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 271 records · Page 15Linked to original sources

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↗

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↗

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↗

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↗

PubMed2000

New algorithm for the Ising problem: partition function for finite lattice graphs.

We present a new efficient method to find the Ising problem partition function for finite lattice graphs embeddable on an arbitrary orientable surface, with integral coupling constants bounded in the absolute value by a polynomial of the size of the lattice graph. The algorithm has been implemented for toroidal lattices using modular arithmetic and the generalized nested dissection method. The implementation has substantially better performance than any other as far as we know.

Journal Article↗

PubMed2002

Leading off-diagonal correction to the form factor of large graphs.

Using periodic-orbit theory beyond the diagonal approximation we investigate the form factor, K(tau), of a generic quantum graph with mixing classical dynamics and time-reversal symmetry. We calculate the contribution from pairs of self-intersecting orbits that differ from each other only in the orientation of a single loop. In the limit of large graphs, these pairs produce a contribution -2tau(2) to the form factor which agrees with random-matrix theory.

Journal Article↗

PubMed2000

Application of graph theory to detect disconnected structures in a crystallographic database: copper oxide perovskites as a case study

Every crystal structure can be described as a graph with atoms as vertices and bonds as edges. Although such a graph loses the space arrangement of atoms and symmetry elements, it can mathematically represent the connectivity between atoms. This topological approach was used to develop a new method for detecting disconnected structures, in which individual atoms or structural fragments are located too far from each other, forming impossibly large gaps. Approximately 2300 perovskite-related crystal structures have been extracted from the Inorganic Crystal Structure Database (in 1999) and the maximum disconnecting distances, and the relations between them and the ionic radii of elements, have been analysed. Several disconnected structures, which are erroneous by our definition, have been revealed. Conventional tests for crystallographic data checking did not detect those entries.

Journal Article↗

PubMed2001

Automated graph-based analysis and correction of cortical volume topology.

The human cerebral cortex is topologically equivalent to a sheet and can be considered topologically spherical if it is closed at the brain stem. Low-level segmentation of magnetic resonance (MR) imagery typically produces cerebral volumes whose tessellations are not topologically spherical. We present a novel algorithm that analyzes and constrains the topology of a volumetric object. Graphs are formed that represent the connectivity of voxel segments in the foreground and background of the image. These graphs are analyzed and minimal corrections to the volume are made prior to tessellation. We apply the algorithm to a simple test object and to cerebral white matter masks generated by a low-level tissue identification sequence. We tessellate the resulting objects using the marching cubes algorithm and verify their topology by computing their Euler characteristics. A key benefit of the algorithm is that it localizes the change to a volume to the specific areas of its topological defects.

Algorithms↗

PubMed1992

An approach based on two-dimensional graph theory for structural cluster detection and its histopathological application.

An approach based on graph theory is described for detecting clusters of cells in tissue specimens (two-dimensional space). With a set of discrete basic elements (cell nuclei) having several measurable features (area, surface, main and minor axis of best-fitting ellipses) a graph is defined as having attributes associated with edges. Different minimum spanning trees (MSTs) can be constructed using different weight functions on the attributes (attributed MST). Analysis of the MST and of an attributed MST by use of a decomposition function allows detection of image areas with similar local properties. These clusters, which are then clusters of the tree, describe, for example, partial growth in different directions in a case of a human fibrosarcoma assuming that tumour cell nuclei are homogeneous with respect to their configuration and size. The model allows the separation of clusters of tumour cells growing in different directions and the approximation of the different growth angles. This decomposition also allows us to create new (higher) orders of structure (cluster tree).

Algorithms↗

PubMed1999

The RXc graph in evaluating and monitoring fluid balance in patients with liver cirrhosis.

A recent study, using height-standardized resistance (R/H) and reactance (Xc/H) and assuming a bivariate distribution, has proposed the "RXc graph". We applied this new approach for patients with chronic liver disease in differentiating various degrees of fluid unbalance. Our data showed that a 95% confidence ellipse of patients with chronic hepatitis (CH) overlapped that of healthy control subjects (CONTR), while those of patients with liver cirrhosis (CIR), patients with cirrhosis and ascites (ACIR), and patients with cirrhosis, edemas, and ascites (AECIR) were clearly different for both genders. A progressively shorter mean impedance vector proportional to the stage of liver disease and to the degree of fluid unbalance was found. The lower half of the 50% tolerance ellipse for the healthy population proved to be a threshold for cirrhotics, while almost all the subjects with clinically detectable edema fell outside this limit. The RXc graph was shown to be useful in monitoring the treatment of fluid unbalance and for the immediate selection of patients in whom BIA can precisely assess body composition.

Adolescent↗

PubMed1982

Numbers of receptor sites from Scatchard graphs: facts and fantasies.

Data for ligand and receptor binding presented in the format of a Scatchard graph are compared with the same data shown as bound ligand plotted against the logarithm of free ligand. From this comparison it is apparent that extrapolations in the Scatchard graph to yield total number of receptor sites are generally not correct.

Kinetics↗

PubMed1987

Solvent flow in osmosis and hydraulics: network thermodynamics and representation by bond graphs.

A tutorial introduction to network thermodynamics and bond graphs as a modeling technique for any physiochemical system is presented with a particular emphasis on reaction diffusion systems. It combines the generality of nonequilibrium thermodynamics with the advantages of a graph theory. It is applied to the representation of osmotic and hydraulic flows across a semipermeable membrane on the basis of the solvent diffusion theory of osmosis. This theory allows for an easy derivation of the van't Hoff law of osmotic pressure from the Fick law of diffusion. Molar flows and volume flows are transformed into one another by transducers, the modulus of which is the partial molar volume of water, in such a way that power is conserved by a reciprocal transformation between the chemical potential and the pressure. Osmotic and hydraulic resistances are calculated, and their dependence on pore size is estimated.

Diffusion↗