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PubMed1976

The corticosteroid dose graph. Use in determination of corticosteroid requirements, characterization of patients, and prevention of seasonal exacerbation in corticosteroid-dependent patients.

Sixty-three corticosteroid(CS)-dependent asthmatics were evaluated by a method which records asthmatic exacerbations as a function of change in CS dosage. This method, the Corticosteroid Dose Graph (CSDG), is a graphic representation of the patients' narrative charts. It is useful in assessing and directing the care of these patients and in evaluating the efficacy of altered therapeutic regimens in asthmatics. The CSDG categorizes cooperative patients (CP) and distinguishes these patients from those who are less cooperative (LCP). Evaluation of the progress of CP by the graphic analysis system showed that CP have fewer severe exacerbations of asthma than LCPs. Evaluation of the 63 patients by this graphic method shows a significantly increased incidence of asthmatic exacerbations in the Chicago area in October as compared to other months. The CSDG also demonstrates that some individuals experienced significantly increased numbers of asthma exacerbations at certain times of the year unique to themselves. Because the CSDG predicts exacerbations, it was shown to be applicable to prevent such exacerbations by prophylactic increase in CS dose during a high-risk season for selected CS-dependent asthmatics.

Adolescent↗

PubMed1995

A study of chemical systems using signal flow graph theory.

Photochemistry of giant planets and their satellites is characterized by numerous reactions involving a lot of chemical species. In the present paper, chemical systems are modeled by signal flow graphs. Such a technique evaluates the transmission of any input into the system (solar flux, electrons ... ) and gives access to the identification of the most important mechanisms in the chemical system. This method is applied to the production of hydrocarbons in the atmospheres of giant planets. In particular, the production of C2H6 in the atmosphere of Neptune from the photodissociation of CH4 is investigated. Different pathways of dissociation of CH4 are possible from L alpha radiation. A chemical system containing 14 species and 30 reactions including these different pathways of dissociation is integrated. The main mechanism of production of C2H6 is identified and evaluated for each model of dissociation. The importance of various reaction pathways as a function of time is presented.

Ethane↗

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↗

PubMed2026

Robust error-minimization in the genetic code across physicochemical metrics and variant codes: A graph-theoretic analysis in GF(2)6.

The standard genetic code reduces the impact of point mutations, but the robustness of this property across physicochemical metrics, naturally occurring variant codes, and codon-reassignment mechanisms remains incompletely quantified. Embedding the 64 codons in GF(2)6 represents the hypercube Q6 as a coordinate-dependent subgraph of the encoding-independent single-nucleotide mutation graph H(3,4), and enables continuous ρ-interpolation between the two. Under a quartet-pattern shuffle null (n=10,000), the standard code is significantly low-cost across four established, code-independent physicochemical distance metrics with partially overlapping content (Grant ham p=0.0062; Miyata p<0.001; Woese polar requirement p=0.003; Kyte-Doolittle hydropathy p=0.001), and the signal strengthens monotonically as ρ moves Q6→H(3,4). A structure-aware sensitivity analysis under the alignment-derived ProtSub matrix (Jia & Jernigan 2021) yields the most extreme percentile of any measure tested (p=0.0004; all five p-values pass Bonferroni at α=0.05). Across the 27 NCBI translation tables, near-optimality is preserved: 11 of 12 informative-distance variants retain top-5% placement after BH-FDR correction. Natural codon reassignments avoid disrupting codon-family connectivity: under the encoding-independent H(3,4) adjacency, observed events are topology-breaking at relative risk 0.32 versus the candidate landscape (permutation p≤10-4). The H(3,4) result is stable by construction; the Q6 decomposition is representation-specific and fails to show depletion under 8 of 24 base-to-bit encodings, so we report H(3,4) as the primary test and Q6 as a sensitivity. Event-level conditional-logit modelling shows that topology avoidance and local physicochemical cost provide complementary, only weakly correlated signal (rs=0.15), and that topology adds explanatory value beyond physicochemistry under both Q6 and encoding-independent H(3,4) adjacency. Retrospective reanalysis of nine genome-recoding datasets is consistent with codon-family topology operating as an evolutionary-trajectory constraint distinct from acute engineering fitness. The contribution is the second axis: code evolution is jointly constrained by physicochemical smoothness and codon-family topological integrity, and these two constraints are partly independent.

