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PubMed1992

MEPS parameters and graph analysis for the use of recombination to construct ordered sets of overlapping clones.

Homologous recombination can provide a basis for the construction of an ordered set of overlapping clones. The principle is to make two libraries, each in a vector that has a different selectable marker flanking the insert site. Recombination between the flanking markers, leading to a selectable phenotype, can only occur as the consequence of crossing over between inserts. The two libraries are crossed in a matrix, allowing the construction of an ordered set. The logic, akin to S. Benzer's (1961, Genetics 47:403-415) for the arrangement of deletion and point mutations, has a graph theoretic formulation, which helps to cope with the complex and noisy data inherent in the physical mapping of genomes rich in repeated sequences. The minimum length of identity required for homologous recombination is called the MEPS (minimum efficient processing segment) and is a property of each recombination pathway. The amount and the type of sequence similarity required for two sequences to recombine is different from that implied by either the conservation of restriction sites or by most procedures of hybridization.

Chromosome Deletion↗

PubMed2002

Simultaneous determination of dorzolamide HCL and timolol maleate in eye drops by two different spectroscopic methods.

Two-component mixtures of dorzolamide hydrochloride and timolol maleate were assayed by first derivative and ratio derivative spectrophotometric methods. The first method, derivative spectrophotometry, by the zero-crossing measurements, was used due to the drugs closely overlapping absorption spectra. Linear calibration graphs of first derivative values at 250.3 nm for dorzolamide hydrochloride and 315.8 nm for timolol maleate. The second method, is based on ratio first derivative spectrophotometry, the amplitudes in the first derivative of the ratio spectra at 242.9 and at 223.5 nm were selected to determine dorzolamide and timolol maleate in the binary mixture. Calibration graphs were established for 8.0-30.0 microg ml(-1) for dorzolamide hydrochloride and 3.0-24.6 microg ml(-1) for timolol maleate in binary mixture. Good linearity, precision and selectivity were found, and the proposed methods were applied successfully to the pharmaceutical dosage from containing the above-mentioned drug combination without any interference by the excipients. Vierordt's method was also developed for a comparison method.

Adrenergic beta-Antagonists↗

PubMed2002

Noninvasive estimation of both systolic and diastolic pulmonary artery pressure from Doppler analysis of tricuspid regurgitant velocity spectrum in patients with chronic heart failure.

BACKGROUND: Noninvasive estimation of pulmonary artery systolic and diastolic pressures usually requires the investigation of both tricuspid and pulmonary regurgitant jets and an estimate of right atrial pressure. A new, noninvasive method to obtain pulmonary diastolic pressure (based on the hemodynamic demonstration that right ventricular systolic pressure and pulmonary artery diastolic pressure are equal at the time of pulmonary valve opening) from the analysis of tricuspid regurgitation alone has been described in a small cohort of patients. We sought to verify the accuracy of this method in a large population of patients with heart failure. METHODS: An estimate of pulmonary artery diastolic pressure was obtained by transposing the pulmonary opening time (from the onset of the R wave on the electrocardiographic tracing to the beginning of pulmonic forward flow on Doppler examination) onto the tricuspid regurgitant velocity curve and calculating the pulmonary artery diastolic pressure value as the pressure gradient between the right ventricle and right atrium at this time. The study group included 86 consecutive patients (64 men, aged 52 +/- 11 years) with heart failure (New York Heart Association class > or =II, 94%) who were in stable clinical condition with a chiefly idiopathic (57%), ischemic (24%), or other form (13%) of dilated cardiomyopathy. Noninvasive, right-sided pressures were compared with invasive measurements obtained during right heart catheterization performed within 24 hours. The Bland and Altman graphic method was used together with the calculation of the Lin concordance correlation coefficient and its 95% CI to assess the agreement between hemodynamic and echocardiographic measurements. RESULTS: Catheter-derived pulmonary artery systolic pressure ranged from 8 to 119 mm Hg (mean 42 +/- 21 mm Hg), pulmonary artery diastolic pressure from 1 to 59 mm Hg (mean 20 +/- 11 mm Hg), and right atrial pressure from -5 to 20 mm Hg (mean 6 +/- 5 mm Hg). Tricuspid regurgitation was detected in 75 of 86 patients (87%). Pulmonary artery systolic pressure ranged from 13 to 110 mm Hg (mean 44 +/- 21 mm Hg); the pressure gradient between the right ventricle and right atrium at time t of the pulmonary valve opening on the tricuspid regurgitation velocity curve was measurable in 70 of 75 (93%) cases and ranged from 3.5 to 64 mm Hg (mean 22 +/- 11 mm Hg). Good agreement was observed not only for pulmonary artery systolic pressure but also for pulmonary artery diastolic pressure, based on the analysis of the tricuspid regurgitation velocity jet, with a slight difference between measurements (-1.8 and 0.1, respectively), no evident pattern of point scattering, and a high concordance correlation coefficient that was elicited by the virtually total overlapping of lines on the graph. Overall results were not significantly different whether patients with depressed right ventricular function (right ventricular ejection fraction < or =35%), with a tricuspid regurgitation grade > or =2 and atrial fibrillation were included in the analysis. CONCLUSIONS: The narrow paired difference for the estimate of pulmonary artery systolic pressure and the even better difference for pulmonary artery diastolic pressure using the tricuspid regurgitation velocity curve analysis indicates that this new method reliably estimates invasive right-sided pressures over a wide range of pressure values in patients with heart failure. The overall good correlation with invasive values indicates that Doppler examination of tricuspid regurgitation alone may provide a simple and comprehensive new method for the noninvasive evaluation of right ventricular and pulmonary hemodynamics in patients with heart failure.

