MotifMark: Finding regulatory motifs in DNA sequences.
Hassanzadeh, Hamid Reza; Kolhe, Pushkar; Isbell, Charles L; Wang, May D
2017-07-01
The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding sites and the specificity of target proteins in binding to these regions are two important steps in understanding the mechanisms of these biological activities. A number of high-throughput technologies have recently emerged that try to quantify the affinity between proteins and DNA motifs. Despite their success, these technologies have their own limitations and fall short in precise characterization of motifs, and as a result, require further downstream analysis to extract useful and interpretable information from a haystack of noisy and inaccurate data. Here we propose MotifMark, a new algorithm based on graph theory and machine learning, that can find binding sites on candidate probes and rank their specificity in regard to the underlying transcription factor. We developed a pipeline to analyze experimental data derived from compact universal protein binding microarrays and benchmarked it against two of the most accurate motif search methods. Our results indicate that MotifMark can be a viable alternative technique for prediction of motif from protein binding microarrays and possibly other related high-throughput techniques.
DNA motif elucidation using belief propagation
Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei
2013-01-01
Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ?10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/?wkc/kmerHMM. 2013 The Author(s).
DNA motif elucidation using belief propagation.
Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei
2013-09-01
Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k=8∼10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/∼wkc/kmerHMM.
DNA motif elucidation using belief propagation
Wong, Ka-Chun
2013-06-29
Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ?10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors\\' websites: e.g. http://www.cs.toronto.edu/?wkc/kmerHMM. 2013 The Author(s).
MotifMark: Finding Regulatory Motifs in DNA Sequences
Hassanzadeh, Hamid Reza; Kolhe, Pushkar; Isbell, Charles L.; Wang, May D.
2017-01-01
The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding sites and the specificity of target proteins in binding to these regions are two important steps in understanding the mechanisms of these biological activities. A number of high-throughput technologies have recently emerged that try to quantify the affinity be...
The limits of de novo DNA motif discovery.
David Simcha
Full Text Available A major challenge in molecular biology is reverse-engineering the cis-regulatory logic that plays a major role in the control of gene expression. This program includes searching through DNA sequences to identify "motifs" that serve as the binding sites for transcription factors or, more generally, are predictive of gene expression across cellular conditions. Several approaches have been proposed for de novo motif discovery-searching sequences without prior knowledge of binding sites or nucleotide patterns. However, unbiased validation is not straightforward. We consider two approaches to unbiased validation of discovered motifs: testing the statistical significance of a motif using a DNA "background" sequence model to represent the null hypothesis and measuring performance in predicting membership in gene clusters. We demonstrate that the background models typically used are "too null," resulting in overly optimistic assessments of significance, and argue that performance in predicting TF binding or expression patterns from DNA motifs should be assessed by held-out data, as in predictive learning. Applying this criterion to common motif discovery methods resulted in universally poor performance, although there is a marked improvement when motifs are statistically significant against real background sequences. Moreover, on synthetic data where "ground truth" is known, discriminative performance of all algorithms is far below the theoretical upper bound, with pronounced "over-fitting" in training. A key conclusion from this work is that the failure of de novo discovery approaches to accurately identify motifs is basically due to statistical intractability resulting from the fixed size of co-regulated gene clusters, and thus such failures do not necessarily provide evidence that unfound motifs are not active biologically. Consequently, the use of prior knowledge to enhance motif discovery is not just advantageous but necessary. An implementation of
PISMA: A Visual Representation of Motif Distribution in DNA Sequences
Rogelio Alcántara-Silva
2017-03-01
Full Text Available Background: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code–like, as a gene-map–like, and as a transcript scheme. Results: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes. Also, we present 2 analyses: one of DNA motifs associated with either methylation-resistant or methylation-sensitive CpG islands and another analysis of motifs associated with exosome RNA secretion. Availability and Implementation: PISMA is developed in Java; it is executable in any type of hardware and in diverse operating systems. PISMA is freely available to noncommercial users. The English version and the User Manual are provided in Supplementary Files 1 and 2, and a Spanish version is available at www.biomedicas.unam.mx/wp-content/software/pisma.zip and www.biomedicas.unam.mx/wp-content/pdf/manual/pisma.pdf .
Hybrid DNA i-motif: Aminoethylprolyl-PNA (pC5) enhance the stability of DNA (dC5) i-motif structure.
Gade, Chandrasekhar Reddy; Sharma, Nagendra K
2017-12-15
This report describes the synthesis of C-rich sequence, cytosine pentamer, of aep-PNA and its biophysical studies for the formation of hybrid DNA:aep-PNAi-motif structure with DNA cytosine pentamer (dC 5 ) under acidic pH conditions. Herein, the CD/UV/NMR/ESI-Mass studies strongly support the formation of stable hybrid DNA i-motif structure with aep-PNA even near acidic conditions. Hence aep-PNA C-rich sequence cytosine could be considered as potential DNA i-motif stabilizing agents in vivo conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.
Presence of a consensus DNA motif at nearby DNA sequence of the mutation susceptible CG nucleotides.
Chowdhury, Kaushik; Kumar, Suresh; Sharma, Tanu; Sharma, Ankit; Bhagat, Meenakshi; Kamai, Asangla; Ford, Bridget M; Asthana, Shailendra; Mandal, Chandi C
2018-01-10
Complexity in tissues affected by cancer arises from somatic mutations and epigenetic modifications in the genome. The mutation susceptible hotspots present within the genome indicate a non-random nature and/or a position specific selection of mutation. An association exists between the occurrence of mutations and epigenetic DNA methylation. This study is primarily aimed at determining mutation status, and identifying a signature for predicting mutation prone zones of tumor suppressor (TS) genes. Nearby sequences from the top five positions having a higher mutation frequency in each gene of 42 TS genes were selected from a cosmic database and were considered as mutation prone zones. The conserved motifs present in the mutation prone DNA fragments were identified. Molecular docking studies were done to determine putative interactions between the identified conserved motifs and enzyme methyltransferase DNMT1. Collective analysis of 42 TS genes found GC as the most commonly replaced and AT as the most commonly formed residues after mutation. Analysis of the top 5 mutated positions of each gene (210 DNA segments for 42 TS genes) identified that CG nucleotides of the amino acid codons (e.g., Arginine) are most susceptible to mutation, and found a consensus DNA "T/AGC/GAGGA/TG" sequence present in these mutation prone DNA segments. Similar to TS genes, analysis of 54 oncogenes not only found CG nucleotides of the amino acid Arg as the most susceptible to mutation, but also identified the presence of similar consensus DNA motifs in the mutation prone DNA fragments (270 DNA segments for 54 oncogenes) of oncogenes. Docking studies depicted that, upon binding of DNMT1 methylates to this consensus DNA motif (C residues of CpG islands), mutation was likely to occur. Thus, this study proposes that DNMT1 mediated methylation in chromosomal DNA may decrease if a foreign DNA segment containing this consensus sequence along with CG nucleotides is exogenously introduced to dividing
DNA mutation motifs in the genes associated with inherited diseases.
Michal Růžička
Full Text Available Mutations in human genes can be responsible for inherited genetic disorders and cancer. Mutations can arise due to environmental factors or spontaneously. It has been shown that certain DNA sequences are more prone to mutate. These sites are termed hotspots and exhibit a higher mutation frequency than expected by chance. In contrast, DNA sequences with lower mutation frequencies than expected by chance are termed coldspots. Mutation hotspots are usually derived from a mutation spectrum, which reflects particular population where an effect of a common ancestor plays a role. To detect coldspots/hotspots unaffected by population bias, we analysed the presence of germline mutations obtained from HGMD database in the 5-nucleotide segments repeatedly occurring in genes associated with common inherited disorders, in particular, the PAH, LDLR, CFTR, F8, and F9 genes. Statistically significant sequences (mutational motifs rarely associated with mutations (coldspots and frequently associated with mutations (hotspots exhibited characteristic sequence patterns, e.g. coldspots contained purine tract while hotspots showed alternating purine-pyrimidine bases, often with the presence of CpG dinucleotide. Using molecular dynamics simulations and free energy calculations, we analysed the global bending properties of two selected coldspots and two hotspots with a G/T mismatch. We observed that the coldspots were inherently more flexible than the hotspots. We assume that this property might be critical for effective mismatch repair as DNA with a mutation recognized by MutSα protein is noticeably bent.
DMINDA: an integrated web server for DNA motif identification and analyses.
Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying
2014-07-01
DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data.
Ozaki, Haruka; Iwasaki, Wataru
2016-08-01
As a key mechanism of gene regulation, transcription factors (TFs) bind to DNA by recognizing specific short sequence patterns that are called DNA-binding motifs. A single TF can accept ambiguity within its DNA-binding motifs, which comprise both canonical (typical) and non-canonical motifs. Clarification of such DNA-binding motif ambiguity is crucial for revealing gene regulatory networks and evaluating mutations in cis-regulatory elements. Although chromatin immunoprecipitation sequencing (ChIP-seq) now provides abundant data on the genomic sequences to which a given TF binds, existing motif discovery methods are unable to directly answer whether a given TF can bind to a specific DNA-binding motif. Here, we report a method for clarifying the DNA-binding motif ambiguity, MOCCS. Given ChIP-Seq data of any TF, MOCCS comprehensively analyzes and describes every k-mer to which that TF binds. Analysis of simulated datasets revealed that MOCCS is applicable to various ChIP-Seq datasets, requiring only a few minutes per dataset. Application to the ENCODE ChIP-Seq datasets proved that MOCCS directly evaluates whether a given TF binds to each DNA-binding motif, even if known position weight matrix models do not provide sufficient information on DNA-binding motif ambiguity. Furthermore, users are not required to provide numerous parameters or background genomic sequence models that are typically unavailable. MOCCS is implemented in Perl and R and is freely available via https://github.com/yuifu/moccs. By complementing existing motif-discovery software, MOCCS will contribute to the basic understanding of how the genome controls diverse cellular processes via DNA-protein interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.
DNA motif alignment by evolving a population of Markov chains.
Bi, Chengpeng
2009-01-30
Deciphering cis-regulatory elements or de novo motif-finding in genomes still remains elusive although much algorithmic effort has been expended. The Markov chain Monte Carlo (MCMC) method such as Gibbs motif samplers has been widely employed to solve the de novo motif-finding problem through sequence local alignment. Nonetheless, the MCMC-based motif samplers still suffer from local maxima like EM. Therefore, as a prerequisite for finding good local alignments, these motif algorithms are often independently run a multitude of times, but without information exchange between different chains. Hence it would be worth a new algorithm design enabling such information exchange. This paper presents a novel motif-finding algorithm by evolving a population of Markov chains with information exchange (PMC), each of which is initialized as a random alignment and run by the Metropolis-Hastings sampler (MHS). It is progressively updated through a series of local alignments stochastically sampled. Explicitly, the PMC motif algorithm performs stochastic sampling as specified by a population-based proposal distribution rather than individual ones, and adaptively evolves the population as a whole towards a global maximum. The alignment information exchange is accomplished by taking advantage of the pooled motif site distributions. A distinct method for running multiple independent Markov chains (IMC) without information exchange, or dubbed as the IMC motif algorithm, is also devised to compare with its PMC counterpart. Experimental studies demonstrate that the performance could be improved if pooled information were used to run a population of motif samplers. The new PMC algorithm was able to improve the convergence and outperformed other popular algorithms tested using simulated and biological motif sequences.
Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells
Wong, Ka-Chun; Li, Yue; Peng, Chengbin
2015-01-01
Motivation: The protein-DNA interactions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcription. The identification of the DNA motifs is a vital task for downstream analysis. Unfortunately, the long-range coupling information between different DNA motifs is still lacking. To fill the void, as the first-of-its-kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in human. Results: The coupling DNA motif pairs exhibit substantially higher DNase accessibility than the background sequences. Half of the DNA motifs involved are matched to the existing motif databases, although nearly all of them are enriched with at least one gene ontology term. Their motif instances are also found statistically enriched on the promoter and enhancer regions. Especially, we introduce a novel measurement called motif pairing multiplicity which is defined as the number of motifs that are paired with a given motif on chromatin interactions. Interestingly, we observe that motif pairing multiplicity is linked to several characteristics such as regulatory region type, motif sequence degeneracy, DNase accessibility and pairing genomic distance. Taken into account together, we believe the coupling DNA motif pairs identified in this study can shed lights on the gene transcription mechanism under long-range chromatin interactions. © The Author 2015. Published by Oxford University Press.
Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells
Wong, Ka-Chun
2015-09-27
Motivation: The protein-DNA interactions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcription. The identification of the DNA motifs is a vital task for downstream analysis. Unfortunately, the long-range coupling information between different DNA motifs is still lacking. To fill the void, as the first-of-its-kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in human. Results: The coupling DNA motif pairs exhibit substantially higher DNase accessibility than the background sequences. Half of the DNA motifs involved are matched to the existing motif databases, although nearly all of them are enriched with at least one gene ontology term. Their motif instances are also found statistically enriched on the promoter and enhancer regions. Especially, we introduce a novel measurement called motif pairing multiplicity which is defined as the number of motifs that are paired with a given motif on chromatin interactions. Interestingly, we observe that motif pairing multiplicity is linked to several characteristics such as regulatory region type, motif sequence degeneracy, DNase accessibility and pairing genomic distance. Taken into account together, we believe the coupling DNA motif pairs identified in this study can shed lights on the gene transcription mechanism under long-range chromatin interactions. © The Author 2015. Published by Oxford University Press.
Probing structural changes of self assembled i-motif DNA
Lee, Iljoon; Patil, Sachin; Fhayli, Karim; Alsaiari, Shahad K.; Khashab, Niveen M.
2015-01-01
We report an i-motif structural probing system based on Thioflavin T (ThT) as a fluorescent sensor. This probe can discriminate the structural changes of RET and Rb i-motif sequences according to pH change. This journal is
DNA regulatory motif selection based on support vector machine ...