Codon reassignment↗

PubMed2005

Linear indices of the 'macromolecular graph's nucleotides adjacency matrix' as a promising approach for bioinformatics studies. Part 1: prediction of paromomycin's affinity constant with HIV-1 psi-RNA packaging region.

The design of novel anti-HIV compounds has now become a crucial area for scientists around the world. In this paper a new set of macromolecular descriptors (that are calculated from the macromolecular graph's nucleotide adjacency matrix) of relevance to nucleic acid QSAR/QSPR studies, nucleic acids' linear indices. A study of the interaction of the antibiotic Paromomycin with the packaging region of the HIV-1 psi-RNA has been performed as example of this approach. A multiple linear regression model predicted the local binding affinity constants [Log K (10(-4) M(-1))] between a specific nucleotide and the aforementioned antibiotic. The linear model explains more than 87% of the variance of the experimental Log K (R = 0.93 and s = 0.102 x 10(-4) M(-1)) and leave-one-out press statistics evidenced its predictive ability (q2 = 0.82 and s(cv) = 0.108 x 10(-4) M(-1)). The comparison with other approaches (macromolecular quadratic indices, Markovian Negentropies and 'stochastic' spectral moments) reveals a good behavior of our method.

Anti-Bacterial Agents↗

PubMed2006

Switching mechanism for branched biochemical fluxes: graph-theoretical analysis.

A graph-theoretical method is applied to characterize the structure of a simplest switching mechanism of common biochemical importance. This mechanism is based on competition of two coupled substrate-binding pathways for a single substrate. No other regulatory interactions are shown to be needed for the switching phenomenon to be observed. It is shown that switch in branch effluxes is observed as bistability or reciprocal oscillations, depending on the value of steady influx. Frequency of reciprocal efflux oscillations in branches is regulated by steady influx. Therefore, the switching mechanism can function as the coding mechanism in the manner of "influx steady level-efflux frequency". The calculated kinetic equations for the switching mechanism demonstrate very steep transitions in the branch fluxes without using high non-linearity of these equations.

Enzymes↗

PubMed2006

Pattern detection in forensic case data using graph theory: application to heroin cutting agents.

Pattern recognition techniques can be very useful in forensic sciences to point out to relevant sets of events and potentially encourage an intelligence-led style of policing. In this study, these techniques have been applied to categorical data corresponding to cutting agents found in heroin seizures. An application of graph theoretic methods has been performed, in order to highlight the possible relationships between the location of seizures and co-occurrences of particular heroin cutting agents. An analysis of the co-occurrences to establish several main combinations has been done. Results illustrate the practical potential of mathematical models in forensic data analysis.

Journal Article↗

PubMed2004

Null bar and null zone are better than the error bar to compare group means in graphs.

THE PROBLEM: Conventional graphs often include error bars around the group means. Regardless of what these bars depict, they are uninformative as to whether a difference between the groups is statistically significant. THE SOLUTION: This article suggests plotting the null bar or null zone: that is, the range or area in which the means of the two groups fall if the null hypothesis of no difference cannot be rejected. The bar and zone are simply derived from the confidence interval around the difference, obtained from the t-test.

Data Display↗

PubMed2006

Correlation of stylet activities by the glassy-winged sharpshooter, Homalodisca coagulata (Say), with electrical penetration graph (EPG) waveforms.

