scholarly journals Towards the Development of K-Map Model in Visualizing the Dengue Hotspot Using Venn Diagram and AHP Technique

2012 ◽  
Vol 2 (1) ◽  
pp. 7-13 ◽  
Author(s):  
Az-Azira Abdul Aziz ◽  
Rusli Abdullah, Hamidah Ibrahim
Keyword(s):  
Venn Diagram

scholarly journals Screen Key Genes Associated with Distraction-Induced Osteogenesis of Stem Cells Using Bioinformatics Methods

2021 ◽  
Vol 22 (12) ◽  
pp. 6505
Author(s):  
Jishizhan Chen ◽  
Jia Hua ◽  
Wenhui Song
Keyword(s):  
Stem Cells ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Negative Control ◽  
Gene Set Enrichment Analysis ◽  
Venn Diagram ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Two Samples ◽  
Key Genes

Applying mesenchymal stem cells (MSCs), together with the distraction osteogenesis (DO) process, displayed enhanced bone quality and shorter treatment periods. The DO guides the differentiation of MSCs by providing mechanical clues. However, the underlying key genes and pathways are largely unknown. The aim of this study was to screen and identify hub genes involved in distraction-induced osteogenesis of MSCs and potential molecular mechanisms. Material and Methods: The datasets were downloaded from the ArrayExpress database. Three samples of negative control and two samples subjected to 5% cyclic sinusoidal distraction at 0.25 Hz for 6 h were selected for screening differentially expressed genes (DEGs) and then analysed via bioinformatics methods. The Gene Ontology (GO) terms and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment were investigated. The protein–protein interaction (PPI) network was visualised through the Cytoscape software. Gene set enrichment analysis (GSEA) was conducted to verify the enrichment of a self-defined osteogenic gene sets collection and identify osteogenic hub genes. Results: Three hub genes (IL6, MMP2, and EP300) that were highly associated with distraction-induced osteogenesis of MSCs were identified via the Venn diagram. These hub genes could provide a new understanding of distraction-induced osteogenic differentiation of MSCs and serve as potential gene targets for optimising DO via targeted therapies.

scholarly journals Venn diagram analysis overestimates the extent of circadian rhythm reprogramming

FEBS Journal ◽  
2021 ◽  
Author(s):  
Anne Pelikan ◽  
Hanspeter Herzel ◽  
Achim Kramer ◽  
Bharath Ananthasubramaniam
Keyword(s):  
Circadian Rhythm ◽  
Venn Diagram ◽  
Diagram Analysis

scholarly journals Identification BCL6 and miR-30 family associating with Ibrutinib resistance in activated B-cell-like diffuse large B-cell lymphoma

2021 ◽  
Vol 38 (4) ◽  
Author(s):  
Jiazheng Li ◽  
Yan Huang ◽  
Yun Zhang ◽  
Jingjing Wen ◽  
Yanxin Chen ◽  
...  
Keyword(s):  
B Cell ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Genetic Alterations ◽  
Venn Diagram ◽  
Potential Candidate ◽  
Large B Cell Lymphoma ◽  
Ibrutinib Resistance ◽  
Large B Cell ◽  
Geo Database

AbstractIbrutinib has clear efficacy for activated B-cell-like diffuse large B cell lymphoma (ABC-DLBCL) in previous clinical researches. However, the resistance of Ibrutinib has limited its therapeutic benefit and the potential mechanism remains unclear. This study was aimed to identify potential candidate genes and miRNA targets to overcome Ibrutinib resistance in ABC-DLBCL. First, two expression profiles were downloaded from the GEO database, which used to identify the DEGs related to Ibrutinib resistance in ABC-DLBCL cell lines by GEO2R analysis separately. And the common DEGs were obtained though Venn diagram. Then Gene ontology (GO) and pathway enrichment analysis were conducted by DAVID database. From STRING database, BCL6, IL10, IL2RB, IRF4, CD80, PRDM1and GZMB were determined to be the hub genes by protein–protein interaction (PPI) network. Through miRNA-mRNA targeting network, we found that BCL6, IRF4, CD80, and PRDM1 were common target genes of miR-30 family. The cBioPortal database showed that BCL6 had the highest level of genetic alterations among DLBCL. In addition, another expression profile from GEO database showed that BCL6 was significantly high expression in no responsive patients after Ibrutinib treatment, and the receiver operating characteristic (ROC) curve which was used to evaluate the relationship between BCL6 expression and its effect was 0.67. MTT assay showed that treatment with FX1 (a BCL6 inhibitor) can enhance the sensitivity of Ibrutinib in C481S BTK HBL-1 cells. The results suggested that BCL6 and miR-30 family maybe associate with Ibrutinib resistance in ABC-DLBCL.

