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At least 433 records · Page 24Linked to original sources

PubMed1990

A computer designed graph for administration of atracurium by i.v. infusion.

A bi-exponential mathematical computer model was used to develop a guidance graph for atracurium infusions. The model permitted variation in infusion rates, in pharmacokinetic parameters and in "effect" thresholds. Systematic experiments revealed a relationship between the rate of recovery from a fixed bolus loading dose and the most appropriate initial infusion rate. This relationship was expressed as a guidance graph or "ready reckoner". The quality of guidance was assessed in 50 anaesthetics, given consecutively. In 39 patients optimal myoneural block for surgery was maintained for the duration of the infusion without adjustments or supplementary bolus doses. The mean operating time was 92 min and the mean duration of infusion was 59 min.

Adult↗

PubMed1988

A box-graph method for illustrating relative-size relationships in a 2 x 2 table.

The proportional relationships of the four numbers in a 2 x 2 table can be displayed using two types of box graphs. In one approach, a 'unitary square' is first divided according to the denominator proportions of the two groups formed in a cohort or case-control study, and then re-divided according to the numerator proportions in each group. In the second method, the numbers are arranged as four squares, proportionately sized according to the square root of each number, and contiguously adjacent to a central reference point. The methods offer a pictorial format for showing contingency counts in a manner analogous to the graphs used for other forms of data.

Data Interpretation, Statistical↗

PubMed2003

Enumeration and simulation of marriage node graphs on zero-loop pedigrees.

We present a method that for the marriage node graph of a zero-loop pedigree will enumerate all possible pedigrees that share the same underlying tree structure. The enumeration method leads naturally to a scheme for simulating from a uniform distribution on such pedigrees. This is extended to simulating pedigrees for which the underlying marriage node graph is a tree of any particular size.

Female↗

PubMed2006

Estimating the parameters of a model for protein-protein interaction graphs.

We find accurate approximations for the expected number of three-cycles and unchorded four-cycles under a stochastic distribution for graphs that has been proposed for modelling yeast two-hybrid protein-protein interaction networks. We show that unchorded four-cycles are characteristic motifs under this model and that the count of unchorded four-cycles in the graph is a reliable statistic on which to base parameter estimation. Finally, we test our model against a range of experimental data, obtain parameter estimates from these data and investigate possible improvements in the model. Characterization of this model lays the foundation for its use as a prior distribution in a Bayesian analysis of yeast two-hybrid networks that can potentially aid in identifying false-positive and false-negative results.

Algorithms↗

PubMed2025

Reference-Free Variant Calling with Local Graph Construction with ska lo (SKA).

The study of genomic variants is increasingly important for public health surveillance of pathogens. Traditional variant-calling methods from whole-genome sequencing data rely on reference-based alignment, which can introduce biases and require significant computational resources. Alignment- and reference-free approaches offer an alternative by leveraging k-mer-based methods, but existing implementations often suffer from sensitivity limitations, particularly in high mutation density genomic regions. Here, we present ska lo, a graph-based algorithm that aims to identify within-strain variants in pathogen whole-genome sequencing data by traversing a colored De Bruijn graph and building variant groups (i.e. sets of variant combinations). Through in silico benchmarking and real-world dataset analyses, we demonstrate that ska lo achieves high sensitivity in single-nucleotide polymorphism (SNP) calls while also enabling the detection of insertions and deletions, as well as SNP positioning on a reference genome for recombination analyses. These findings highlight ska lo as a simple, fast, and effective tool for pathogen genomic epidemiology, extending the range of reference-free variant-calling approaches. ska lo is freely available as part of the SKA program (https://github.com/bacpop/ska.rust).

Polymorphism, Single Nucleotide↗

PubMed2006

A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites.

Given a set of known binding sites for a specific transcription factor, it is possible to build a model of the transcription factor binding site, usually called a motif model, and use this model to search for other sites that bind the same transcription factor. Typically, this search is performed using a position-specific scoring matrix (PSSM), also known as a position weight matrix. In this paper we analyze a set of eukaryotic transcription factor binding sites and show that there is extensive clustering of similar k-mers in eukaryotic motifs, owing to both functional and evolutionary constraints. The apparent limitations of probabilistic models in representing complex nucleotide dependencies lead us to a graph-based representation of motifs. When deciding whether a candidate k-mer is part of a motif or not, we base our decision not on how well the k-mer conforms to a model of the motif as a whole, but how similar it is to specific, known k-mers in the motif. We elucidate the reasons why we expect graph-based methods to perform well on motif data. Our MotifScan algorithm shows greatly improved performance over the prevalent PSSM-based method for the detection of eukaryotic motifs.

Algorithms↗

PubMed2006

Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm.