... machine (SVM) and its application in microarray experiment of Kashin-Beck disease. ... speed and amount of the corresponding mRNA in gene replication process. ... and revealed that some motifs may be related to the immune reactions.
A single thiazole orange molecule forms an exciplex in a DNA i-motif.
Xu, Baochang; Wu, Xiangyang; Yeow, Edwin K L; Shao, Fangwei
2014-06-18
A fluorescent exciplex of thiazole orange (TO) is formed in a single-dye conjugated DNA i-motif. The exciplex fluorescence exhibits a large Stokes shift, high quantum yield, robust response to pH oscillation and little structural disturbance to the DNA quadruplex, which can be used to monitor the folding of high-order DNA structures.
I-motif DNA structures are formed in the nuclei of human cells
Zeraati, Mahdi; Langley, David B.; Schofield, Peter; Moye, Aaron L.; Rouet, Romain; Hughes, William E.; Bryan, Tracy M.; Dinger, Marcel E.; Christ, Daniel
2018-06-01
Human genome function is underpinned by the primary storage of genetic information in canonical B-form DNA, with a second layer of DNA structure providing regulatory control. I-motif structures are thought to form in cytosine-rich regions of the genome and to have regulatory functions; however, in vivo evidence for the existence of such structures has so far remained elusive. Here we report the generation and characterization of an antibody fragment (iMab) that recognizes i-motif structures with high selectivity and affinity, enabling the detection of i-motifs in the nuclei of human cells. We demonstrate that the in vivo formation of such structures is cell-cycle and pH dependent. Furthermore, we provide evidence that i-motif structures are formed in regulatory regions of the human genome, including promoters and telomeric regions. Our results support the notion that i-motif structures provide key regulatory roles in the genome.
Argo_CUDA: Exhaustive GPU based approach for motif discovery in large DNA datasets.
Vishnevsky, Oleg V; Bocharnikov, Andrey V; Kolchanov, Nikolay A
2018-02-01
The development of chromatin immunoprecipitation sequencing (ChIP-seq) technology has revolutionized the genetic analysis of the basic mechanisms underlying transcription regulation and led to accumulation of information about a huge amount of DNA sequences. There are a lot of web services which are currently available for de novo motif discovery in datasets containing information about DNA/protein binding. An enormous motif diversity makes their finding challenging. In order to avoid the difficulties, researchers use different stochastic approaches. Unfortunately, the efficiency of the motif discovery programs dramatically declines with the query set size increase. This leads to the fact that only a fraction of top "peak" ChIP-Seq segments can be analyzed or the area of analysis should be narrowed. Thus, the motif discovery in massive datasets remains a challenging issue. Argo_Compute Unified Device Architecture (CUDA) web service is designed to process the massive DNA data. It is a program for the detection of degenerate oligonucleotide motifs of fixed length written in 15-letter IUPAC code. Argo_CUDA is a full-exhaustive approach based on the high-performance GPU technologies. Compared with the existing motif discovery web services, Argo_CUDA shows good prediction quality on simulated sets. The analysis of ChIP-Seq sequences revealed the motifs which correspond to known transcription factor binding sites.
Bai, Xuejia; Huang, Wenqiu; Zhang, Chenguang; Niu, Jing; Ding, Wei
2016-03-01
One of the basic leucine zipper transcription factors, BATF2, has been found to suppress cancer growth and migration. However, little is known about the genes downstream of BATF2. HeLa cells were stably transfected with BATF2, then chromatin immunoprecipitation-sequencing was employed to identify the DNA motifs responsive to BATF2. Comprehensive bioinformatics analyses indicated that the most significant motif discovered as TTCCATT[CT]GATTCCATTC[AG]AT was primarily distributed among the chromosome centromere regions and mostly within human type II satellite DNA. Such motifs were able to prime the transcription of type II satellite DNA in a directional and asymmetrical manner. Consistently, satellite II transcription was up-regulated in BATF2-overexpressing cells. The present study provides insight into understanding the role of BATF2 in tumours and the importance of satellite DNA in the maintenance of genomic stability. Copyright© 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.
Fauteux, François; Strömvik, Martina V
2009-01-01
Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP) gene promoters from three plant families, namely Brassicaceae (mustards), Fabaceae (legumes) and Poaceae (grasses) using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L.) Heynh.), soybean (Glycine max (L.) Merr.) and rice (Oryza sativa L.) respectively. We have identified three conserved motifs (two RY-like and one ACGT-like) in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination of conserved motifs
Fauteux François
2009-10-01
Full Text Available Abstract Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP gene promoters from three plant families, namely Brassicaceae (mustards, Fabaceae (legumes and Poaceae (grasses using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L. Heynh., soybean (Glycine max (L. Merr. and rice (Oryza sativa L. respectively. We have identified three conserved motifs (two RY-like and one ACGT-like in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination
Accurate quantification of microRNA via single strand displacement reaction on DNA origami motif.
Jie Zhu
Full Text Available DNA origami is an emerging technology that assembles hundreds of staple strands and one single-strand DNA into certain nanopattern. It has been widely used in various fields including detection of biological molecules such as DNA, RNA and proteins. MicroRNAs (miRNAs play important roles in post-transcriptional gene repression as well as many other biological processes such as cell growth and differentiation. Alterations of miRNAs' expression contribute to many human diseases. However, it is still a challenge to quantitatively detect miRNAs by origami technology. In this study, we developed a novel approach based on streptavidin and quantum dots binding complex (STV-QDs labeled single strand displacement reaction on DNA origami to quantitatively detect the concentration of miRNAs. We illustrated a linear relationship between the concentration of an exemplary miRNA as miRNA-133 and the STV-QDs hybridization efficiency; the results demonstrated that it is an accurate nano-scale miRNA quantifier motif. In addition, both symmetrical rectangular motif and asymmetrical China-map motif were tested. With significant linearity in both motifs, our experiments suggested that DNA Origami motif with arbitrary shape can be utilized in this method. Since this DNA origami-based method we developed owns the unique advantages of simple, time-and-material-saving, potentially multi-targets testing in one motif and relatively accurate for certain impurity samples as counted directly by atomic force microscopy rather than fluorescence signal detection, it may be widely used in quantification of miRNAs.
Accurate Quantification of microRNA via Single Strand Displacement Reaction on DNA Origami Motif
Lou, Jingyu; Li, Weidong; Li, Sheng; Zhu, Hongxin; Yang, Lun; Zhang, Aiping; He, Lin; Li, Can
2013-01-01
DNA origami is an emerging technology that assembles hundreds of staple strands and one single-strand DNA into certain nanopattern. It has been widely used in various fields including detection of biological molecules such as DNA, RNA and proteins. MicroRNAs (miRNAs) play important roles in post-transcriptional gene repression as well as many other biological processes such as cell growth and differentiation. Alterations of miRNAs' expression contribute to many human diseases. However, it is still a challenge to quantitatively detect miRNAs by origami technology. In this study, we developed a novel approach based on streptavidin and quantum dots binding complex (STV-QDs) labeled single strand displacement reaction on DNA origami to quantitatively detect the concentration of miRNAs. We illustrated a linear relationship between the concentration of an exemplary miRNA as miRNA-133 and the STV-QDs hybridization efficiency; the results demonstrated that it is an accurate nano-scale miRNA quantifier motif. In addition, both symmetrical rectangular motif and asymmetrical China-map motif were tested. With significant linearity in both motifs, our experiments suggested that DNA Origami motif with arbitrary shape can be utilized in this method. Since this DNA origami-based method we developed owns the unique advantages of simple, time-and-material-saving, potentially multi-targets testing in one motif and relatively accurate for certain impurity samples as counted directly by atomic force microscopy rather than fluorescence signal detection, it may be widely used in quantification of miRNAs. PMID:23990889
Accurate quantification of microRNA via single strand displacement reaction on DNA origami motif.
Zhu, Jie; Feng, Xiaolu; Lou, Jingyu; Li, Weidong; Li, Sheng; Zhu, Hongxin; Yang, Lun; Zhang, Aiping; He, Lin; Li, Can
2013-01-01
DNA origami is an emerging technology that assembles hundreds of staple strands and one single-strand DNA into certain nanopattern. It has been widely used in various fields including detection of biological molecules such as DNA, RNA and proteins. MicroRNAs (miRNAs) play important roles in post-transcriptional gene repression as well as many other biological processes such as cell growth and differentiation. Alterations of miRNAs' expression contribute to many human diseases. However, it is still a challenge to quantitatively detect miRNAs by origami technology. In this study, we developed a novel approach based on streptavidin and quantum dots binding complex (STV-QDs) labeled single strand displacement reaction on DNA origami to quantitatively detect the concentration of miRNAs. We illustrated a linear relationship between the concentration of an exemplary miRNA as miRNA-133 and the STV-QDs hybridization efficiency; the results demonstrated that it is an accurate nano-scale miRNA quantifier motif. In addition, both symmetrical rectangular motif and asymmetrical China-map motif were tested. With significant linearity in both motifs, our experiments suggested that DNA Origami motif with arbitrary shape can be utilized in this method. Since this DNA origami-based method we developed owns the unique advantages of simple, time-and-material-saving, potentially multi-targets testing in one motif and relatively accurate for certain impurity samples as counted directly by atomic force microscopy rather than fluorescence signal detection, it may be widely used in quantification of miRNAs.
Dragon polya spotter: Predictor of poly(A) motifs within human genomic DNA sequences
Kalkatawi, Manal M.
2011-11-15
Motivation: Recognition of poly(A) signals in mRNA is relatively straightforward due to the presence of easily recognizable polyadenylic acid tail. However, the task of identifying poly(A) motifs in the primary genomic DNA sequence that correspond to poly(A) signals in mRNA is a far more challenging problem. Recognition of poly(A) signals is important for better gene annotation and understanding of the gene regulation mechanisms. In this work, we present one such poly(A) motif prediction method based on properties of human genomic DNA sequence surrounding a poly(A) motif. These properties include thermodynamic, physico-chemical and statistical characteristics. For predictions, we developed Artificial Neural Network and Random Forest models. These models are trained to recognize 12 most common poly(A) motifs in human DNA. Our predictors are available as a free web-based tool accessible at http://cbrc.kaust.edu.sa/dps. Compared with other reported predictors, our models achieve higher sensitivity and specificity and furthermore provide a consistent level of accuracy for 12 poly(A) motif variants. The Author(s) 2011. Published by Oxford University Press. All rights reserved.
On fuzzy semantic similarity measure for DNA coding.
Ahmad, Muneer; Jung, Low Tang; Bhuiyan, Md Al-Amin
2016-02-01
A coding measure scheme numerically translates the DNA sequence to a time domain signal for protein coding regions identification. A number of coding measure schemes based on numerology, geometry, fixed mapping, statistical characteristics and chemical attributes of nucleotides have been proposed in recent decades. Such coding measure schemes lack the biologically meaningful aspects of nucleotide data and hence do not significantly discriminate coding regions from non-coding regions. This paper presents a novel fuzzy semantic similarity measure (FSSM) coding scheme centering on FSSM codons׳ clustering and genetic code context of nucleotides. Certain natural characteristics of nucleotides i.e. appearance as a unique combination of triplets, preserving special structure and occurrence, and ability to own and share density distributions in codons have been exploited in FSSM. The nucleotides׳ fuzzy behaviors, semantic similarities and defuzzification based on the center of gravity of nucleotides revealed a strong correlation between nucleotides in codons. The proposed FSSM coding scheme attains a significant enhancement in coding regions identification i.e. 36-133% as compared to other existing coding measure schemes tested over more than 250 benchmarked and randomly taken DNA datasets of different organisms. Copyright © 2015 Elsevier Ltd. All rights reserved.
Marlowe, Ashley E.; Singh, Abhishek; Semichaevsky, Andrey V.; Yingling, Yaroslava G.
2009-03-01
Nucleic acid nanoparticles can self-assembly through the formation of complementary loop-loop interactions or stem-stem interactions. Presence and concentration of ions can significantly affect the self-assembly process and the stability of the nanostructure. In this presentation we use explicit molecular dynamics simulations to examine the variations in cationic distributions and hydration environment around DNA and RNA helices and loop-loop interactions. Our simulations show that the potassium and sodium ionic distributions are different around RNA and DNA motifs which could be indicative of ion mediated relative stability of loop-loop complexes. Moreover in RNA loop-loop motifs ions are consistently present and exchanged through a distinct electronegative channel. We will also show how we used the specific RNA loop-loop motif to design a RNA hexagonal nanoparticle.
Rtt107/Esc4 binds silent chromatin and DNA repair proteins using different BRCT motifs
Jockusch Rebecca A
2006-11-01
Full Text Available Abstract Background By screening a plasmid library for proteins that could cause silencing when targeted to the HMR locus in Saccharomyces cerevisiae, we previously reported the identification of Rtt107/Esc4 based on its ability to establish silent chromatin. In this study we aimed to determine the mechanism of Rtt107/Esc4 targeted silencing and also learn more about its biological functions. Results Targeted silencing by Rtt107/Esc4 was dependent on the SIR genes, which encode obligatory structural and enzymatic components of yeast silent chromatin. Based on its sequence, Rtt107/Esc4 was predicted to contain six BRCT motifs. This motif, originally identified in the human breast tumor suppressor gene BRCA1, is a protein interaction domain. The targeted silencing activity of Rtt107/Esc4 resided within the C-terminal two BRCT motifs, and this region of the protein bound to Sir3 in two-hybrid tests. Deletion of RTT107/ESC4 caused sensitivity to the DNA damaging agent MMS as well as to hydroxyurea. A two-hybrid screen showed that the N-terminal BRCT motifs of Rtt107/Esc4 bound to Slx4, a protein previously shown to be involved in DNA repair and required for viability in a strain lacking the DNA helicase Sgs1. Like SLX genes, RTT107ESC4 interacted genetically with SGS1; esc4Δ sgs1Δ mutants were viable, but exhibited a slow-growth phenotype and also a synergistic DNA repair defect. Conclusion Rtt107/Esc4 binds to the silencing protein Sir3 and the DNA repair protein Slx4 via different BRCT motifs, thus providing a bridge linking silent chromatin to DNA repair enzymes.