Blood Pressure↗

PubMed2026

Rawsamble: overlapping raw nanopore signals using a hash-based seeding mechanism.

MOTIVATION: Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the signals to bases (i.e. without basecalling). However, existing solutions cannot interpret raw signals directly if a reference genome is unknown due to a lack of accurate mechanisms to handle increased noise in pairwise raw signal comparison. Our goal is to enable the direct analysis of raw signals without a reference genome. To this end, we propose Rawsamble, the first mechanism that can identify regions of similarity between all raw signal pairs, known as all-vs-all overlapping, using a hash-based search mechanism. RESULTS: We use these overlaps to construct de novo assembly graphs with an existing assembler, miniasm, off-the-shelf. To our knowledge, these are the first de novo assemblies ever constructed directly from raw signals without basecalling. Our extensive evaluations across multiple genomes of varying sizes show that Rawsamble provides a significant speedup (on average by 5.01× and up to 23.10×) and reduces peak memory usage (on average by 5.74× and up to by 22.00×) compared to a conventional genome assembly pipeline using the state-of-the-art tools for basecalling (Dorado's fastest mode) and overlapping (minimap2) on a CPU. We find that around one-third of Rawsamble's overlapping pairs are also found by minimap2. We find that when we use overlapping reads from Rawsamble, we can construct unitigs that are (i) as accurate as those built from minimap2's overlaps and (ii) up to half a chromosome in length (e.g. 2.3 million bases for E. coli). AVAILABILITY AND IMPLEMENTATION: Rawsamble is available at https://github.com/CMU-SAFARI/RawHash. We also provide the scripts to fully reproduce our results on our GitHub page.

Nanopores↗

PubMedDate not supplied

Errors caused by combination of Di-4 ANEPPS and Fluo3/4 for simultaneous measurements of transmembrane potentials and intracellular calcium.

Intracellular calcium concentration and transmembrane potentials are two important measurements used to study the mechanisms of cardiac activity. Fluorescent dyes have been used to measure these separately but not simultaneously in cardiac tissue. Fluo-3 and Fluo-4 (a recently improved version of Fluo-3) have been used to measure changes in intracellular calcium concentration and Di-4 ANEPPS has been used to measure transmembrane potentials. This paper addresses the feasibility of using these fluorescent dyes together in order to measure transmembrane potentials and intracellular calcium concentration simultaneously. For the dyes to be used simultaneously, their respective fluorescence spectra must be sufficiently separated in wavelength in order to allow them to be separated by optical filters or spectrographs. An apparatus was constructed to measure the dyes' spectra in a fluorescence imaging chamber as well as in an isolated perfused rabbit heart. The measured spectra were mathematically modeled in order to assess the spectral overlap error under different conditions. Error graphs were constructed which may help researchers select optical filters and dye concentrations that will result in an acceptable error.

Aniline Compounds↗

PubMed1982

Computer-assisted sequencing, interval graphs, and molecular evolution.