A phage-display library of random peptides is a combinatorial experimental technique that can be harnessed for studying antibody-antigen interactions. In this technique, a phage peptide library is scanned against an antibody molecule to obtain a set of peptides that are bound by the antibody with high affinity. This set of peptides is regarded as mimicking the genuine epitope of the antibody's interacting antigen and can be used to define it. Here we present PepSurf, an algorithm for mapping a set of affinity-selected peptides onto the solved structure of the antigen. The problem of epitope mapping is converted into the task of aligning a set of query peptides to a graph representing the surface of the antigen. The best match of each peptide is found by aligning it against virtually all possible paths in the graph. Following a clustering step, which combines the most significant matches, a predicted epitope is inferred. We show that PepSurf accurately predicts the epitope in four cases for which the epitope is known from a solved antibody-antigen co-crystal complex. We further examine the capabilities of PepSurf for predicting other types of protein-protein interfaces. The performance of PepSurf is compared to other available epitope mapping programs.

Algorithms↗

PubMed1991

Similarity graphing and enzyme-reaction database: methods to detect sequence regions of importance for recognition of chemical structures.

We developed a new method which searches sequence segments responsible for the recognition of a given chemical structure. These segments are detected as those locally conserved among a sequence to be analyzed (target sequence) and a set of sequences (reference sequences). Reference sequences are the sequences of functionally related proteins, ligands of which contain a common chemical substructure in their molecular structures. 'Similarity graphing' cuts target sequences into segments, aligns them with reference sequence pairwise, calculates the degree of similarity for each alignment, and shows graphically cumulative similarity values on target sequence. Any locally conserved regions, short or long in length and weak or strong in similarity, are detected at their optimal conditions by adjusting three parameters. The 'enzyme-reaction database' contains chemical structures and their related enzymes. When a chemical substructure is input into the database, sequences of the enzymes related to the input substructure are systematically searched from the NBRF sequence database and output as reference sequences. Examples of analysis using similarity graphing in combination with the enzyme-reaction database showed a great potentiality in the systematic analysis of the relationships between sequences and molecular recognitions for protein engineering.

Algorithms↗

PubMed2002

Measurement of cerebral blood flow using graph plot analysis and I-123 iodoamphetamine.

PURPOSE: N-isopropyl-p[I-123]iodoamphetamin (IMP) is transiently taken up by the lungs after intravenous injection and its concentration in arterial blood varies depending on the degree of I-123 IMP uptake and subsequent washout. A method that does not require arterial blood sampling would be valuable to measure cerebral blood flow (CBF) using I-123 IMP. METHODS: The authors developed a new theory and a convenient new method of CBF determination using I-123 IMP that does not require blood sampling. Dynamic images of the head and chest were acquired immediately after intravenous injection of I-123 IMP in a series of 42 consecutive patients with cerebrovascular disorders or other brain diseases (31 men, 11 women; mean age, 58 +/- 11 years). Changes in the I-123 IMP counts of the regions of interest set in the head and pulmonary trunk were analyzed by the graph plot method, and the F values (CBF index slope) determined were compared with the mean CBF levels obtained by simultaneous autoradiography. RESULT: The F values correlated well with the mean CBF obtained by autoradiography (r = 0.818, P < 0.001). CONCLUSIONS: This innovative I-123 IMP graph plot analysis method using the time-activity curve of the head and pulmonary trunk alone is a noninvasive, convenient way to measure CBF. It is expected to become the most useful clinical technique for measuring CBF with I-123 IMP. This method can be used for patient follow-up and for comparing different patient groups evaluated in regional CBF studies.

Amphetamines↗

PubMed2005

Undirected graphs of frequency-dependent functional connectivity in whole brain networks.

We explored properties of whole brain networks based on multivariate spectral analysis of human functional magnetic resonance imaging (fMRI) time-series measured in 90 cortical and subcortical subregions in each of five healthy volunteers studied in the (no-task) resting state. We note that undirected graphs representing conditional independence between multivariate time-series can be more readily approached in the frequency domain than the time domain. Estimators of partial coherency and normalized partial mutual information phi, an integrated measure of partial coherence over an arbitrary frequency band, are applied. Using these tools, we replicate the prior observations that bilaterally homologous brain regions tend to be strongly connected and functional connectivity is generally greater at low frequencies [0.0004, 0.1518 Hz]. We also show that long-distance intrahemispheric connections between regions of prefrontal and parietal cortex were more salient at low frequencies than at frequencies greater than 0.3 Hz, whereas many local or short-distance connections, such as those comprising segregated dorsal and ventral paths in posterior cortex, were also represented in the graph of high-frequency connectivity. We conclude that the partial coherency spectrum between a pair of human brain regional fMRI time-series depends on the anatomical distance between regions: long-distance (greater than 7 cm) edges represent conditional dependence between bilaterally symmetric neocortical regions, and between regions of prefrontal and parietal association cortex in the same hemisphere, are predominantly subtended by low-frequency components.

