Use of reentrant nets in modular analysis of colored nets

2005 ◽  
pp. 58-77 ◽  
Author(s):  
Ghassan Chehaibar
Keyword(s):  
Modular Analysis

scholarly journals Modular Analysis of Peripheral Blood Gene Expression in Rheumatoid Arthritis Captures Reproducible Gene Expression Changes in Tumor Necrosis Factor Responders

2015 ◽  
Vol 67 (2) ◽  
pp. 344-351 ◽  
Author(s):  
Michaela Oswald ◽  
Mark E. Curran ◽  
Sarah L. Lamberth ◽  
Robert M. Townsend ◽  
Jennifer D. Hamilton ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gene Expression ◽  
Tumor Necrosis Factor ◽  
Peripheral Blood ◽  
Tumor Necrosis ◽  
Blood Gene Expression ◽  
Peripheral Blood Gene Expression ◽  
Modular Analysis ◽  
Necrosis Factor

scholarly journals Incremental and Modular Context-sensitive Analysis

2021 ◽  
pp. 1-48
Author(s):  
ISABEL GARCIA-CONTRERAS ◽  
JOSÉ F. MORALES ◽  
MANUEL V. HERMENEGILDO
Keyword(s):  
Global Analysis ◽  
Memory Consumption ◽  
Sensitive Analysis ◽  
Analysis Techniques ◽  
Context Sensitive ◽  
Fine Grained ◽  
Fine Grain ◽  
Modular Analysis ◽  
Modular Algorithm ◽  
Modular Structures

Abstract Context-sensitive global analysis of large code bases can be expensive, which can make its use impractical during software development. However, there are many situations in which modifications are small and isolated within a few components, and it is desirable to reuse as much as possible previous analysis results. This has been achieved to date through incremental global analysis fixpoint algorithms that achieve cost reductions at fine levels of granularity, such as changes in program lines. However, these fine-grained techniques are neither directly applicable to modular programs nor are they designed to take advantage of modular structures. This paper describes, implements, and evaluates an algorithm that performs efficient context-sensitive analysis incrementally on modular partitions of programs. The experimental results show that the proposed modular algorithm shows significant improvements, in both time and memory consumption, when compared to existing non-modular, fine-grain incremental analysis techniques. Furthermore, thanks to the proposed intermodular propagation of analysis information, our algorithm also outperforms traditional modular analysis even when analyzing from scratch.

Abstract O.29: Transcriptional Profiling Discriminates Complete and Incomplete KD from Human Adenovirus

Circulation ◽  
2015 ◽  
Vol 131 (suppl_2) ◽  
Author(s):  
Preeti Jaggi ◽  
Asuncion Mejias ◽  
Adriana Tremoulet ◽  
Jane Burns ◽  
Wei Wang ◽  
...  
Keyword(s):  
Transcriptional Profiling ◽  
Myeloid Cell ◽  
Human Adenovirus ◽  
Response To Therapy ◽  
Transcriptional Analysis ◽  
Coagulation Cascade ◽  
Prediction Algorithm ◽  
Prognostic Information ◽  
Class Prediction ◽  
Modular Analysis

Background: The diagnosis of Kawasaki disease (KD) is often difficult to distinguish from HAdV. Objective: 1) To characterize the specific transcriptional profiles of KD patients versus acute HAdV infection 2) To determine whether the molecular distance to health (MDTH) score (a molecular score that reflects the perturbation derived from whole genome transcriptional analysis) correlates with response to therapy. Methods: Whole blood RNA samples collected in Tempus tubes were analyzed using Illumina chips and GeneSpring software 7.4 from 76 pediatric patients with complete KD, 13 with incomplete KD, and 19 patients with HadV, and 20 age- and sex-matched healthy controls (HC). We used class comparison algorithms (Mann-Whitney p< 0.01, Benjamini-Hochberg, and 1.25- fold change filter) and modular analysis to define the KD profiles; class prediction algorithm was used to identify genes that best differentiate KD and HAdV. Results: Statistical group comparisons identified 7,899 genes differentially expressed in 39 complete KD patients versus HC (KD biosignature). This signature was validated in another 37 patients with complete KD and in 13 patients with incomplete KD. Modular analysis in children with complete KD demonstrated overexpression of inflammation, neutrophils, myeloid cell, coagulation cascade, and cell cycle genes. The class prediction algorithm identified 25-classifier genes that differentiated children with KD vs HAdV infection in two independent cohorts of patients with 92% (95% CI [73%-99%]) sensitivity and 90% [67%-98%] specificity. MDTH scores in KD patients significantly correlated with the baseline c-reactive protein (R=0.29, p=0.008) and was four fold higher than in children with HAdV (p<0.01). In addition, KD patients that remained febrile 36 hours after treatment with IVIG (non-responders) demonstrated higher baseline, pre-treatment MDTH values compared with responders [12,290 vs. 5572 respectively; p=0.009]. Conclusion: Transcriptional signatures can be used as a tool to discriminate between KD and HAdV infection, and may also provide prognostic information.

scholarly journals webCEMiTool: Co-expression Modular Analysis Made Easy

2019 ◽  
Vol 10 ◽  
Author(s):  
Lucas E. Cardozo ◽  
Pedro S. T. Russo ◽  
Bruno Gomes-Correia ◽  
Mariana Araujo-Pereira ◽  
Gonzalo Sepúlveda-Hermosilla ◽  
...  
Keyword(s):  
Modular Analysis

scholarly journals Modular analysis of hipposin, a histone-derived antimicrobial peptide consisting of membrane translocating and membrane permeabilizing fragments

2014 ◽  
Vol 1838 (9) ◽  
pp. 2228-2233 ◽  
Author(s):  
Maria E. Bustillo ◽  
Alexandra L. Fischer ◽  
Maria A. LaBouyer ◽  
Julia A. Klaips ◽  
Andrew C. Webb ◽  
...  
Keyword(s):  
Antimicrobial Peptide ◽  
Modular Analysis

scholarly journals Comparative modular analysis of gene expression in vertebrate organs

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 124 ◽  
Author(s):  
Barbara Piasecka ◽  
Zoltan Kutalik ◽  
Julien Roux ◽  
Sven Bergmann ◽  
Marc Robinson-Rechavi
Keyword(s):  
Gene Expression ◽  
Modular Analysis
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