STUDYING THE INFLUENCE OF THE PYRENE INTERCALATOR TINA ON THE STABILITY OF DNA i-MOTIFS
El-Sayed, Ahmed A.; Pedersen, Erik Bjerregaard; Khaireldin, Nahid A.
2012-01-01
Certain cytosine-rich (C-rich) DNA sequences can fold into secondary structures as four-stranded i-motifs with hemiprotonated base pairs. Here we synthesized C-rich TINA-intercalating oligonucleotides by inserting a nonnucleotide pyrene moiety between two C-rich regions. The stability of their i-...
Dragon polya spotter: Predictor of poly(A) motifs within human genomic DNA sequences
Kalkatawi, Manal M.; Rangkuti, Farania; Schramm, Michael C.; Jankovic, Boris R.; Kamau, Allan; Chowdhary, Rajesh; Archer, John A.C.; Bajic, Vladimir B.
2011-01-01
. These models are trained to recognize 12 most common poly(A) motifs in human DNA. Our predictors are available as a free web-based tool accessible at http://cbrc.kaust.edu.sa/dps. Compared with other reported predictors, our models achieve higher sensitivity
New scoring schema for finding motifs in DNA Sequences
Nowzari-Dalini Abbas
2009-03-01
Full Text Available Abstract Background Pattern discovery in DNA sequences is one of the most fundamental problems in molecular biology with important applications in finding regulatory signals and transcription factor binding sites. An important task in this problem is to search (or predict known binding sites in a new DNA sequence. For this reason, all subsequences of the given DNA sequence are scored based on an scoring function and the prediction is done by selecting the best score. By assuming no dependency between binding site base positions, most of the available tools for known binding site prediction are designed. Recently Tomovic and Oakeley investigated the statistical basis for either a claim of dependence or independence, to determine whether such a claim is generally true, and they presented a scoring function for binding site prediction based on the dependency between binding site base positions. Our primary objective is to investigate the scoring functions which can be used in known binding site prediction based on the assumption of dependency or independency in binding site base positions. Results We propose a new scoring function based on the dependency between all positions in biding site base positions. This scoring function uses joint information content and mutual information as a measure of dependency between positions in transcription factor binding site. Our method for modeling dependencies is simply an extension of position independency methods. We evaluate our new scoring function on the real data sets extracted from JASPAR and TRANSFAC data bases, and compare the obtained results with two other well known scoring functions. Conclusion The results demonstrate that the new approach improves known binding site discovery and show that the joint information content and mutual information provide a better and more general criterion to investigate the relationships between positions in the TFBS. Our scoring function is formulated by simple
Motif finding in DNA sequences based on skipping nonconserved positions in background Markov chains.
Zhao, Xiaoyan; Sze, Sing-Hoi
2011-05-01
One strategy to identify transcription factor binding sites is through motif finding in upstream DNA sequences of potentially co-regulated genes. Despite extensive efforts, none of the existing algorithms perform very well. We consider a string representation that allows arbitrary ignored positions within the nonconserved portion of single motifs, and use O(2(l)) Markov chains to model the background distributions of motifs of length l while skipping these positions within each Markov chain. By focusing initially on positions that have fixed nucleotides to define core occurrences, we develop an algorithm to identify motifs of moderate lengths. We compare the performance of our algorithm to other motif finding algorithms on a few benchmark data sets, and show that significant improvement in accuracy can be obtained when the sites are sufficiently conserved within a given sample, while comparable performance is obtained when the site conservation rate is low. A software program (PosMotif ) and detailed results are available online at http://faculty.cse.tamu.edu/shsze/posmotif.
A Comparison Study for DNA Motif Modeling on Protein Binding Microarray
Wong, Ka-Chun; Li, Yue; Peng, Chengbin; Wong, Hau-San
2015-01-01
Transcription Factor Binding Sites (TFBSs) are relatively short (5-15 bp) and degenerate. Identifying them is a computationally challenging task. In particular, Protein Binding Microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner; for instance, a typical PBM experiment can measure binding signal intensities of a protein to all possible DNA k-mers (k=810). Since proteins can often bind to DNA with different binding intensities, one of the major challenges is to build motif models which can fully capture the quantitative binding affinity data. To learn DNA motif models from the non-convex objective function landscape, several optimization methods are compared and applied to the PBM motif model building problem. In particular, representative methods from different optimization paradigms have been chosen for modeling performance comparison on hundreds of PBM datasets. The results suggest that the multimodal optimization methods are very effective for capturing the binding preference information from PBM data. In particular, we observe a general performance improvement using di-nucleotide modeling over mono-nucleotide modeling. In addition, the models learned by the best-performing method are applied to two independent applications: PBM probe rotation testing and ChIP-Seq peak sequence prediction, demonstrating its biological applicability.
A Comparison Study for DNA Motif Modeling on Protein Binding Microarray
Wong, Ka-Chun
2015-06-11
Transcription Factor Binding Sites (TFBSs) are relatively short (5-15 bp) and degenerate. Identifying them is a computationally challenging task. In particular, Protein Binding Microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner; for instance, a typical PBM experiment can measure binding signal intensities of a protein to all possible DNA k-mers (k=810). Since proteins can often bind to DNA with different binding intensities, one of the major challenges is to build motif models which can fully capture the quantitative binding affinity data. To learn DNA motif models from the non-convex objective function landscape, several optimization methods are compared and applied to the PBM motif model building problem. In particular, representative methods from different optimization paradigms have been chosen for modeling performance comparison on hundreds of PBM datasets. The results suggest that the multimodal optimization methods are very effective for capturing the binding preference information from PBM data. In particular, we observe a general performance improvement using di-nucleotide modeling over mono-nucleotide modeling. In addition, the models learned by the best-performing method are applied to two independent applications: PBM probe rotation testing and ChIP-Seq peak sequence prediction, demonstrating its biological applicability.
Poly(A) motif prediction using spectral latent features from human DNA sequences
Xie, Bo; Jankovic, Boris R.; Bajic, Vladimir B.; Song, Le; Gao, Xin
2013-01-01
Motivation: Polyadenylation is the addition of a poly(A) tail to an RNA molecule. Identifying DNA sequence motifs that signal the addition of poly(A) tails is essential to improved genome annotation and better understanding of the regulatory mechanisms and stability of mRNA.Existing poly(A) motif predictors demonstrate that information extracted from the surrounding nucleotide sequences of candidate poly(A) motifs can differentiate true motifs from the false ones to a great extent. A variety of sophisticated features has been explored, including sequential, structural, statistical, thermodynamic and evolutionary properties. However, most of these methods involve extensive manual feature engineering, which can be time-consuming and can require in-depth domain knowledge.Results: We propose a novel machine-learning method for poly(A) motif prediction by marrying generative learning (hidden Markov models) and discriminative learning (support vector machines). Generative learning provides a rich palette on which the uncertainty and diversity of sequence information can be handled, while discriminative learning allows the performance of the classification task to be directly optimized. Here, we used hidden Markov models for fitting the DNA sequence dynamics, and developed an efficient spectral algorithm for extracting latent variable information from these models. These spectral latent features were then fed into support vector machines to fine-tune the classification performance.We evaluated our proposed method on a comprehensive human poly(A) dataset that consists of 14 740 samples from 12 of the most abundant variants of human poly(A) motifs. Compared with one of the previous state-of-the-art methods in the literature (the random forest model with expert-crafted features), our method reduces the average error rate, false-negative rate and false-positive rate by 26, 15 and 35%, respectively. Meanwhile, our method makes ?30% fewer error predictions relative to the other
Poly(A) motif prediction using spectral latent features from human DNA sequences
Xie, Bo
2013-06-21
Motivation: Polyadenylation is the addition of a poly(A) tail to an RNA molecule. Identifying DNA sequence motifs that signal the addition of poly(A) tails is essential to improved genome annotation and better understanding of the regulatory mechanisms and stability of mRNA.Existing poly(A) motif predictors demonstrate that information extracted from the surrounding nucleotide sequences of candidate poly(A) motifs can differentiate true motifs from the false ones to a great extent. A variety of sophisticated features has been explored, including sequential, structural, statistical, thermodynamic and evolutionary properties. However, most of these methods involve extensive manual feature engineering, which can be time-consuming and can require in-depth domain knowledge.Results: We propose a novel machine-learning method for poly(A) motif prediction by marrying generative learning (hidden Markov models) and discriminative learning (support vector machines). Generative learning provides a rich palette on which the uncertainty and diversity of sequence information can be handled, while discriminative learning allows the performance of the classification task to be directly optimized. Here, we used hidden Markov models for fitting the DNA sequence dynamics, and developed an efficient spectral algorithm for extracting latent variable information from these models. These spectral latent features were then fed into support vector machines to fine-tune the classification performance.We evaluated our proposed method on a comprehensive human poly(A) dataset that consists of 14 740 samples from 12 of the most abundant variants of human poly(A) motifs. Compared with one of the previous state-of-the-art methods in the literature (the random forest model with expert-crafted features), our method reduces the average error rate, false-negative rate and false-positive rate by 26, 15 and 35%, respectively. Meanwhile, our method makes ?30% fewer error predictions relative to the other
DistAMo: A web-based tool to characterize DNA-motif distribution on bacterial chromosomes
Patrick eSobetzko
2016-03-01
Full Text Available Short DNA motifs are involved in a multitude of functions such as for example chromosome segregation, DNA replication or mismatch repair. Distribution of such motifs is often not random and the specific chromosomal pattern relates to the respective motif function. Computational approaches which quantitatively assess such chromosomal motif patterns are necessary. Here we present a new computer tool DistAMo (Distribution Analysis of DNA Motifs. The algorithm uses codon redundancy to calculate the relative abundance of short DNA motifs from single genes to entire chromosomes. Comparative genomics analyses of the GATC-motif distribution in γ-proteobacterial genomes using DistAMo revealed that (i genes beside the replication origin are enriched in GATCs, (ii genome-wide GATC distribution follows a distinct pattern and (iii genes involved in DNA replication and repair are enriched in GATCs. These features are specific for bacterial chromosomes encoding a Dam methyltransferase. The new software is available as a stand-alone or as an easy-to-use web-based server version at http://www.computational.bio.uni-giessen.de/distamo.
Human telomeric DNA: G-quadruplex, i-motif and Watson–Crick double helix
Phan, Anh Tuân; Mergny, Jean-Louis
2002-01-01
Human telomeric DNA composed of (TTAGGG/CCCTAA)n repeats may form a classical Watson–Crick double helix. Each individual strand is also prone to quadruplex formation: the G-rich strand may adopt a G-quadruplex conformation involving G-quartets whereas the C-rich strand may fold into an i-motif based on intercalated C·C+ base pairs. Using an equimolar mixture of the telomeric oligonucleotides d[AGGG(TTAGGG)3] and d[(CCCTAA)3CCCT], we defined which structures existed and which would be the predominant species under a variety of experimental conditions. Under near-physiological conditions of pH, temperature and salt concentration, telomeric DNA was predominantly in a double-helix form. However, at lower pH values or higher temperatures, the G-quadruplex and/or the i-motif efficiently competed with the duplex. We also present kinetic and thermodynamic data for duplex association and for G-quadruplex/i-motif unfolding. PMID:12409451
Yang, Peng; Wu, Min; Guo, Jing; Kwoh, Chee Keong; Przytycka, Teresa M; Zheng, Jie
2014-02-17
As a fundamental genomic element, meiotic recombination hotspot plays important roles in life sciences. Thus uncovering its regulatory mechanisms has broad impact on biomedical research. Despite the recent identification of the zinc finger protein PRDM9 and its 13-mer binding motif as major regulators for meiotic recombination hotspots, other regulators remain to be discovered. Existing methods for finding DNA sequence motifs of recombination hotspots often rely on the enrichment of co-localizations between hotspots and short DNA patterns, which ignore the cross-individual variation of recombination rates and sequence polymorphisms in the population. Our objective in this paper is to capture signals encoded in genetic variations for the discovery of recombination-associated DNA motifs. Recently, an algorithm called "LDsplit" has been designed to detect the association between single nucleotide polymorphisms (SNPs) and proximal meiotic recombination hotspots. The association is measured by the difference of population recombination rates at a hotspot between two alleles of a candidate SNP. Here we present an open source software tool of LDsplit, with integrative data visualization for recombination hotspots and their proximal SNPs. Applying LDsplit on SNPs inside an established 7-mer motif bound by PRDM9 we observed that SNP alleles preserving the original motif tend to have higher recombination rates than the opposite alleles that disrupt the motif. Running on SNP windows around hotspots each containing an occurrence of the 7-mer motif, LDsplit is able to guide the established motif finding algorithm of MEME to recover the 7-mer motif. In contrast, without LDsplit the 7-mer motif could not be identified. LDsplit is a software tool for the discovery of cis-regulatory DNA sequence motifs stimulating meiotic recombination hotspots by screening and narrowing down to hotspot associated SNPs. It is the first computational method that utilizes the genetic variation of
Kanno, Shin-ichiro; Kuzuoka, Hiroyuki; Sasao, Shigeru; Hong, Zehui; Lan, Li; Nakajima, Satoshi; Yasui, Akira
2007-01-01
DNA damage causes genome instability and cell death, but many of the cellular responses to DNA damage still remain elusive. We here report a human protein, PALF (PNK and APTX-like FHA protein), with an FHA (forkhead-associated) domain and novel zinc-finger-like CYR (cysteine–tyrosine–arginine) motifs that are involved in responses to DNA damage. We found that the CYR motif is widely distributed among DNA repair proteins of higher eukaryotes, and that PALF, as well as a Drosophila protein with...