In 1945, Fox developed the strategy for sequencing long proteins by using overlapping fragments. We show how the formal mathematical technique for the construction of interval graphs (Gilmore and Hoffman, 1964) is useful both pedagogically for understanding the underlying logic of sequencing linear molecules and is more amenable to automation because of its algorithmic nature. We also present a computer program, that employs the interval graph algorithm, which can be used to sequence proteins when given digest data. An example is given to illustrate all the steps involved in the algorithmic processing of the data. The need for such developments with respect to molecular evolution is discussed.

Amino Acid Sequence↗

PubMed1988

Neuroblastoma--when are urinary catecholamines and their metabolites 'normal'?

The overproduction of catecholamines and their metabolites is a well recognised feature of neuroblastoma. Published data are scarce for their urinary excretion in children with neuroblastoma and in ill children in whom this diagnosis may be considered. We have determined a graphical upper reference limit for total catecholamines, total metadrenalines and HMMA in urine, expressed as a ratio to the creatinine concentration, for a group of 174 children with neuroblastoma and 704 hospitalised children with other disorders. This graph has been determined by examining the overlap region between the results for the two groups of children and avoids the irregularities caused by statistical outliers. The sensitivity and specificity of the individual tests indicate that total catecholamines is marginally the best single test to perform when trying to diagnose neuroblastoma, with the best clinical sensitivity being achieved by examining both total catecholamines and HMMA. Only two of the 174 children with neuroblastoma would not have been detected using these two tests. Total metadrenalines did not appear to add any further information and could be dropped from the repertoire in favour of the other two measurements.

Adolescent↗

PubMedDate not supplied

Classifying binormal diagnostic tests using separation-asymmetry diagrams with constant-performance curves.

A method is proposed for classifying diagnostic tests that have underlying binormal distributions. The method involves using the parameters that characterize these distributions as axes of a two-dimensional graph called a separation-asymmetry (S-A) diagram. Each point on an S-A diagram corresponds to a possible diagnostic test. The diagram also has superimposed on it any of three possible families of curves of constant performance: curves of constant area under the ROC graph (iso-AUR), curves of constant overlap area (iso-OA), and curves of constant maximum information (iso-MaxInfo). Thus, the performance of any test can be determined immediately by identifying the iso-performance curve of the desired type that passes through the corresponding point of the S-A diagram. The concept of "eccentric" diagnostic tests is defined and incorporated into the S-A diagrams. The classification scheme is applied to 28 diagnostic tests. Excellent agreement is found in the ranking between the iso-OA and iso-MaxInfo measures of performance, but the iso-AUR produces markedly different results. Only three of the 28 tests were found to be eccentric. Several other interesting patterns emerged.

Bias↗

PubMed2006

Hybridization-ligation versus parallel overlap assembly: an experimental comparison of initial pool generation for direct-proportional length-based DNA computing.

Previously, direct-proportional length-based DNA computing (DPLB-DNAC) for solving weighted graph problems has been reported. The proposed DPLB-DNAC has been successfully applied to solve the shortest path problem, which is an instance of weighted graph problems. The design and development of DPLB-DNAC is important in order to extend the capability of DNA computing for solving numerical optimization problem. According to DPLB-DNAC, after the initial pool generation, the initial solution is subjected to amplification by polymerase chain reaction and, finally, the output of the computation is visualized by gel electrophoresis. In this paper, however, we give more attention to the initial pool generation of DPLB-DNAC. For this purpose, two kinds of initial pool generation methods, which are generally used for solving weighted graph problems, are evaluated. Those methods are hybridization-ligation and parallel overlap assembly (POA). It is found that for DPLB-DNAC, POA is better than that of the hybridization-ligation method, in terms of population size, generation time, material usage, and efficiency, as supported by the results of actual experiments.

Base Sequence↗

PubMed2006

CFinder: locating cliques and overlapping modules in biological networks.

UNLABELLED: Most cellular tasks are performed not by individual proteins, but by groups of functionally associated proteins, often referred to as modules. In a protein association network modules appear as groups of densely interconnected nodes, also called communities or clusters. These modules often overlap with each other and form a network of their own, in which nodes (links) represent the modules (overlaps). We introduce CFinder, a fast program locating and visualizing overlapping, densely interconnected groups of nodes in undirected graphs, and allowing the user to easily navigate between the original graph and the web of these groups. We show that in gene (protein) association networks CFinder can be used to predict the function(s) of a single protein and to discover novel modules. CFinder is also very efficient for locating the cliques of large sparse graphs. AVAILABILITY: CFinder (for Windows, Linux and Macintosh) and its manual can be downloaded from http://angel.elte.hu/clustering. SUPPLEMENTARY INFORMATION: Supplementary data are available on Bioinformatics online.