Brain↗

PubMed2026

SwinePan for pig graph-based pangenome and multiomics data mining.

Pigs are one of the most important livestock species worldwide. Although multiple high-quality reference genomes exist, reliance on a single linear reference limits the detection of structural variants (SVs) and the characterization of population-specific genetic diversity. To address this limitation, we developed SwinePan, a comprehensive and integrated multiomics database for pigs built on a graph-based pangenome framework. SwinePan incorporates a variome derived from the graph-based pangenome, covering 2,598 individuals across 35 breeds, including 185,759 SVs, 117 million SNPs, and 6.8 million indels. The database also integrates transcriptomic data from liver, loin muscle, abdominal fat, and backfat, along with over 150,000 phenotypic records. The online toolkit deployed in SwinePan enables genome-wide association studies (GWAS), expression quantitative trait locus (eQTL) mapping, and colocalization, while interactive modules visualize population structure and multiomics associations, streamlining candidate gene and variant exploration. Additionally, two proof-of-concept analyses demonstrate how SwinePan pinpoints trait-associated loci and deciphers their potential regulatory mechanisms.

Journal Article↗

PubMed2000

Branching annihilating random walk on random regular graphs

The branching annihilating random walk is studied on a random graph whose sites have a uniform number of neighbors (z). The Monte Carlo simulations in agreement with the generalized mean-field analysis indicate that the concentration decreases linearly with the branching rate for z>/=4, while the coefficient of the linear term becomes zero if z=3. These properties are described by a modified mean-field theory taking explicitly into consideration the probability of mutual annihilation of the parent and its offspring particles using the returning features of a single walker on the same graph.

Journal Article↗

PubMed2001

Freezing in random graph ferromagnets.

Using T=0 Monte Carlo and simulated annealing simulation, we study the energy relaxation of ferromagnetic Ising and Potts models on random graphs. In addition to the expected exponential decay to a zero energy ground state, a range of connectivities for which there is power law relaxation and freezing to a metastable state is found. For some connectivities this freezing persists even using simulated annealing to find the ground state. The freezing is caused by dynamic frustration in the graphs, and is a feature of the local search nature of the Monte Carlo dynamics used. The implications of the freezing on agent-based complex system models are briefly considered.

Journal Article↗

PubMed2002

Random graph coloring: statistical physics approach.

The problem of vertex coloring in random graphs is studied using methods of statistical physics and probability. Our analytical results are compared to those obtained by exact enumeration and Monte Carlo simulations. We critically discuss the merits and shortcomings of the various methods, and interpret the results obtained. We present an exact analytical expression for the two-coloring problem as well as general replica symmetric approximated solutions for the thermodynamics of the graph coloring problem with p colors and K-body edges.

Journal Article↗

PubMed2002

General formalism for inhomogeneous random graphs.

We present and investigate an extension of the classical random graph to a general class of inhomogeneous random graph models, where vertices come in different types, and the probability of realizing an edge depends on the types of its terminal vertices. This approach provides a general framework for the analysis of a large class of models. The generic phase structure is derived using generating function techniques, and relations to other classes of models are pointed out.

Journal Article↗

PubMed2003

Resilience to damage of graphs with degree correlations.

The existence or nonexistence of a percolation threshold on power law correlated graphs is a fundamental question for which a general criterion is lacking. In this work we investigate the problems of site and bond percolation on graphs with degree correlations and their connection with spreading phenomena. We obtain some general expressions that allow the computation of the transition thresholds or their bounds. Using these results we study the effects of assortative and disassortative correlations on the resilience to damage of networks.

Journal Article↗

PubMed2003

Explicit analytical solution for scaling quantum graphs.

We show that scaling quantum graphs with arbitrary topology are explicitly analytically solvable. This is surprising since quantum graphs are excellent models of quantum chaos and quantum chaotic systems are not usually explicitly analytically solvable.

Journal Article↗

PubMed2004

Universal spectral statistics in Wigner-Dyson, chiral, and Andreev star graphs. I. Construction and numerical results.

In a series of two papers we investigate the universal spectral statistics of chaotic quantum systems in the ten known symmetry classes of quantum mechanics. In this first paper we focus on the construction of appropriate ensembles of star graphs in the ten symmetry classes. A generalization of the Bohigas-Giannoni-Schmit conjecture is given that covers all these symmetry classes. The conjecture is supported by numerical results that demonstrate the fidelity of the spectral statistics of star graphs to the corresponding Gaussian random-matrix theories.

Journal Article↗