overwhelming respiratory failure may assist in the selection of candidates for new therapeutic techniques. We have evaluated, both retrospectively and prospectively, a simple scoring system for neonatal respiratory insufficiency. During the first 24 hr of life, serial inspired oxygen values (FiO2) are plotted with serial pH measurements against time on a graph. With pulmonary insufficiency, the lines cross. The severity of the insufficiency is quantified by integrating the area between the crossed lines. The 25 infants in our Regional Intensive Care Unit Nursery who died with respiratory distress syndrome (RDS) during 1976 were compared with surviving infants matched for gestational age, birth weight, and admission date; all patients received similar conventional management. The difference in the mean 24-hr cumulative scores between the two groups was significant (p < 0.01). Only 1 infant with a score over 40 U ultimately survived (96% specificity). From January 1978 through June 1979, data were graphed at the bedside on 100 neonates who required respiratory support, and analyzed without knowledge of the eventual outcome. Overall, the scoring system predicted the final outcome in 95% of the cases. False positive determinations were minimal, the system accurately selecting 86/87 ultimate survivors (98.8% specificity). These data suggest that this simple scoring system may prove useful in identifying infants with overwhelming respiratory distress. Such infants may be considered for specialized care or innovative yet unproven treatment modalities.

Humans↗