scholarly journals Differential Expression of mRNAs in Peripheral Blood Related to Prodrome and Progression of Alzheimer’s Disease

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Weishuang Xue ◽  
Jinwei Li ◽  
Kailei Fu ◽  
Weiyu Teng
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Peripheral Blood ◽  
Bioinformatics Analysis ◽  
Gene Expression Omnibus ◽  
Venn Diagram ◽  
Ppi Network ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Ppi Networks

Alzheimer’s disease (AD) is a chronic progressive neurodegenerative disease that affects the quality of life of elderly individuals, while the pathogenesis of AD is still unclear. Based on the bioinformatics analysis of differentially expressed genes (DEGs) in peripheral blood samples, we investigated genes related to mild cognitive impairment (MCI), AD, and late-stage AD that might be used for predicting the conversions. Methods. We obtained the DEGs in MCI, AD, and advanced AD patients from the Gene Expression Omnibus (GEO) database. A Venn diagram was used to identify the intersecting genes. Gene Ontology (GO) and Kyoto Gene and Genomic Encyclopedia (KEGG) were used to analyze the functions and pathways of the intersecting genes. Protein-protein interaction (PPI) networks were constructed to visualize the network of the proteins coded by the related genes. Hub genes were selected based on the PPI network. Results. Bioinformatics analysis indicated that there were 61 DEGs in both the MCI and AD groups and 27 the same DEGs among the three groups. Using GO and KEGG analyses, we found that these genes were related to the function of mitochondria and ribosome. Hub genes were determined by bioinformatics software based on the PPI network. Conclusions. Mitochondrial and ribosomal dysfunction in peripheral blood may be early signs in AD patients and related to the disease progression. The identified hub genes may provide the possibility for predicting AD progression or be the possible targets for treatments.

Some Possibilities of Modeling Colored Petri Nets

2021 ◽  
pp. 77-91
Author(s):  
Goharik Petrosyan ◽  
Armen Gaboutchian ◽  
Vladimir Knyaz
Keyword(s):  
Petri Nets ◽  
Petri Net ◽  
Optimal Allocation ◽  
Production Systems ◽  
Oriented Graph ◽  
Discrete Systems ◽  
Colored Petri Nets ◽  
Venn Diagram ◽  
Colored Petri Net ◽  
Language Class

Petri nets are a mathematical apparatus for modelling dynamic discrete systems. Their feature is the ability to display parallelism, asynchrony and hierarchy. First was described by Karl Petri in 1962 [1,2,8]. The Petri net is a bipartite oriented graph consisting of two types of vertices - positions and transitions connected by arcs between each other; vertices of the same type cannot be directly connected. Positions can be placed by tags (markers) that can move around the network. [2] Petri Nets (PN) used for modelling real systems is sometimes referred to as Condition/Events nets. Places identify the conditions of the parts of the system (working, idling, queuing, and failing), and transitions describe the passage from one state to another (end of a task, failure, repair...). An event occurs (a transition fire) when all the conditions are satisfied (input places are marked) and give concession to the event. The occurrence of the event entirely or partially modifies the status of the conditions (marking). The number of tokens in a place can be used to identify the number of resources lying in the condition denoted by that place [1,2,8]. Coloured Petri nets (CPN) is a graphical oriented language for design, specification, simulation and verification of systems [3-6,9,15]. It is in particular well-suited for systems that consist of several processes which communicate and synchronize. Typical examples of application areas are communication protocols, distributed systems, automated production systems, workflow analysis and VLSI chips. In the Classical Petri Net, tokens do not differ; we can say that they are colourless. Unlike standard Petri nets in Colored Petri Net of a position can contain tokens of arbitrary complexity, such as lists, etc., that enables modelling to be more reliable. The article is devoted to the study of the possibilities of modelling Colored Petri nets. The article discusses the interrelation of languages of the Colored Petri nets and traditional formal languages. The Venn diagram, which the author has modified, shows the relationship between the languages of the Colored Petri nets and some traditional languages. The language class of the Colored Petri nets includes a whole class of Context-free languages and some other classes. The paper shows modelling the task synchronization Patil using Colored Petri net, which can't be modeled using well- known operations P and V or by classical Petri network, since the operations P and V and classical Petri networks have limited mathematical properties which do not allow to model the mechanisms in which the process should be synchronized with the optimal allocation of resources.