DNA methylation requires a DNMT1 ubiquitin interacting motif (UIM) and histone ubiquitination.
Qin, Weihua; Wolf, Patricia; Liu, Nan; Link, Stephanie; Smets, Martha; La Mastra, Federica; Forné, Ignasi; Pichler, Garwin; Hörl, David; Fellinger, Karin; Spada, Fabio; Bonapace, Ian Marc; Imhof, Axel; Harz, Hartmann; Leonhardt, Heinrich
2015-08-01
DNMT1 is recruited by PCNA and UHRF1 to maintain DNA methylation after replication. UHRF1 recognizes hemimethylated DNA substrates via the SRA domain, but also repressive H3K9me3 histone marks with its TTD. With systematic mutagenesis and functional assays, we could show that chromatin binding further involved UHRF1 PHD binding to unmodified H3R2. These complementation assays clearly demonstrated that the ubiquitin ligase activity of the UHRF1 RING domain is required for maintenance DNA methylation. Mass spectrometry of UHRF1-deficient cells revealed H3K18 as a novel ubiquitination target of UHRF1 in mammalian cells. With bioinformatics and mutational analyses, we identified a ubiquitin interacting motif (UIM) in the N-terminal regulatory domain of DNMT1 that binds to ubiquitinated H3 tails and is essential for DNA methylation in vivo. H3 ubiquitination and subsequent DNA methylation required UHRF1 PHD binding to H3R2. These results show the manifold regulatory mechanisms controlling DNMT1 activity that require the reading and writing of epigenetic marks by UHRF1 and illustrate the multifaceted interplay between DNA and histone modifications. The identification and functional characterization of the DNMT1 UIM suggests a novel regulatory principle and we speculate that histone H2AK119 ubiquitination might also lead to UIM-dependent recruitment of DNMT1 and DNA methylation beyond classic maintenance.
qPMS7: a fast algorithm for finding (ℓ, d-motifs in DNA and protein sequences.
Hieu Dinh
Full Text Available Detection of rare events happening in a set of DNA/protein sequences could lead to new biological discoveries. One kind of such rare events is the presence of patterns called motifs in DNA/protein sequences. Finding motifs is a challenging problem since the general version of motif search has been proven to be intractable. Motifs discovery is an important problem in biology. For example, it is useful in the detection of transcription factor binding sites and transcriptional regulatory elements that are very crucial in understanding gene function, human disease, drug design, etc. Many versions of the motif search problem have been proposed in the literature. One such is the (ℓ, d-motif search (or Planted Motif Search (PMS. A generalized version of the PMS problem, namely, Quorum Planted Motif Search (qPMS, is shown to accurately model motifs in real data. However, solving the qPMS problem is an extremely difficult task because a special case of it, the PMS Problem, is already NP-hard, which means that any algorithm solving it can be expected to take exponential time in the worse case scenario. In this paper, we propose a novel algorithm named qPMS7 that tackles the qPMS problem on real data as well as challenging instances. Experimental results show that our Algorithm qPMS7 is on an average 5 times faster than the state-of-art algorithm. The executable program of Algorithm qPMS7 is freely available on the web at http://pms.engr.uconn.edu/downloads/qPMS7.zip. Our online motif discovery tools that use Algorithm qPMS7 are freely available at http://pms.engr.uconn.edu or http://motifsearch.com.
The Q Motif Is Involved in DNA Binding but Not ATP Binding in ChlR1 Helicase.
Hao Ding
Full Text Available Helicases are molecular motors that couple the energy of ATP hydrolysis to the unwinding of structured DNA or RNA and chromatin remodeling. The conversion of energy derived from ATP hydrolysis into unwinding and remodeling is coordinated by seven sequence motifs (I, Ia, II, III, IV, V, and VI. The Q motif, consisting of nine amino acids (GFXXPXPIQ with an invariant glutamine (Q residue, has been identified in some, but not all helicases. Compared to the seven well-recognized conserved helicase motifs, the role of the Q motif is less acknowledged. Mutations in the human ChlR1 (DDX11 gene are associated with a unique genetic disorder known as Warsaw Breakage Syndrome, which is characterized by cellular defects in genome maintenance. To examine the roles of the Q motif in ChlR1 helicase, we performed site directed mutagenesis of glutamine to alanine at residue 23 in the Q motif of ChlR1. ChlR1 recombinant protein was overexpressed and purified from HEK293T cells. ChlR1-Q23A mutant abolished the helicase activity of ChlR1 and displayed reduced DNA binding ability. The mutant showed impaired ATPase activity but normal ATP binding. A thermal shift assay revealed that ChlR1-Q23A has a melting point value similar to ChlR1-WT. Partial proteolysis mapping demonstrated that ChlR1-WT and Q23A have a similar globular structure, although some subtle conformational differences in these two proteins are evident. Finally, we found ChlR1 exists and functions as a monomer in solution, which is different from FANCJ, in which the Q motif is involved in protein dimerization. Taken together, our results suggest that the Q motif is involved in DNA binding but not ATP binding in ChlR1 helicase.
Kanno, Shin-ichiro; Kuzuoka, Hiroyuki; Sasao, Shigeru; Hong, Zehui; Lan, Li; Nakajima, Satoshi; Yasui, Akira
2007-01-01
DNA damage causes genome instability and cell death, but many of the cellular responses to DNA damage still remain elusive. We here report a human protein, PALF (PNK and APTX-like FHA protein), with an FHA (forkhead-associated) domain and novel zinc-finger-like CYR (cysteine–tyrosine–arginine) motifs that are involved in responses to DNA damage. We found that the CYR motif is widely distributed among DNA repair proteins of higher eukaryotes, and that PALF, as well as a Drosophila protein with tandem CYR motifs, has endo- and exonuclease activities against abasic site and other types of base damage. PALF accumulates rapidly at single-strand breaks in a poly(ADP-ribose) polymerase 1 (PARP1)-dependent manner in human cells. Indeed, PALF interacts directly with PARP1 and is required for its activation and for cellular resistance to methyl-methane sulfonate. PALF also interacts directly with KU86, LIGASEIV and phosphorylated XRCC4 proteins and possesses endo/exonuclease activity at protruding DNA ends. Various treatments that produce double-strand breaks induce formation of PALF foci, which fully coincide with γH2AX foci. Thus, PALF and the CYR motif may play important roles in DNA repair of higher eukaryotes. PMID:17396150
Fan, Li; Arval, Andrew S.; Cooper, Priscilla K.; Iwai, Shigenori; Hanaoka, Fumio; Tainer, John A.
2005-04-01
The human xeroderma pigmentosum group B (XPB) helicase is essential for transcription, nucleotide excision repair, and TFIIH functional assembly. Here, we determined crystal structures of an Archaeoglobus fulgidus XPB homolog (AfXPB) that characterize two RecA-like XPB helicase domains and discover a DNA damage recognition domain (DRD), a unique RED motif, a flexible thumb motif (ThM), and implied conformational changes within a conserved functional core. RED motif mutations dramatically reduce helicase activity, and the DRD and ThM, which flank the RED motif, appear structurally as well as functionally analogous to the MutS mismatch recognition and DNA polymerase thumb domains. Substrate specificity is altered by DNA damage, such that AfXPB unwinds dsDNA with 3' extensions, but not blunt-ended dsDNA, unless it contains a lesion, as shown for CPD or (6-4) photoproducts. Together, these results provide an unexpected mechanism of DNA unwinding with Implications for XPB damage verification in nucleotide excision repair.
Discovery of cell-type specific DNA motif grammar in cis-regulatory elements using random Forest.
Wang, Xin; Lin, Peijie; Ho, Joshua W K
2018-01-19
It has been observed that many transcription factors (TFs) can bind to different genomic loci depending on the cell type in which a TF is expressed in, even though the individual TF usually binds to the same core motif in different cell types. How a TF can bind to the genome in such a highly cell-type specific manner, is a critical research question. One hypothesis is that a TF requires co-binding of different TFs in different cell types. If this is the case, it may be possible to observe different combinations of TF motifs - a motif grammar - located at the TF binding sites in different cell types. In this study, we develop a bioinformatics method to systematically identify DNA motifs in TF binding sites across multiple cell types based on published ChIP-seq data, and address two questions: (1) can we build a machine learning classifier to predict cell-type specificity based on motif combinations alone, and (2) can we extract meaningful cell-type specific motif grammars from this classifier model. We present a Random Forest (RF) based approach to build a multi-class classifier to predict the cell-type specificity of a TF binding site given its motif content. We applied this RF classifier to two published ChIP-seq datasets of TF (TCF7L2 and MAX) across multiple cell types. Using cross-validation, we show that motif combinations alone are indeed predictive of cell types. Furthermore, we present a rule mining approach to extract the most discriminatory rules in the RF classifier, thus allowing us to discover the underlying cell-type specific motif grammar. Our bioinformatics analysis supports the hypothesis that combinatorial TF motif patterns are cell-type specific.
Fragile DNA Motifs Trigger Mutagenesis at Distant Chromosomal Loci in Saccharomyces cerevisiae
Saini, Natalie; Zhang, Yu; Nishida, Yuri; Sheng, Ziwei; Choudhury, Shilpa; Mieczkowski, Piotr; Lobachev, Kirill S.
2013-01-01
DNA sequences capable of adopting non-canonical secondary structures have been associated with gross-chromosomal rearrangements in humans and model organisms. Previously, we have shown that long inverted repeats that form hairpin and cruciform structures and triplex-forming GAA/TTC repeats induce the formation of double-strand breaks which trigger genome instability in yeast. In this study, we demonstrate that breakage at both inverted repeats and GAA/TTC repeats is augmented by defects in DNA replication. Increased fragility is associated with increased mutation levels in the reporter genes located as far as 8 kb from both sides of the repeats. The increase in mutations was dependent on the presence of inverted or GAA/TTC repeats and activity of the translesion polymerase Polζ. Mutagenesis induced by inverted repeats also required Sae2 which opens hairpin-capped breaks and initiates end resection. The amount of breakage at the repeats is an important determinant of mutations as a perfect palindromic sequence with inherently increased fragility was also found to elevate mutation rates even in replication-proficient strains. We hypothesize that the underlying mechanism for mutagenesis induced by fragile motifs involves the formation of long single-stranded regions in the broken chromosome, invasion of the undamaged sister chromatid for repair, and faulty DNA synthesis employing Polζ. These data demonstrate that repeat-mediated breaks pose a dual threat to eukaryotic genome integrity by inducing chromosomal aberrations as well as mutations in flanking genes. PMID:23785298
Construction of a fuzzy and all Boolean logic gates based on DNA
M. Zadegan, Reza; Jepsen, Mette D E; Hildebrandt, Lasse
2015-01-01
to the operation of the six Boolean logic gates AND, NAND, OR, NOR, XOR, and XNOR. The logic gate complex is shown to work also when implemented in a three-dimensional DNA origami box structure, where it controlled the position of the lid in a closed or open position. Implementation of multiple microRNA sensitive...... DNA locks on one DNA origami box structure enabled fuzzy logical operation that allows biosensing of complex molecular signals. Integrating logic gates with DNA origami systems opens a vast avenue to applications in the fields of nanomedicine for diagnostics and therapeutics....
Role of specific cations and water entropy on the stability of branched DNA motif structures.
Pascal, Tod A; Goddard, William A; Maiti, Prabal K; Vaidehi, Nagarajan
2012-10-11
DNA three-way junctions (TWJs) are important intermediates in various cellular processes and are the simplest of a family of branched nucleic acids being considered as scaffolds for biomolecular nanotechnology. Branched nucleic acids are stabilized by divalent cations such as Mg(2+), presumably due to condensation and neutralization of the negatively charged DNA backbone. However, electrostatic screening effects point to more complex solvation dynamics and a large role of interfacial waters in thermodynamic stability. Here, we report extensive computer simulations in explicit water and salt on a model TWJ and use free energy calculations to quantify the role of ionic character and strength on stability. We find that enthalpic stabilization of the first and second hydration shells by Mg(2+) accounts for 1/3 and all of the free energy gain in 50% and pure MgCl(2) solutions, respectively. The more distorted DNA molecule is actually destabilized in pure MgCl(2) compared to pure NaCl. Notably, the first shell, interfacial waters have very low translational and rotational entropy (i.e., mobility) compared to the bulk, an entropic loss that is overcompensated by increased enthalpy from additional electrostatic interactions with Mg(2+). In contrast, the second hydration shell has anomalously high entropy as it is trapped between an immobile and bulklike layer. The nonmonotonic entropic signature and long-range perturbations of the hydration shells to Mg(2+) may have implications in the molecular recognition of these motifs. For example, we find that low salt stabilizes the parallel configuration of the three-way junction, whereas at normal salt we find antiparallel configurations deduced from the NMR. We use the 2PT analysis to follow the thermodynamics of this transition and find that the free energy barrier is dominated by entropic effects that result from the decreased surface area of the antiparallel form which has a smaller number of low entropy waters in the first
Ahmad, Muneer; Jung, Low Tan; Bhuiyan, Al-Amin
2017-10-01
Digital signal processing techniques commonly employ fixed length window filters to process the signal contents. DNA signals differ in characteristics from common digital signals since they carry nucleotides as contents. The nucleotides own genetic code context and fuzzy behaviors due to their special structure and order in DNA strand. Employing conventional fixed length window filters for DNA signal processing produce spectral leakage and hence results in signal noise. A biological context aware adaptive window filter is required to process the DNA signals. This paper introduces a biological inspired fuzzy adaptive window median filter (FAWMF) which computes the fuzzy membership strength of nucleotides in each slide of window and filters nucleotides based on median filtering with a combination of s-shaped and z-shaped filters. Since coding regions cause 3-base periodicity by an unbalanced nucleotides' distribution producing a relatively high bias for nucleotides' usage, such fundamental characteristic of nucleotides has been exploited in FAWMF to suppress the signal noise. Along with adaptive response of FAWMF, a strong correlation between median nucleotides and the Π shaped filter was observed which produced enhanced discrimination between coding and non-coding regions contrary to fixed length conventional window filters. The proposed FAWMF attains a significant enhancement in coding regions identification i.e. 40% to 125% as compared to other conventional window filters tested over more than 250 benchmarked and randomly taken DNA datasets of different organisms. This study proves that conventional fixed length window filters applied to DNA signals do not achieve significant results since the nucleotides carry genetic code context. The proposed FAWMF algorithm is adaptive and outperforms significantly to process DNA signal contents. The algorithm applied to variety of DNA datasets produced noteworthy discrimination between coding and non-coding regions contrary
Nomura, Yusuke; Tanaka, Yoichiro; Fukunaga, Jun-ichi; Fujiwara, Kazuya; Chiba, Manabu; Iibuchi, Hiroaki; Tanaka, Taku; Nakamura, Yoshikazu; Kawai, Gota; Kozu, Tomoko; Sakamoto, Taiichi
2013-12-01
AML1/RUNX1 is an essential transcription factor involved in the differentiation of hematopoietic cells. AML1 binds to the Runt-binding double-stranded DNA element (RDE) of target genes through its N-terminal Runt domain. In a previous study, we obtained RNA aptamers against the AML1 Runt domain by systematic evolution of ligands by exponential enrichment and revealed that RNA aptamers exhibit higher affinity for the Runt domain than that for RDE and possess the 5'-GCGMGNN-3' and 5'-N'N'CCAC-3' conserved motif (M: A or C; N and N' form Watson-Crick base pairs) that is important for Runt domain binding. In this study, to understand the structural basis of recognition of the Runt domain by the aptamer motif, the solution structure of a 22-mer RNA was determined using nuclear magnetic resonance. The motif contains the AH(+)-C mismatch and base triple and adopts an unusual backbone structure. Structural analysis of the aptamer motif indicated that the aptamer binds to the Runt domain by mimicking the RDE sequence and structure. Our data should enhance the understanding of the structural basis of DNA mimicry by RNA molecules.