Glassy-winged sharpshooter, Homalodisca coagulata (Say), is an efficient vector of Xylella fastidiosa (Xf), the causal bacterium of Pierce's disease, and leaf scorch in almond and oleander. Acquisition and inoculation of Xf occur sometime during the process of stylet penetration into the plant. That process is most rigorously studied via electrical penetration graph (EPG) monitoring of insect feeding. This study provides part of the crucial biological meanings that define the waveforms of each new insect species recorded by EPG. By synchronizing AC EPG waveforms with high-magnification video of H. coagulata stylet penetration in artifical diet, we correlated stylet activities with three previously described EPG pathway waveforms, A1, B1 and B2, as well as one ingestion waveform, C. Waveform A1 occured at the beginning of stylet penetration. This waveform was correlated with salivary sheath trunk formation, repetitive stylet movements involving retraction of both maxillary stylets and one mandibular stylet, extension of the stylet fascicle, and the fluttering-like movements of the maxillary stylet tips. Waveform B1 was ubitquious, interspersed throughout the other waveforms. B1 sub-type B1w was correlated with salivation followed by maxillary tip fluttering. This tip fluttering also occurred before and during B1 sub-type B1s, but was not directly correlated with either the occurrence or frequency of this waveform. Waveform B2 was correlated with sawing-like maxillary stylet movements, which usually occurred during salivary sheath branching. Waveform C was correlated with ingestion. Fluid outflow was also observed as a mechanism to clear the maxillary tips from debris during waveform C. This detailed understanding of stylet penetration behaviors of H. coagulata is an important step toward identifying the instant of bacterial inoculation which, in turn, will be applied to studies of disease epidemiology and development of host plant resistance.

Animals↗

PubMed2006

Comparative genomics and protein domain graph analyses link ubiquitination and RNA metabolism.

The human gene parkin, known to cause familial Parkinson disease, as well as several other genes, likely involved in other neurodegenerative diseases or in cancer, encode proteins of the RBR family of ubiquitin ligases. Here, we describe the structural diversity of the RBR family in order to infer their functional roles. Of particular interest is a relationship detected between RBR-mediated ubiquitination and RNA metabolism: a few RBR proteins contain RNA binding domains and DEAH-box RNA helicase domains. Global protein domain graph analyses demonstrate that this connection is not RBR-specific, but instead many other proteins contain both ubiquitination and RNA-related domains. These proteins are present in animals, plants and fungi, suggesting that the link between these two cellular processes is ancient. Our results show that global bioinformatic approaches, involving comparative genomics and domain network analyses, may unearth novel functional relationships involving well-known and thoroughly studied groups of proteins.

Algorithms↗

PubMed2006

Use of the cumulative proportion of responders analysis graph to present pain data over a range of cut-off points: making clinical trial data more understandable.

In randomized controlled trials, no single definition of response is ideal for all purposes. We propose a method to present in a simple fashion the likelihood of response over a full range of response levels, which will facilitate a better understanding of clinical trial data. We present the technique called the cumulative proportion of responders analysis (CPRA) and its application to four pain clinical trial data sets as examples. The CPRA can be used to present the proportion of responders over the entire range of possible cut-off points as a graph. This allows the reader to compare treatment groups at any responder level that is valid for their patient population. Whether as a primary or secondary approach to a clinical trial of pain therapy, the display of data in a CPRA format may be useful in the understanding of results and applicability to patient care.

Analgesics↗

PubMed2004

A graph model for the evolution of specificity in humoral immunity.

The immune system protects the body against health-threatening entities, known as antigens, through very complex interactions involving the antigens and the system's own entities. One remarkable feature resulting from such interactions is the immune system's ability to improve its capability to fight antigens commonly found in the individual's environment. This adaptation process is called the evolution of specificity. In this paper, we introduce a new mathematical model for the evolution of specificity in humoral immunity, based on Jerne's functional, or idiotypic, network. The evolution of specificity is modeled as the dynamic updating of connection weights in a dynamic graph whose nodes are related to the network's idiotypes. At the core of this weight-updating mechanism are the increase in specificity caused by clonal selection and the decrease in specificity due to the insertion of uncorrelated idiotypes by the bone marrow. As we demonstrate through numerous computer experiments, for appropriate choices of parameters the new model correctly reproduces, in qualitative terms, several immune functions.

Antibody Formation↗

PubMed2005

Directed graphs of DNA sequences and their numerical characterization.

In this paper we (1) introduce a directed graphical representation of DNA primary sequences; (2) describe a scheme that transforms the directed graph of a DNA sequence into an upper triangular matrix; (3) investigate whether or not the existing matrix-based invariants of DNA sequences are compatible for the upper triangular matrix representation. The utility of our method is illustrated by an examination of the similarity between human and other seven species.

Base Sequence↗

PubMed2006

Using graph theoretical analysis of multi channel EEG to evaluate the neural efficiency hypothesis.