Biology↗

PubMed2003

Effect of Veau-Wardill-Kilner type of cleft palate repair on long-term midfacial growth.

There is a common concern that the Veau-Wardill-Kilner type of cleft palate repair causes extensive denudation of the palate, resulting in inhibition of maxillary growth. The evidence for this belief is equivocal in the literature. The authors present some long-term results of this technique from a pure sample of nonsyndromic complete unilateral cleft lip and palate patients operated on by a single intermediate-volume cleft surgeon over a period of 25 years. Twenty-five patients, all born between 1977 and 1989, met the above inclusion criteria. Their age at the time of collection of study models and cephalograms was 9 to 17 years (average, 12 years). Midfacial growth was studied using 12-year dental models and lateral cephalograms taken before definitive orthodontic treatment. These were evaluated using the GOSLON Yardstick and digital cephalometric analysis. The final GOSLON results show that 72 percent of the patients had a good or satisfactory outcome, with a GOSLON score of 1, 2, or 3, and only 28 percent ended with a poor score of 4 or 5. The poor sensitivity of cephalometrics in discerning statistically significant differences was highlighted by the huge overlaps observed in the 95 percent confidence interval graph of mean sella-nasion-subspinale angle (S-N-A) values when comparing the results of the Eurocleft centers with those of the authors' center. The results suggest that satisfactory long-term midfacial growth can be obtained with Veau-Wardill-Kilner cleft palate repair.

Adolescent↗

PubMed2005

Motion layer extraction in the presence of occlusion using graph cuts.

Extracting layers from video is very important for video representation, analysis, compression, and synthesis. Assuming that a scene can be approximately described by multiple planar regions, this paper describes a robust and novel approach to automatically extract a set of affine or projective transformations induced by these regions, detect the occlusion pixels over multiple consecutive frames, and segment the scene into several motion layers. First, after determining a number of seed regions using correspondences in two frames, we expand the seed regions and reject the outliers employing the graph cuts method integrated with level set representation. Next, these initial regions are merged into several initial layers according to the motion similarity. Third, an occlusion order constraint on multiple frames is explored, which enforces that the occlusion area increases with the temporal order in a short period and effectively maintains segmentation consistency over multiple consecutive frames. Then, the correct layer segmentation is obtained by using a graph cuts algorithm and the occlusions between the overlapping layers are explicitly determined. Several experimental results are demonstrated to show that our approach is effective and robust.

Algorithms↗

PubMed1994

An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA.

An algorithm is described for mapping DNA contigs based on an interval graph (IG) representation. In general terms, the input to the algorithm is a set of binary overlapping relations among finite intervals spread along a real line, from which the algorithm generates sets of ordered overlapping fragments spanning that line. The implications of a more general case of the IG, called a probe interval graph (PIG), in which only a subset of cosmids are used as probes, are also discussed. In the specific case of cosmids hybridizing to regions of a YAC, the algorithm takes cross-hybridization information using the cosmids as probes, and orders them along the YAC; if gaps exist due to insufficient coverage of cosmid contigs along the length of the YAC, repetitive use of the algorithm generates sets of ordered overlapping fragments. Both the IG and the PIG can expose problems caused by false overlaps, such as hybridizations due to repetitive elements. The algorithm, has been coded in C; CPU time is essentially linear with respect to the number of cosmids analyzed. Results are presented for the application of a PIG to cosmid contig assembly along a human chromosome 13-specific YAC. An alignment of 67 cosmids spanning a YAC took 0.28 seconds of CPU time on a Convex 220 computer.

Algorithms↗

PubMed1996

Analysis of binary mixtures of cephalothin and cefoxitin by using first-derivative spectrophotometry.

A method for the analysis of two-component mixtures of cephalothin and cefoxitin using zero-crossing first-derivative spectrophotometry is described. This technique permits the quantification of these drugs with closely overlapping spectral bands without any separation step. Linear calibration graphs of first-derivative values at 235.00 and 236.75 nm for cephalothin and cefoxitin, respectively, with negligible intercepts were obtained versus concentration in the range 4.0-32.0 micrograms ml-1 for both antibiotics. This paper presents a systematic examination of the experimental data by applying an exhaustive statistical analysis to demonstrate the validity of the method. The results of the determination of these antibiotics in mixtures of injectable dosage forms are also presented, together with their determinations in physiological serum and glucosed physiological serum.