Distance-dependent duplex DNA destabilization proximal to G-quadruplex/i-motif sequences
König, Sebastian L. B.; Huppert, Julian L.; Sigel, Roland K. O.; Evans, Amanda C.
2013-01-01
G-quadruplexes and i-motifs are complementary examples of non-canonical nucleic acid substructure conformations. G-quadruplex thermodynamic stability has been extensively studied for a variety of base sequences, but the degree of duplex destabilization that adjacent quadruplex structure formation can cause has yet to be fully addressed. Stable in vivo formation of these alternative nucleic acid structures is likely to be highly dependent on whether sufficient spacing exists between neighbouring duplex- and quadruplex-/i-motif-forming regions to accommodate quadruplexes or i-motifs without disrupting duplex stability. Prediction of putative G-quadruplex-forming regions is likely to be assisted by further understanding of what distance (number of base pairs) is required for duplexes to remain stable as quadruplexes or i-motifs form. Using oligonucleotide constructs derived from precedented G-quadruplexes and i-motif-forming bcl-2 P1 promoter region, initial biophysical stability studies indicate that the formation of G-quadruplex and i-motif conformations do destabilize proximal duplex regions. The undermining effect that quadruplex formation can have on duplex stability is mitigated with increased distance from the duplex region: a spacing of five base pairs or more is sufficient to maintain duplex stability proximal to predicted quadruplex/i-motif-forming regions. PMID:23771141
Soyoung Chang
2018-04-01
Full Text Available The unique biological features of supramolecular DNA have led to an increasing interest in biomedical applications such as biosensors. We have developed an i-motif and G-rich DNA conjugated single-walled carbon nanotube hybrid materials, which shows reversible conformational switching upon external stimuli such as pH (5 and 8 and presence of ions (Li+ and K+. We observed reversible electrochemical redox activity upon external stimuli in a quick and robust manner. Given the ease and the robustness of this method, we believe that pH- and ion-driven reversible DNA structure transformations will be utilized for future applications for developing novel biosensors.
Chakraborty, Mohua; Dhar, Bishal; Ghosh, Sankar Kumar
2017-11-01
The DNA barcodes are generally interpreted using distance-based and character-based methods. The former uses clustering of comparable groups, based on the relative genetic distance, while the latter is based on the presence or absence of discrete nucleotide substitutions. The distance-based approach has a limitation in defining a universal species boundary across the taxa as the rate of mtDNA evolution is not constant throughout the taxa. However, character-based approach more accurately defines this using a unique set of nucleotide characters. The character-based analysis of full-length barcode has some inherent limitations, like sequencing of the full-length barcode, use of a sparse-data matrix and lack of a uniform diagnostic position for each group. A short continuous stretch of a fragment can be used to resolve the limitations. Here, we observe that a 154-bp fragment, from the transversion-rich domain of 1367 COI barcode sequences can successfully delimit species in the three most diverse orders of freshwater fishes. This fragment is used to design species-specific barcode motifs for 109 species by the character-based method, which successfully identifies the correct species using a pattern-matching program. The motifs also correctly identify geographically isolated population of the Cypriniformes species. Further, this region is validated as a species-specific mini-barcode for freshwater fishes by successful PCR amplification and sequencing of the motif (154 bp) using the designed primers. We anticipate that use of such motifs will enhance the diagnostic power of DNA barcode, and the mini-barcode approach will greatly benefit the field-based system of rapid species identification. © 2017 John Wiley & Sons Ltd.
Mitchell, Michael S.; Rao, Venigalla B.
2004-01-01
Bacteriophage terminases constitute a very interesting class of viral-coded multifunctional ATPase 'motors' that apparently drive directional translocation of DNA into an empty viral capsid. A common Walker A motif and other conserved signatures of a critical ATPase catalytic center are identified in the N-terminal half of numerous large terminase proteins. However, several terminases, including the well-characterized λ and SPP1 terminases, seem to lack the classic Walker A in the N-terminus. Using sequence alignment approaches, we discovered the presence of deviant Walker A motifs in these and many other phage terminases. One deviation, the presence of a lysine at the beginning of P-loop, may represent a 3D equivalent of the universally conserved lysine in the Walker A GKT/S signature. This and other novel putative Walker A motifs that first came to light through this study help define the ATPase centers of phage and viral terminases as well as elicit important insights into the molecular functioning of this fundamental motif in biological systems
Chojnowski, Grzegorz, E-mail: gchojnowski@genesilico.pl [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); Waleń, Tomasz [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); University of Warsaw, Banacha 2, 02-097 Warsaw (Poland); Piątkowski, Paweł; Potrzebowski, Wojciech [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); Bujnicki, Janusz M. [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); Adam Mickiewicz University, Umultowska 89, 61-614 Poznan (Poland)
2015-03-01
A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.
Chojnowski, Grzegorz; Waleń, Tomasz; Piątkowski, Paweł; Potrzebowski, Wojciech; Bujnicki, Janusz M.
2015-01-01
A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx
Hipp, Katharina; Rau, Peter; Schäfer, Benjamin [Institut für Biomaterialien und biomolekulare Systeme, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart (Germany); Gronenborn, Bruno [Institut des Sciences du Végétal, CNRS, 91198 Gif-sur-Yvette (France); Jeske, Holger, E-mail: holger.jeske@bio.uni-stuttgart.de [Institut für Biomaterialien und biomolekulare Systeme, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart (Germany)
2014-08-15
Geminiviruses, single-stranded DNA plant viruses, encode a replication-initiator protein (Rep) that is indispensable for virus replication. A potential cyclin interaction motif (RXL) in the sequence of African cassava mosaic virus Rep may be an alternative link to cell cycle controls to the known interaction with plant homologs of retinoblastoma protein (pRBR). Mutation of this motif abrogated rereplication in fission yeast induced by expression of wildtype Rep suggesting that Rep interacts via its RXL motif with one or several yeast proteins. The RXL motif is essential for viral infection of Nicotiana benthamiana plants, since mutation of this motif in infectious clones prevented any symptomatic infection. The cell-cycle link (Clink) protein of a nanovirus (faba bean necrotic yellows virus) was investigated that activates the cell cycle by binding via its LXCXE motif to pRBR. Expression of wildtype Clink and a Clink mutant deficient in pRBR-binding did not trigger rereplication in fission yeast. - Highlights: • A potential cyclin interaction motif is conserved in geminivirus Rep proteins. • In ACMV Rep, this motif (RXL) is essential for rereplication of fission yeast DNA. • Mutating RXL abrogated viral infection completely in Nicotiana benthamiana. • Expression of a nanovirus Clink protein in yeast did not induce rereplication. • Plant viruses may have evolved multiple routes to exploit host DNA synthesis.
Hipp, Katharina; Rau, Peter; Schäfer, Benjamin; Gronenborn, Bruno; Jeske, Holger
2014-01-01
Geminiviruses, single-stranded DNA plant viruses, encode a replication-initiator protein (Rep) that is indispensable for virus replication. A potential cyclin interaction motif (RXL) in the sequence of African cassava mosaic virus Rep may be an alternative link to cell cycle controls to the known interaction with plant homologs of retinoblastoma protein (pRBR). Mutation of this motif abrogated rereplication in fission yeast induced by expression of wildtype Rep suggesting that Rep interacts via its RXL motif with one or several yeast proteins. The RXL motif is essential for viral infection of Nicotiana benthamiana plants, since mutation of this motif in infectious clones prevented any symptomatic infection. The cell-cycle link (Clink) protein of a nanovirus (faba bean necrotic yellows virus) was investigated that activates the cell cycle by binding via its LXCXE motif to pRBR. Expression of wildtype Clink and a Clink mutant deficient in pRBR-binding did not trigger rereplication in fission yeast. - Highlights: • A potential cyclin interaction motif is conserved in geminivirus Rep proteins. • In ACMV Rep, this motif (RXL) is essential for rereplication of fission yeast DNA. • Mutating RXL abrogated viral infection completely in Nicotiana benthamiana. • Expression of a nanovirus Clink protein in yeast did not induce rereplication. • Plant viruses may have evolved multiple routes to exploit host DNA synthesis
The Runt domain of AML1 (RUNX1) binds a sequence-conserved RNA motif that mimics a DNA element.
Fukunaga, Junichi; Nomura, Yusuke; Tanaka, Yoichiro; Amano, Ryo; Tanaka, Taku; Nakamura, Yoshikazu; Kawai, Gota; Sakamoto, Taiichi; Kozu, Tomoko
2013-07-01
AML1 (RUNX1) is a key transcription factor for hematopoiesis that binds to the Runt-binding double-stranded DNA element (RDE) of target genes through its N-terminal Runt domain. Aberrations in the AML1 gene are frequently found in human leukemia. To better understand AML1 and its potential utility for diagnosis and therapy, we obtained RNA aptamers that bind specifically to the AML1 Runt domain. Enzymatic probing and NMR analyses revealed that Apt1-S, which is a truncated variant of one of the aptamers, has a CACG tetraloop and two stem regions separated by an internal loop. All the isolated aptamers were found to contain the conserved sequence motif 5'-NNCCAC-3' and 5'-GCGMGN'N'-3' (M:A or C; N and N' form Watson-Crick base pairs). The motif contains one AC mismatch and one base bulged out. Mutational analysis of Apt1-S showed that three guanines of the motif are important for Runt binding as are the three guanines of RDE, which are directly recognized by three arginine residues of the Runt domain. Mutational analyses of the Runt domain revealed that the amino acid residues used for Apt1-S binding were similar to those used for RDE binding. Furthermore, the aptamer competed with RDE for binding to the Runt domain in vitro. These results demonstrated that the Runt domain of the AML1 protein binds to the motif of the aptamer that mimics DNA. Our findings should provide new insights into RNA function and utility in both basic and applied sciences.
Sequence-specific DNA binding by MYC/MAX to low-affinity non-E-box motifs.
Michael Allevato
Full Text Available The MYC oncoprotein regulates transcription of a large fraction of the genome as an obligatory heterodimer with the transcription factor MAX. The MYC:MAX heterodimer and MAX:MAX homodimer (hereafter MYC/MAX bind Enhancer box (E-box DNA elements (CANNTG and have the greatest affinity for the canonical MYC E-box (CME CACGTG. However, MYC:MAX also recognizes E-box variants and was reported to bind DNA in a "non-specific" fashion in vitro and in vivo. Here, in order to identify potential additional non-canonical binding sites for MYC/MAX, we employed high throughput in vitro protein-binding microarrays, along with electrophoretic mobility-shift assays and bioinformatic analyses of MYC-bound genomic loci in vivo. We identified all hexameric motifs preferentially bound by MYC/MAX in vitro, which include the low-affinity non-E-box sequence AACGTT, and found that the vast majority (87% of MYC-bound genomic sites in a human B cell line contain at least one of the top 21 motifs bound by MYC:MAX in vitro. We further show that high MYC/MAX concentrations are needed for specific binding to the low-affinity sequence AACGTT in vitro and that elevated MYC levels in vivo more markedly increase the occupancy of AACGTT sites relative to CME sites, especially at distal intergenic and intragenic loci. Hence, MYC binds diverse DNA motifs with a broad range of affinities in a sequence-specific and dose-dependent manner, suggesting that MYC overexpression has more selective effects on the tumor transcriptome than previously thought.