scholarly journals VennPlex–A Novel Venn Diagram Program for Comparing and Visualizing Datasets with Differentially Regulated Datapoints

PLoS ONE ◽  
2013 ◽  
Vol 8 (1) ◽  
pp. e53388 ◽  
Author(s):  
Huan Cai ◽  
Hongyu Chen ◽  
Tie Yi ◽  
Caitlin M. Daimon ◽  
John P. Boyle ◽  
...  
Keyword(s):  
Venn Diagram

scholarly journals Venn Diagram Approach to Heisenberg Inequalities

2012 ◽  
Vol 4 (2) ◽  
Author(s):  
Nassar H. S. Haidar
Keyword(s):  
Venn Diagram ◽  
Diagram Approach

scholarly journals Estimation of a closed population size of tadpoles in temporary pond

2017 ◽  
Vol 78 (2) ◽  
pp. 328-336
Author(s):  
M. S. C. S. Lima ◽  
J. Pederassi ◽  
C. A. S. Souza
Keyword(s):  
Population Size ◽  
Bayes Theorem ◽  
Venn Diagram ◽  
Temporary Pond ◽  
Larval Phase ◽  
Closed Population ◽  
Lotic Environment ◽  
Capture Recapture ◽  
Kolmogorov Smirnov ◽  
Smirnov Test

Abstract The practice of capture-recapture to estimate the diversity is well known to many animal groups, however this practice in the larval phase of anuran amphibians is incipient. We aimed at evaluating the Lincoln estimator, Venn diagram and Bayes theorem in the inference of population size of a larval phase anurocenose from lotic environment. The adherence of results was evaluated using the Kolmogorov-Smirnov test. The marking of tadpoles for later recapture and methods measurement was made with eosin methylene blue. When comparing the results of Lincoln-Petersen estimator corresponding to the Venn diagram and Bayes theorem, we detected percentage differences per sampling, i.e., the proportion of sampled anuran genera is kept among the three methods, although the values are numerically different. By submitting these results to the Kolmogorov-Smirnov test we have found no significant differences. Therefore, no matter the estimator, the measured value is adherent and estimates the total population. Together with the marking methodology, which did not change the behavior of tadpoles, the present study helps to fill the need of more studies on larval phase of amphibians in Brazil, especially in semi-arid northeast.

Separate is Never Equal: Sylvia Mendez and Her Family’s Fight for Desegregation: written by Duncan Tonatiuh

2017 ◽  
Vol 12 (1) ◽  
pp. 1-8
Author(s):  
Elizabeth Sturm
Keyword(s):  
Negative Impact ◽  
Lesson Plan ◽  
School Desegregation ◽  
Position Statement ◽  
Venn Diagram ◽  
School Segregation ◽  
Content Type ◽  
The Impact ◽  
Segregated Schooling ◽  
Compare And Contrast

Purpose The purpose of this paper is to use Separate is Never Equal: Sylvia Mendez and Her Family’s Fight for Desegregation, by Duncan Tonatiuh, along with other materials on school segregation to address the question, is separate ever equal? Design/methodology/approach Students compare and contrast segregated schooling using a Venn diagram, then research other instances of school segregation, paying attention to the time periods, geographic locations, and impact on segregated individuals. In pairs, students identify these locations on a US map and create a class timeline of the instances of segregation they uncover. Using their research, the class then discusses segregation and its impact on the segregated groups and individuals. Afterwards, students compare their school to the schools researched to determine if segregation exists in their school, and form a class position statement on the importance and benefits of school desegregation. Findings Students will build an understanding of the importance and benefits of school desegregation and the negative impact of segregation. Originality/value This lesson plan brings together multiple texts that illustrate the impact of segregation on various cultures in America.

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