Previous studies demonstrated that intelligence is significantly related to an impressive array of psychological, social, biological and genetic factors and that working memory (WM) can be considered as a general cognitive resource strongly related with a wide variety of higher order cognitive competencies and intelligence. Also, evaluating the WM of subjects might allow one to test the neural efficiency hypothesis (NEH). WM typically involves functional interactions between frontal and parietal cortices. We recorded EEG signals to study neuronal interactions during one WM test in individuals who had few years of formal education (LE) as compared to individuals with university degrees (UE). The two groups of individuals differed in the scores they obtained in psychological tests. To quantify the synchronization between EEG channels in several frequency bands, we evaluated the "synchronization likelihood" (SL), which takes into consideration nonlinear processes as well as linear ones. SL was then converted into graphs to estimate the distance from "small-world network" (SWN) organization, i.e., an optimally organized network that would give rise to the data. In comparison to LE subjects, those with university degrees exhibited less prominent SWN properties in most frequency bands during the WM task. This finding supports the NEH and suggests that the connections between brain areas of well-educated subjects engaged in WM tasks are not as well-organized in the sense of SWN.

Adult↗

PubMed2005

Recursive neural networks for processing graphs with labelled edges: theory and applications.

In this paper, we introduce a new recursive neural network model able to process directed acyclic graphs with labelled edges. The model uses a state transition function which considers the edge labels and is independent both from the number and the order of the children of each node. The computational capabilities of the new recursive architecture are assessed. Moreover, in order to test the proposed architecture on a practical challenging application, the problem of object detection in images is also addressed. In fact, the localization of target objects is a preliminary step in any recognition system. The proposed technique is general and can be applied in different detection systems, since it does not exploit any a priori knowledge on the particular problem. Some experiments on face detection, carried out on scenes acquired by an indoor camera, are reported, showing very promising results.

Computer Simulation↗

PubMed2005

An incremental regression method for graph structured data.

In this paper, we consider learning problems defined on graph-structured data. We propose an incremental supervised learning algorithm for network-based estimators using diffusion kernels. Diffusion kernel nodes are iteratively added in the training process. For each new node added, the kernel function center and the output connection weight are decided according to an empirical risk driven rule based on an extended chained version of the Nadaraja-Watson estimator. Then the diffusion parameters are determined by a genetic-like optimization technique.

Algorithms↗

PubMed1997

The selection of ELISA cut-off points for testing antibody to Newcastle disease by two-graph receiver operating characteristic (TG-ROC) analysis.

Two hundred and sixty field serum samples were tested for Newcastle disease (ND) antibodies using a commercial enzyme-linked immunosorbent assay (ELISA) and the haemagglutination inhibition test (HI). The HI test was regarded as the reference method. Reciprocal titres of 16 and above were considered positive. In this study the two-graph receiver operating characteristic (TG-ROC) analysis was used as a tool for selecting cut-off points. Sensitivity, specificity, efficiency and Youden's index were used as indices of test accuracy. The positive and negative predictive values of the ELISA results were analysed for various prevalence rates.

Animals↗

PubMed2003

Characterisation of the feeding behaviour of western flower thrips in terms of electrical penetration graph (EPG) waveforms.

Western flower thrips, Frankliniella occidentalis (Pergande) causes damage to plants when they are feeding. Also, this thrips species transmits Tomato spotted wilt virus (TSWV) during stylet penetration. We investigated the penetration behaviour (probing) of thrips on pepper leaves and on liquid diet by electrical penetration graph (EPG, DC-system) recording. In addition, we used high-magnification video observations to correlate EPG waveforms with the insect's posture, head movements, and muscle contractions. Also, EPGs were correlated with probing on liquid diets containing radio-active tracers to distinguish and quantify ingestion waveforms. The previously described waveforms P, Q, and R were distinguished and additionally, a new waveform 'S' was distinguished. Waveform P could be linked with mandibular leaf penetration, waveform Q presumably with insertion of the maxillary stylets, and waveform R with ingestion of cell contents, whereas waveform S could not be correlated with any behavioural activity. Histology of the feeding damage in pepper leaves shows that thrips ingests the contents of multiple cells per probe.

Animals↗