Grimm, Guido W.; Renner, Susanne S.; Stamatakis, Alexandros; Hemleben, Vera
2007-01-01
The multi-copy internal transcribed spacer (ITS) region of nuclear ribosomal DNA is widely used to infer phylogenetic relationships among closely related taxa. Here we use maximum likelihood (ML) and splits graph analyses to extract phylogenetic information from ~ 600 mostly cloned ITS sequences, representing 81 species and subspecies of Acer, and both species of its sister Dipteronia. Additional analyses compared sequence motifs in Acer and several hundred Anacardiaceae, Burseraceae, Meliaceae, Rutaceae, and Sapindaceae ITS sequences in GenBank. We also assessed the effects of using smaller data sets of consensus sequences with ambiguity coding (accounting for within-species variation) instead of the full (partly redundant) original sequences. Neighbor-nets and bipartition networks were used to visualize conflict among character state patterns. Species clusters observed in the trees and networks largely agree with morphology-based classifications; of de Jong’s (1994) 16 sections, nine are supported in neighbor-net and bipartition networks, and ten by sequence motifs and the ML tree; of his 19 series, 14 are supported in networks, motifs, and the ML tree. Most nodes had higher bootstrap support with matrices of 105 or 40 consensus sequences than with the original matrix. Within-taxon ITS divergence did not differ between diploid and polyploid Acer, and there was little evidence of differentiated parental ITS haplotypes, suggesting that concerted evolution in Acer acts rapidly. PMID:19455198
Guido W. Grimm
2006-01-01
Full Text Available The multi-copy internal transcribed spacer (ITS region of nuclear ribosomal DNA is widely used to infer phylogenetic relationships among closely related taxa. Here we use maximum likelihood (ML and splits graph analyses to extract phylogenetic information from ~ 600 mostly cloned ITS sequences, representing 81 species and subspecies of Acer, and both species of its sister Dipteronia. Additional analyses compared sequence motifs in Acer and several hundred Anacardiaceae, Burseraceae, Meliaceae, Rutaceae, and Sapindaceae ITS sequences in GenBank. We also assessed the effects of using smaller data sets of consensus sequences with ambiguity coding (accounting for within-species variation instead of the full (partly redundant original sequences. Neighbor-nets and bipartition networks were used to visualize conflict among character state patterns. Species clusters observed in the trees and networks largely agree with morphology-based classifications; of de Jong’s (1994 16 sections, nine are supported in neighbor-net and bipartition networks, and ten by sequence motifs and the ML tree; of his 19 series, 14 are supported in networks, motifs, and the ML tree. Most nodes had higher bootstrap support with matrices of 105 or 40 consensus sequences than with the original matrix. Within-taxon ITS divergence did not differ between diploid and polyploid Acer, and there was little evidence of differentiated parental ITS haplotypes, suggesting that concerted evolution in Acer acts rapidly.
Zheng, Tao; Jiang, Pan; Cao, Bo; Cheng, Qiuxiang; Kong, Lingxin; Zheng, Xiaoqing; Hu, Qinghai; You, Delin
2016-01-15
Phosphorothioate (PT) modification of DNA, in which the non-bridging oxygen of the backbone phosphate group is replaced by sulfur, is governed by the DndA-E proteins in prokaryotes. To better understand the biochemical mechanism of PT modification, functional analysis of the recently found PT-modifying enzyme DndEi, which has an additional domain compared with canonical DndE, from Riemerella anatipestifer is performed in this study. The additional domain is identified as a DNA helicase, and functional deletion of this domain in vivo leads to PT modification deficiency, indicating an essential role of helicase activity in PT modification. Subsequent analysis reveals that the additional domain has an ATPase activity. Intriguingly, the ATPase activity is strongly stimulated by DNA substrate containing a GAAC/GTTC motif (i.e. the motif at which PT modifications occur in R. anatipestifer) when the additional domain and the other domain (homologous to canonical DndE) are co-expressed as a full-length DndEi. These results reveal that PT modification is a biochemical process with DNA strand separation and intense ATP hydrolysis. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.
Li, Jun; Shi, Jian-Li; Wu, Xiao-Yan; Fu, Fang; Yu, Jiang; Yuan, Xiao-Yuan; Peng, Zhe; Cong, Xiao-Yan; Xu, Shao-Jian; Sun, Wen-Bo; Cheng, Kai-Hui; Du, Yi-Jun; Wu, Jia-Qiang; Wang, Jin-Bao; Huang, Bao-Hua
2015-06-01
Nowadays, adjuvant is still important for boosting immunity and improving resistance in animals. In order to boost the immunity of porcine circovirus type 2 (PCV2) DNA vaccine, CpG motifs were inserted. In this study, the dose-effect was studied, and the immunity of PCV2 DNA vaccines by recombinant open reading frame 2 (ORF2) gene and CpG motifs was evaluated. Three-week-old Changbai piglets were inoculated intramuscularly with 200 μg, 400 μg, and 800 μg DNA vaccines containing 14 and 18 CpG motifs, respectively. Average gain and rectum temperature were recorded everyday during the experiments. Blood was collected from the piglets after vaccination to detect the changes of specific antibodies, interleukin-2, and immune cells every week. Tissues were collected for histopathology and polymerase chain reaction. The results indicated that compared to those of the control piglets, all concentrations of two DNA vaccines could induce PCV2-specific antibodies. A cellular immunity test showed that PCV2-specific lymphocytes proliferated the number of TH, TC, and CD3+ positive T-cells raised in the blood of DNA vaccine immune groups. There was no distinct pathological damage and viremia occurring in pigs that were inoculated with DNA vaccines, but there was some minor pathological damage in the control group. The results demonstrated that CpG motifs as an adjuvant could boost the humoral and cellular immunity of pigs to PCV2, especially in terms of cellular immunity. Comparing two DNA vaccines that were constructed, the one containing 18 CpG motifs was more effective. This is the first report that CpG motifs as an adjuvant insert to the PCV2 DNA vaccine could boost immunity.
Counting of oligomers in sequences generated by markov chains for DNA motif discovery.
Shan, Gao; Zheng, Wei-Mou
2009-02-01
By means of the technique of the imbedded Markov chain, an efficient algorithm is proposed to exactly calculate first, second moments of word counts and the probability for a word to occur at least once in random texts generated by a Markov chain. A generating function is introduced directly from the imbedded Markov chain to derive asymptotic approximations for the problem. Two Z-scores, one based on the number of sequences with hits and the other on the total number of word hits in a set of sequences, are examined for discovery of motifs on a set of promoter sequences extracted from A. thaliana genome. Source code is available at http://www.itp.ac.cn/zheng/oligo.c.
Morellet, Nelly; Li, Xianghong; Wieninger, Silke A; Taylor, Jennifer L; Bischerour, Julien; Moriau, Séverine; Lescop, Ewen; Bardiaux, Benjamin; Mathy, Nathalie; Assrir, Nadine; Bétermier, Mireille; Nilges, Michael; Hickman, Alison B; Dyda, Fred; Craig, Nancy L; Guittet, Eric
2018-01-01
Abstract The piggyBac transposase (PB) is distinguished by its activity and utility in genome engineering, especially in humans where it has highly promising therapeutic potential. Little is known, however, about the structure–function relationships of the different domains of PB. Here, we demonstrate in vitro and in vivo that its C-terminal Cysteine-Rich Domain (CRD) is essential for DNA breakage, joining and transposition and that it binds to specific DNA sequences in the left and right transposon ends, and to an additional unexpectedly internal site at the left end. Using NMR, we show that the CRD adopts the specific fold of the cross-brace zinc finger protein family. We determine the interaction interfaces between the CRD and its target, the 5′-TGCGT-3′/3′-ACGCA-5′ motifs found in the left, left internal and right transposon ends, and use NMR results to propose docking models for the complex, which are consistent with our site-directed mutagenesis data. Our results provide support for a model of the PB/DNA interactions in the context of the transpososome, which will be useful for the rational design of PB mutants with increased activity. PMID:29385532
Hosaka, Shuto; Honda, Takuto; Lee, Seon Hwa; Oe, Tomoyuki
2018-06-01
Candidate drugs that can be metabolically transformed into reactive electrophilic products, such as epoxides, quinones, and nitroso compounds, are of special concern because subsequent covalent binding to bio-macromolecules can cause adverse drug reactions, such as allergic reactions, hepatotoxicity, and genotoxicity. Several strategies have been reported for screening reactive metabolites, such as a covalent binding assay with radioisotope-labeled drugs and a trapping method followed by LC-MS/MS analyses. Of these, a trapping method using glutathione is the most common, especially at the early stage of drug development. However, the cysteine of glutathione is not the only nucleophilic site in vivo; lysine, histidine, arginine, and DNA bases are also nucleophilic. Indeed, the glutathione trapping method tends to overlook several types of reactive metabolites, such as aldehydes, acylglucuronides, and nitroso compounds. Here, we introduce an alternate way for screening reactive metabolites as follows: A mixture of the light and heavy isotopes of simplified amino acid motifs and a DNA motif is used as a biomimetic trapping cocktail. This mixture consists of [ 2 H 0 ]/[ 2 H 3 ]-1-methylguanidine (arginine motif, Δ 3 Da), [ 2 H 0 ]/[ 2 H 4 ]-2-mercaptoethanol (cysteine motif, Δ 4 Da), [ 2 H 0 ]/[ 2 H 5 ]-4-methylimidazole (histidine motif, Δ 5 Da), [ 2 H 0 ]/[ 2 H 9 ]-n-butylamine (lysine motif, Δ 9 Da), and [ 13 C 0 , 15 N 0 ]/[ 13 C 1 , 15 N 2 ]-2'-deoxyguanosine (DNA motif, Δ 3 Da). Mass tag triggered data-dependent acquisition is used to find the characteristic doublet peaks, followed by specific identification of the light isotope peak using MS/MS. Forty-two model drugs were examined using an in vitro microsome experiment to validate the strategy. Graphical abstract Biomimetic trapping cocktail to screen reactive metabolites.
Tsai, Zing Tsung-Yeh; Shiu, Shin-Han; Tsai, Huai-Kuang
2015-08-01
Transcription factor (TF) binding is determined by the presence of specific sequence motifs (SM) and chromatin accessibility, where the latter is influenced by both chromatin state (CS) and DNA structure (DS) properties. Although SM, CS, and DS have been used to predict TF binding sites, a predictive model that jointly considers CS and DS has not been developed to predict either TF-specific binding or general binding properties of TFs. Using budding yeast as model, we found that machine learning classifiers trained with either CS or DS features alone perform better in predicting TF-specific binding compared to SM-based classifiers. In addition, simultaneously considering CS and DS further improves the accuracy of the TF binding predictions, indicating the highly complementary nature of these two properties. The contributions of SM, CS, and DS features to binding site predictions differ greatly between TFs, allowing TF-specific predictions and potentially reflecting different TF binding mechanisms. In addition, a "TF-agnostic" predictive model based on three DNA "intrinsic properties" (in silico predicted nucleosome occupancy, major groove geometry, and dinucleotide free energy) that can be calculated from genomic sequences alone has performance that rivals the model incorporating experiment-derived data. This intrinsic property model allows prediction of binding regions not only across TFs, but also across DNA-binding domain families with distinct structural folds. Furthermore, these predicted binding regions can help identify TF binding sites that have a significant impact on target gene expression. Because the intrinsic property model allows prediction of binding regions across DNA-binding domain families, it is TF agnostic and likely describes general binding potential of TFs. Thus, our findings suggest that it is feasible to establish a TF agnostic model for identifying functional regulatory regions in potentially any sequenced genome.
Zing Tsung-Yeh Tsai
2015-08-01
Full Text Available Transcription factor (TF binding is determined by the presence of specific sequence motifs (SM and chromatin accessibility, where the latter is influenced by both chromatin state (CS and DNA structure (DS properties. Although SM, CS, and DS have been used to predict TF binding sites, a predictive model that jointly considers CS and DS has not been developed to predict either TF-specific binding or general binding properties of TFs. Using budding yeast as model, we found that machine learning classifiers trained with either CS or DS features alone perform better in predicting TF-specific binding compared to SM-based classifiers. In addition, simultaneously considering CS and DS further improves the accuracy of the TF binding predictions, indicating the highly complementary nature of these two properties. The contributions of SM, CS, and DS features to binding site predictions differ greatly between TFs, allowing TF-specific predictions and potentially reflecting different TF binding mechanisms. In addition, a "TF-agnostic" predictive model based on three DNA "intrinsic properties" (in silico predicted nucleosome occupancy, major groove geometry, and dinucleotide free energy that can be calculated from genomic sequences alone has performance that rivals the model incorporating experiment-derived data. This intrinsic property model allows prediction of binding regions not only across TFs, but also across DNA-binding domain families with distinct structural folds. Furthermore, these predicted binding regions can help identify TF binding sites that have a significant impact on target gene expression. Because the intrinsic property model allows prediction of binding regions across DNA-binding domain families, it is TF agnostic and likely describes general binding potential of TFs. Thus, our findings suggest that it is feasible to establish a TF agnostic model for identifying functional regulatory regions in potentially any sequenced genome.
The Chilo iridescent virus DNA polymerase promoter contains an essential AAAAT motif
Nalcacioglu, R.; Ince, I.A.; Vlak, J.M.; Demirbag, Z.; Oers, van M.M.
2007-01-01
The delayed-early DNA polymerase promoter of Chilo iridescent virus (CIV), officially known as Invertebrate iridescent virus, was fine mapped by constructing a series of increasing deletions and by introducing point mutations. The effects of these mutations were examined in a luciferase reporter
i-Motif of cytosine-rich human telomere DNA fragments containing natural base lesions
Dvořáková, Zuzana; Renčiuk, Daniel; Kejnovská, Iva; Školáková, Petra; Bednářová, Klára; Sagi, J.; Vorlíčková, Michaela
2018-01-01
Roč. 46, č. 4 (2018), s. 1624-1634 ISSN 1362-4962 R&D Projects: GA ČR(CZ) GA15-06785S; GA ČR GA17-12075S; GA ČR(CZ) GJ17-19170Y; GA MŠk EF15_003/0000477 Institutional support: RVO:68081707 Keywords : pair opening kinetics * g-quadruplex dna Subject RIV: CE - Biochemistry OBOR OECD: Biochemistry and molecular biology
Evaluation of the Stability of DNA i-Motifs in the Nuclei of Living Mammalian Cells
Dzatko, S.; Krafčíková, M.; Haensel-Hertsch, R.; Fessl, T.; Fiala, R.; Loja, T.; Krafčík, D.; Mergny, Jean-Louis; Foldynova-Trantirkova, Silvie; Trantírek, L.