Calibration↗

PubMed2005

Systematic identification of statistically significant network measures.

We present a graph embedding space (i.e., a set of measures on graphs) for performing statistical analyses of networks. Key improvements over existing approaches include discovery of "motif hubs" (multiple overlapping significant subgraphs), computational efficiency relative to subgraph census, and flexibility (the method is easily generalizable to weighted and signed graphs). The embedding space is based on scalars, functionals of the adjacency matrix representing the network. Scalars are global, involving all nodes; although they can be related to subgraph enumeration, there is not a one-to-one mapping between scalars and subgraphs. Improvements in network randomization and significance testing--we learn the distribution rather than assuming Gaussianity--are also presented. The resulting algorithm establishes a systematic approach to the identification of the most significant scalars and suggests machine-learning techniques for network classification.

Algorithms↗

PubMed2004

Quantifying structure-function uncertainty: a graph theoretical exploration into the origins and limitations of protein annotation.

Since the advent of investigations into structural genomics, research has focused on correctly identifying domain boundaries, as well as domain similarities and differences in the context of their evolutionary relationships. As the science of structural genomics ramps up adding more and more information into the databanks, questions about the accuracy and completeness of our classification and annotation systems appear on the forefront of this research. A central question of paramount importance is how structural similarity relates to functional similarity. Here, we begin to rigorously and quantitatively answer these questions by first exploring the consensus between the most common protein domain structure annotation databases CATH, SCOP and FSSP. Each of these databases explores the evolutionary relationships between protein domains using a combination of automatic and manual, structural and functional, continuous and discrete similarity measures. In order to examine the issue of consensus thoroughly, we build a generalized graph out of each of these databases and hierarchically cluster these graphs at interval thresholds. We then employ a distance measure to find regions of greatest overlap. Using this procedure we were able not only to enumerate the level of consensus between the different annotation systems, but also to define the graph-theoretical origins behind the annotation schema of class, family and superfamily by observing that the same thresholds that define the best consensus regions between FSSP, SCOP and CATH correspond to distinct, non-random phase-transitions in the structure comparison graph itself. To investigate the correspondence in divergence between structure and function further, we introduce a measure of functional entropy that calculates divergence in function space. First, we use this measure to calculate the general correlation between structural homology and functional proximity. We extend this analysis further by quantitatively calculating the average amount of functional information gained from our understanding of structural distance and the corollary inherent uncertainty that represents the theoretical limit of our ability to infer function from structural similarity. Finally we show how our measure of functional "entropy" translates into a more intuitive concept of functional annotation into similarity EC classes.

Biochemical Phenomena↗

PubMed2004

Extremal optimization at the phase transition of the three-coloring problem.

We investigate the phase transition in vertex coloring on random graphs, using the extremal optimization heuristic. Three-coloring is among the hardest combinatorial optimization problems and is equivalent to a 3-state anti-ferromagnetic Potts model. Like many other such optimization problems, it has been shown to exhibit a phase transition in its ground state behavior under variation of a system parameter: the graph's mean vertex degree. This phase transition is often associated with the instances of highest complexity. We use extremal optimization to measure the ground state cost and the "backbone," an order parameter related to ground state overlap, averaged over a large number of instances near the transition for random graphs of size n up to 512. For these graphs, benchmarks show that extremal optimization reaches ground states and explores a sufficient number of them to give the correct backbone value after about O (n(3.5)) update steps. Finite size scaling yields a critical mean degree value alpha(c) =4.703 (28). Furthermore, the exploration of the degenerate ground states indicates that the backbone order parameter, measuring the constrainedness of the problem, exhibits a first-order phase transition.

Journal Article↗

PubMed2006

Identification of functional modules in a PPI network by clique percolation clustering.

Large-scale experiments and data integration have provided the opportunity to systematically analyze and comprehensively understand the topology of biological networks and biochemical processes in cells. Modular architecture which encompasses groups of genes/proteins involved in elementary biological functional units is a basic form of the organization of interacting proteins. Here we apply a graph clustering algorithm based on clique percolation clustering to detect overlapping network modules of a protein-protein interaction (PPI) network. Our analysis of the yeast Sacchromyces cerevisiae suggests that most of the detected modules correspond to one or more experimentally functional modules and half of these annotated modules match well with experimentally determined protein complexes. Our method of analysis can of course be applied to protein-protein interaction data for any species and even other biological networks.

Algorithms↗