2018-01-01
Roč. 57, č. 8 (2018), s. 2165-2169 ISSN 1433-7851 R&D Projects: GA MŠk EF15_003/0000477 Institutional support: RVO:68081707 Keywords : g-quadruplex * telomeric dna * base-pairs * molecular switch Subject RIV: CG - Electrochemistry OBOR OECD: Electrochemistry (dry cells, batteries, fuel cells, corrosion metals, electrolysis) Impact factor: 11.994, year: 2016
Tobiason, D M; Buchner, J M; Thiel, W H; Gernert, K M; Karls, A C
2001-02-01
Piv, a site-specific invertase from Moraxella lacunata, exhibits amino acid homology with the transposases of the IS110/IS492 family of insertion elements. The functions of conserved amino acid motifs that define this novel family of both transposases and site-specific recombinases (Piv/MooV family) were examined by mutagenesis of fully conserved amino acids within each motif in Piv. All Piv mutants altered in conserved residues were defective for in vivo inversion of the M. lacunata invertible DNA segment, but competent for in vivo binding to Piv DNA recognition sequences. Although the primary amino acid sequences of the Piv/MooV recombinases do not contain a conserved DDE motif, which defines the retroviral integrase/transposase (IN/Tnps) family, the predicted secondary structural elements of Piv align well with those of the IN/Tnps for which crystal structures have been determined. Molecular modelling of Piv based on these alignments predicts that E59, conserved as either E or D in the Piv/MooV family, forms a catalytic pocket with the conserved D9 and D101 residues. Analysis of Piv E59G confirms a role for E59 in catalysis of inversion. These results suggest that Piv and the related IS110/IS492 transposases mediate DNA recombination by a common mechanism involving a catalytic DED or DDD motif.
Murphy, Derek M
2009-01-01
BACKGROUND: Neuroblastoma, a cancer derived from precursor cells of the sympathetic nervous system, is a major cause of childhood cancer related deaths. The single most important prognostic indicator of poor clinical outcome in this disease is genomic amplification of MYCN, a member of a family of oncogenic transcription factors. METHODOLOGY: We applied MYCN chromatin immunoprecipitation to microarrays (ChIP-chip) using MYCN amplified\\/non-amplified cell lines as well as a conditional knockdown cell line to determine the distribution of MYCN binding sites within all annotated promoter regions. CONCLUSION: Assessment of E-box usage within consistently positive MYCN binding sites revealed a predominance for the CATGTG motif (p<0.0016), with significant enrichment of additional motifs CATTTG, CATCTG, CAACTG in the MYCN amplified state. For cell lines over-expressing MYCN, gene ontology analysis revealed enrichment for the binding of MYCN at promoter regions of numerous molecular functional groups including DNA helicases and mRNA transcriptional regulation. In order to evaluate MYCN binding with respect to other genomic features, we determined the methylation status of all annotated CpG islands and promoter sequences using methylated DNA immunoprecipitation (MeDIP). The integration of MYCN ChIP-chip and MeDIP data revealed a highly significant positive correlation between MYCN binding and DNA hypermethylation. This association was also detected in regions of hemizygous loss, indicating that the observed association occurs on the same homologue. In summary, these findings suggest that MYCN binding occurs more commonly at CATGTG as opposed to the classic CACGTG E-box motif, and that disease associated over expression of MYCN leads to aberrant binding to additional weaker affinity E-box motifs in neuroblastoma. The co-localization of MYCN binding and DNA hypermethylation further supports the dual role of MYCN, namely that of a classical transcription factor affecting the
Andersen, Sofie Dabros; Keijzers, Guido; Rampakakis, Emmanouil
2012-01-01
Human exonuclease 1 (hEXO1) acts directly in diverse DNA processing events, including replication, mismatch repair (MMR), and double strand break repair (DSBR), and it was also recently described to function as damage sensor and apoptosis inducer following DNA damage. In contrast, 14-3-3 proteins...... are specifically induced by replication inhibition leading to protein ubiquitination and degradation. We demonstrate direct and robust interaction between hEXO1 and six of the seven 14-3-3 isoforms in vitro, suggestive of a novel protein interaction network between DNA repair and cell cycle control. Binding...... and most likely a second unidentified binding motif. 14-3-3 associations do not appear to directly influence hEXO1 in vitro nuclease activity or in vitro DNA replication initiation. Moreover, specific phosphorylation variants, including hEXO1 S746A, are efficiently imported to the nucleus; to associate...
Selvam, Sangeetha; Mandal, Shankar; Mao, Hanbin
2017-09-05
The formation of biologically significant tetraplex DNA species, such as G-quadruplexes and i-motifs, is affected by chemical (ions and pH) and mechanical [superhelicity (σ) and molecular crowding] factors. Because of the extremely challenging experimental conditions, the relative importance of these factors on tetraplex folding is unknown. In this work, we quantitatively evaluated the chemical and mechanical effects on the population dynamics of DNA tetraplexes in the insulin-linked polymorphic region using magneto-optical tweezers. By mechanically unfolding individual tetraplexes, we found that ions and pH have the largest effects on the formation of the G-quadruplex and i-motif, respectively. Interestingly, superhelicity has the second largest effect followed by molecular crowding conditions. While chemical effects are specific to tetraplex species, mechanical factors have generic influences. The predominant effect of chemical factors can be attributed to the fact that they directly change the stability of a specific tetraplex, whereas the mechanical factors, superhelicity in particular, reduce the stability of the competing species by changing the kinetics of the melting and annealing of the duplex DNA template in a nonspecific manner. The substantial dependence of tetraplexes on superhelicity provides strong support that DNA tetraplexes can serve as topological sensors to modulate fundamental cellular processes such as transcription.
Stewart, Mikaela; Dunlap, Tori; Dourlain, Elizabeth; Grant, Bryce; McFail-Isom, Lori
2013-01-01
The fine conformational subtleties of DNA structure modulate many fundamental cellular processes including gene activation/repression, cellular division, and DNA repair. Most of these cellular processes rely on the conformational heterogeneity of specific DNA sequences. Factors including those structural characteristics inherent in the particular base sequence as well as those induced through interaction with solvent components combine to produce fine DNA structural variation including helical flexibility and conformation. Cation-pi interactions between solvent cations or their first hydration shell waters and the faces of DNA bases form sequence selectively and contribute to DNA structural heterogeneity. In this paper, we detect and characterize the binding patterns found in cation-pi interactions between solvent cations and DNA bases in a set of high resolution x-ray crystal structures. Specifically, we found that monovalent cations (Tl⁺) and the polarized first hydration shell waters of divalent cations (Mg²⁺, Ca²⁺) form cation-pi interactions with DNA bases stabilizing unstacked conformations. When these cation-pi interactions are combined with electrostatic interactions a pattern of specific binding motifs is formed within the grooves.
Hecker, Andreas; Brand, Luise H; Peter, Sébastien; Simoncello, Nathalie; Kilian, Joachim; Harter, Klaus; Gaudin, Valérie; Wanke, Dierk
2015-07-01
Polycomb-repressive complexes (PRCs) play key roles in development by repressing a large number of genes involved in various functions. Much, however, remains to be discovered about PRC-silencing mechanisms as well as their targeting to specific genomic regions. Besides other mechanisms, GAGA-binding factors in animals can guide PRC members in a sequence-specific manner to Polycomb-responsive DNA elements. Here, we show that the Arabidopsis (Arabidopsis thaliana) GAGA-motif binding factor protein basic pentacysteine6 (BPC6) interacts with like heterochromatin protein1 (LHP1), a PRC1 component, and associates with vernalization2 (VRN2), a PRC2 component, in vivo. By using a modified DNA-protein interaction enzyme-linked immunosorbant assay, we could show that BPC6 was required and sufficient to recruit LHP1 to GAGA motif-containing DNA probes in vitro. We also found that LHP1 interacts with VRN2 and, therefore, can function as a possible scaffold between BPC6 and VRN2. The lhp1-4 bpc4 bpc6 triple mutant displayed a pleiotropic phenotype, extreme dwarfism and early flowering, which disclosed synergistic functions of LHP1 and group II plant BPC members. Transcriptome analyses supported this synergy and suggested a possible function in the concerted repression of homeotic genes, probably through histone H3 lysine-27 trimethylation. Hence, our findings suggest striking similarities between animal and plant GAGA-binding factors in the recruitment of PRC1 and PRC2 components to Polycomb-responsive DNA element-like GAGA motifs, which must have evolved through convergent evolution. © 2015 American Society of Plant Biologists. All Rights Reserved.
Nakamura, Kenta; Katayama, Tsutomu
2010-04-01
Escherichia coli ATP-DnaA initiates chromosomal replication. For preventing extra-initiations, a complex of ADP-Hda and the DNA-loaded replicase clamp promotes DnaA-ATP hydrolysis, yielding inactive ADP-DnaA. However, the Hda-DnaA interaction mode remains unclear except that the Hda Box VII Arg finger (Arg-153) and DnaA sensor II Arg-334 within each AAA(+) domain are crucial for the DnaA-ATP hydrolysis. Here, we demonstrate that direct and functional interaction of ADP-Hda with DnaA requires the Hda residues Ser-152, Phe-118 and Asn-122 as well as Hda Arg-153 and DnaA Arg-334. Structural analyses suggest intermolecular interactions between Hda Ser-152 and DnaA Arg-334 and between Hda Phe-118 and the DnaA Walker B motif region, in addition to an intramolecular interaction between Hda Asn-122 and Arg-153. These interactions likely sustain a specific association of ADP-Hda and DnaA, promoting DnaA-ATP hydrolysis. Consistently, ATP-DnaA and ADP-DnaA interact with the ADP-Hda-DNA-clamp complex with similar affinities. Hda Phe-118 and Asn-122 are contained in the Box VI region, and their hydrophobic and electrostatic features are basically conserved in the corresponding residues of other AAA(+) proteins, suggesting a conserved role for Box VI. These findings indicate novel interaction mechanisms for Hda-DnaA as well as a potentially fundamental mechanism in AAA(+) protein interactions.
Willwand, Kurt; Moroianu, Adela; Hörlein, Rita; Stremmel, Wolfgang; Rommelaere, Jean
2002-07-01
The linear single-stranded DNA genome of minute virus of mice (MVM) is replicated via a double-stranded replicative form (RF) intermediate DNA. Amplification of viral RF DNA requires the structural transition of the right-end palindrome from a linear duplex into a double-hairpin structure, which serves for the repriming of unidirectional DNA synthesis. This conformational transition was found previously to be induced by the MVM nonstructural protein NS1. Elimination of the cognate NS1-binding sites, [ACCA](2), from the central region of the right-end palindrome next to the axis of symmetry was shown to markedly reduce the efficiency of hairpin-primed DNA replication, as measured in a reconstituted in vitro replication system. Thus, [ACCA](2) sequence motifs are essential as NS1-binding elements in the context of the structural transition of the right-end MVM palindrome.
Two sequence motifs from HIF-1α bind to the DNA-binding site of p53
Hansson, Lars O.; Friedler, Assaf; Freund, Stefan; Rüdiger, Stefan; Fersht, Alan R.
2002-01-01
There is evidence that hypoxia-inducible factor-1α (HIF-1α) interacts with the tumor suppressor p53. To characterize the putative interaction, we mapped the binding of the core domain of p53 (p53c) to an array of immobilized HIF-1α-derived peptides and found two peptide-sequence motifs that bound to p53c with micromolar affinity in solution. One sequence was adjacent to and the other coincided with the two proline residues of the oxygen-dependent degradation domain (P402 and P564) that act as...
Bucek, Pavel; Gargallo, Raimundo; Kudrev, Andrei
2010-01-01
The c-kit oncogene shows a cytosine-rich DNA region upstream of the transcription initiation site which forms an i-motif structure at slightly acidic pH values (Bucek et al. ). In the present study, the pH-induced formation of i-motif - forming sequences 5'-CCC CTC CCT CGC GCC CGC CCG-3' (ckitC1, native), 5'-CCC TTC CCT TGT GCC CGC CCG-3' (ckitC2) and 5'-CCCTT CCC TTTTT CCC T CCC T-3' (ckitC3) was studied by spectroscopic techniques, such as UV molecular absorption and circular dichroism (CD), in tandem with two multivariate data analysis methods, the hard modelling-based matrix method and the soft modelling-based MCR-ALS approach. Use of the hard chemical modelling enabled us to propose the equilibrium model, which describes spectral changes as functions of solution acidity. Additionally, the intrinsic protonation constant, K in , and the cooperativity parameters, ω c , and ω a , were calculated from the fitting procedure of the coupled CD and molecular absorption spectra. In the case of ckitC2 and ckitC3, the hard model correctly reproduced the spectral variations observed experimentally. The results indicated that folding was accompanied by a cooperative process, i.e. the enhancement of protonated structure stability upon protonation. In contrast, unfolding was accompanied by an anticooperative process. Finally, folding of the native sequence, ckitC1, seemed to follow a more complex mechanism.
Segura-Puimedon, Maria; Borralleras, Cristina; Pérez-Jurado, Luis A; Campuzano, Victoria
2013-09-25
General transcription factor (TFII-I) is a multi-functional protein involved in the transcriptional regulation of critical developmental genes, encoded by the GTF2I gene located on chromosome 7q11.23. Haploinsufficiency at GTF2I has been shown to play a major role in the neurodevelopmental features of Williams-Beuren syndrome (WBS). Identification of genes regulated by TFII-I is thus critical to detect molecular determinants of WBS as well as to identify potential new targets for specific pharmacological interventions, which are currently absent. We performed a microarray screening for transcriptional targets of TFII-I in cortex and embryonic cells from Gtf2i mutant and wild-type mice. Candidate genes with altered expression were verified using real-time PCR. A novel motif shared by deregulated genes was found and chromatin immunoprecipitation assays in embryonic fibroblasts were used to document in vitro TFII-I binding to this motif in the promoter regions of deregulated genes. Interestingly, the PI3K and TGFβ signaling pathways were over-represented among TFII-I-modulated genes. In this study we have found a highly conserved DNA element, common to a set of genes regulated by TFII-I, and identified and validated novel in vivo neuronal targets of this protein affecting the PI3K and TGFβ signaling pathways. Overall, our data further contribute to unravel the complexity and variability of the different genetic programs orchestrated by TFII-I. © 2013 Elsevier B.V. All rights reserved.
An Improved Fuzzy Based Missing Value Estimation in DNA Microarray Validated by Gene Ranking
Sujay Saha
2016-01-01
Full Text Available Most of the gene expression data analysis algorithms require the entire gene expression matrix without any missing values. Hence, it is necessary to devise methods which would impute missing data values accurately. There exist a number of imputation algorithms to estimate those missing values. This work starts with a microarray dataset containing multiple missing values. We first apply the modified version of the fuzzy theory based existing method LRFDVImpute to impute multiple missing values of time series gene expression data and then validate the result of imputation by genetic algorithm (GA based gene ranking methodology along with some regular statistical validation techniques, like RMSE method. Gene ranking, as far as our knowledge, has not been used yet to validate the result of missing value estimation. Firstly, the proposed method has been tested on the very popular Spellman dataset and results show that error margins have been drastically reduced compared to some previous works, which indirectly validates the statistical significance of the proposed method. Then it has been applied on four other 2-class benchmark datasets, like Colorectal Cancer tumours dataset (GDS4382, Breast Cancer dataset (GSE349-350, Prostate Cancer dataset, and DLBCL-FL (Leukaemia for both missing value estimation and ranking the genes, and the results show that the proposed method can reach 100% classification accuracy with very few dominant genes, which indirectly validates the biological significance of the proposed method.
Cotmore, S F; Christensen, J; Nüesch, J P; Tattersall, P
1995-03-01
A DNA fragment containing the minute virus of mice 3' replication origin was specifically coprecipitated in immune complexes containing the virally coded NS1, but not the NS2, polypeptide. Antibodies directed against the amino- or carboxy-terminal regions of NS1 precipitated the NS1-origin complexes, but antibodies directed against NS1 amino acids 284 to 459 blocked complex formation. Using affinity-purified histidine-tagged NS1 preparations, we have shown that the specific protein-DNA interaction is of moderate affinity, being stable in 0.1 M salt but rapidly lost at higher salt concentrations. In contrast, generalized (or nonspecific) DNA binding by NS1 could be demonstrated only in low salt. Addition of ATP or gamma S-ATP enhanced specific DNA binding by wild-type NS1 severalfold, but binding was lost under conditions which favored ATP hydrolysis. NS1 molecules with mutations in a critical lysine residue (amino acid 405) in the consensus ATP-binding site bound to the origin, but this binding could not be enhanced by ATP addition. DNase I protection assays carried out with wild-type NS1 in the presence of gamma S-ATP gave footprints which extended over 43 nucleotides on both DNA strands, from the middle of the origin bubble sequence to a position some 14 bp beyond the nick site. The DNA-binding site for NS1 was mapped to a 22-bp fragment from the middle of the 3' replication origin which contains the sequence ACCAACCA. This conforms to a reiterated motif (ACCA)2-3, which occurs, in more or less degenerate form, at many sites throughout the minute virus of mice genome (J. W. Bodner, Virus Genes 2:167-182, 1989). Insertion of a single copy of the sequence (ACCA)3 was shown to be sufficient to confer NS1 binding on an otherwise unrecognized plasmid fragment. The functions of NS1 in the viral life cycle are reevaluated in the light of this result.
Martin Převorovský
Full Text Available CSL (CBF1/RBP-Jκ/Suppressor of Hairless/LAG-1 transcription factors are the effector components of the Notch receptor signalling pathway, which is critical for metazoan development. The metazoan CSL proteins (class M can also function in a Notch-independent manner. Recently, two novel classes of CSL proteins, designated F1 and F2, have been identified in fungi. The role of the fungal CSL proteins is unclear, because the Notch pathway is not present in fungi. In fission yeast, the Cbf11 and Cbf12 CSL paralogs play antagonistic roles in cell adhesion and the coordination of cell and nuclear division. Unusually long N-terminal extensions are typical for fungal and invertebrate CSL family members. In this study, we investigate the functional significance of these extended N-termini of CSL proteins.We identify 15 novel CSL family members from 7 fungal species and conduct bioinformatic analyses of a combined dataset containing 34 fungal and 11 metazoan CSL protein sequences. We show that the long, non-conserved N-terminal tails of fungal CSL proteins are likely disordered and enriched in phosphorylation sites and PEST motifs. In a case study of Cbf12 (class F2, we provide experimental evidence that the protein is proteolytically processed and that the N-terminus inhibits the Cbf12-dependent DNA binding activity in an electrophoretic mobility shift assay.This study provides insight into the characteristics of the long N-terminal tails of fungal CSL proteins that may be crucial for controlling DNA-binding and CSL function. We propose that the regulation of DNA binding by Cbf12 via its N-terminal region represents an important means by which fission yeast strikes a balance between the class F1 and class F2 paralog activities. This mode of regulation might be shared with other CSL-positive fungi, some of which are relevant to human disease and biotechnology.
Hüntelmann, Bettina; Staab, Julia; Herrmann-Lingen, Christoph; Meyer, Thomas
2014-01-01
Binding to specific palindromic sequences termed gamma-activated sites (GAS) is a hallmark of gene activation by members of the STAT (signal transducer and activator of transcription) family of cytokine-inducible transcription factors. However, the precise molecular mechanisms involved in the signal-dependent finding of target genes by STAT dimers have not yet been very well studied. In this study, we have characterized a sequence motif in the STAT1 linker domain which is highly conserved among the seven human STAT proteins and includes surface-exposed residues in close proximity to the bound DNA. Using site-directed mutagenesis, we have demonstrated that a lysine residue in position 567 of the full-length molecule is required for GAS recognition. The substitution of alanine for this residue completely abolished both binding to high-affinity GAS elements and transcriptional activation of endogenous target genes in cells stimulated with interferon-γ (IFNγ), while the time course of transient nuclear accumulation and tyrosine phosphorylation were virtually unchanged. In contrast, two glutamic acid residues (E559 and E563) on each monomer are important for the dissociation of dimeric STAT1 from DNA and, when mutated to alanine, result in elevated levels of tyrosine-phosphorylated STAT1 as well as prolonged IFNγ-stimulated nuclear accumulation. In conclusion, our data indicate that the kinetics of signal-dependent GAS binding is determined by an array of glutamic acid residues located at the interior surface of the STAT1 dimer. These negatively charged residues appear to align the long axis of the STAT1 dimer in a position perpendicular to the DNA, thereby facilitating the interaction between lysine 567 and the phosphodiester backbone of a bound GAS element, which is a prerequisite for transient gene induction.
Guo, Xin; Wang, Xue-Mei; Wei, Shuai; Xiao, Shou-Jun
2018-04-12
Design rules for DNA nanotechnology have been mostly learnt from using linear single-stranded (ss) DNA as the source material. For example, the core structure of a typical DAO (double crossover, antiparallel, odd half-turns) tile for assembling 2D lattices is constructed from only two linear ss-oligonucleotide scaffold strands, similar to two ropes making a square knot. Herein, a new type of coupled DAO (cDAO) tile and 2D lattices of small circular ss-oligonucleotides as scaffold strands and linear ss-oligonucleotides as staple strands are reported. A cDAO tile of cDAO-c64nt (c64nt: circular 64 nucleotides), shaped as a solid parallelogram, is constructed with a Holliday junction (HJ) at the center and two HJs at both poles of a c64nt; similarly, cDAO-c84nt, shaped as a crossed quadrilateral composed of two congruent triangles, is formed with a HJ at the center and four three-way junctions at the corners of a c84nt. Perfect 2D lattices were assembled from cDAO tiles: infinite nanostructures of nanoribbons, nanotubes, and nanorings, and finite nanostructures. The structural relationship between the visible lattices imaged by AFM and the corresponding invisible secondary and tertiary molecular structures of HJs, inclination angle of hydrogen bonds against the double-helix axis, and the chirality of the tile can be interpreted very well. This work could shed new light on DNA nanotechnology with unique circular tiles. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Prasad, C. Krishna; Meyers, Craig; Zhan Dejin; You Hong; Chiriva-Internati, Maurizio; Mehta, Jawahar L.; Liu Yong; Hermonat, Paul L.
2003-01-01
Multiple epidemiologic studies show that adeno-associated virus (AAV) is negatively associated with cervical cancer (CX CA), a cancer which is positively associated with human papillomavirus (HPV) infection. Mechanisms for this correlation may be by Rep78's (AAV's major regulatory protein) ability to bind the HPV-16 p97 promoter DNA and inhibit transcription, to bind and interfere with the functions of the E7 oncoprotein of HPV-16, and to bind a variety of HPV-important cellular transcription factors such as Sp1 and TBP. c-Jun is another important cellular factor intimately linked to the HPV life cycle, as well as keratinocyte differentiation and skin development. Skin is the natural host tissue for both HPV and AAV. In this article it is demonstrated that Rep78 directly interacts with c-Jun, both in vitro and in vivo, as analyzed by Western blot, yeast two-hybrid cDNA, and electrophoretic mobility shift-supershift assay (EMSA supershift). Addition of anti-Rep78 antibodies inhibited the EMSA supershift. Investigating the biological implications of this interaction, Rep78 inhibited the c-Jun-dependent c-jun promoter in transient and stable chloramphenicol acetyl-transferase (CAT) assays. Rep78 also inhibited c-Jun-augmented c-jun promoter as well as the HPV-16 p97 promoter activity (also c-Jun regulated) in in vitro transcription assays in T47D nuclear extracts. Finally, the Rep78-c-Jun interaction mapped to the amino-half of Rep78. The ability of Rep78 to interact with c-Jun and down-regulate AP-1-dependent transcription suggests one more mechanism by which AAV may modulate the HPV life cycle and the carcinogenesis process
Rodr?guez, J?ssica; Mosquera, Jes?s; Couceiro, Jose R.; V?zquez, M. Eugenio; Mascare?as, Jos? L.
2015-01-01
We report the development of chimeric DNA binding peptides comprising a DNA binding fragment of natural transcription factors (the basic region of a bZIP protein or a monomeric zinc finger module) and an AT-Hook peptide motif. The resulting peptide conjugates display high DNA affinity and excellent sequence selectivity. Furthermore, the AT-Hook motif also favors the cell internalization of the conjugates.
Blatti, Charles; Sinha, Saurabh
2014-07-01
The Motif Enrichment Tool (MET) provides an online interface that enables users to find major transcriptional regulators of their gene sets of interest. MET searches the appropriate regulatory region around each gene and identifies which transcription factor DNA-binding specificities (motifs) are statistically overrepresented. Motif enrichment analysis is currently available for many metazoan species including human, mouse, fruit fly, planaria and flowering plants. MET also leverages high-throughput experimental data such as ChIP-seq and DNase-seq from ENCODE and ModENCODE to identify the regulatory targets of a transcription factor with greater precision. The results from MET are produced in real time and are linked to a genome browser for easy follow-up analysis. Use of the web tool is free and open to all, and there is no login requirement. ADDRESS: http://veda.cs.uiuc.edu/MET/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
Hiu-Kwan Chow
Full Text Available Minimalist hybrids comprising the DNA-binding domain of bHLH/PAS (basic-helix-loop-helix/Per-Arnt-Sim protein Arnt fused to the leucine zipper (LZ dimerization domain from bZIP (basic region-leucine zipper protein C/EBP were designed to bind the E-box DNA site, CACGTG, targeted by bHLHZ (basic-helix-loop-helix-zipper proteins Myc and Max, as well as the Arnt homodimer. The bHLHZ-like structure of ArntbHLH-C/EBP comprises the Arnt bHLH domain fused to the C/EBP LZ: i.e. swap of the 330 aa PAS domain for the 29 aa LZ. In the yeast one-hybrid assay (Y1H, transcriptional activation from the E-box was strong by ArntbHLH-C/EBP, and undetectable for the truncated ArntbHLH (PAS removed, as detected via readout from the HIS3 and lacZ reporters. In contrast, fluorescence anisotropy titrations showed affinities for the E-box with ArntbHLH-C/EBP and ArntbHLH comparable to other transcription factors (K(d 148.9 nM and 40.2 nM, respectively, but only under select conditions that maintained folded protein. Although in vivo yeast results and in vitro spectroscopic studies for ArntbHLH-C/EBP targeting the E-box correlate well, the same does not hold for ArntbHLH. As circular dichroism confirms that ArntbHLH-C/EBP is a much more strongly alpha-helical structure than ArntbHLH, we conclude that the nonfunctional ArntbHLH in the Y1H must be due to misfolding, leading to the false negative that this protein is incapable of targeting the E-box. Many experiments, including protein design and selections from large libraries, depend on protein domains remaining well-behaved in the nonnative experimental environment, especially small motifs like the bHLH (60-70 aa. Interestingly, a short helical LZ can serve as a folding- and/or solubility-enhancing tag, an important device given the focus of current research on exploration of vast networks of biomolecular interactions.
Smets, P
1995-01-01
We start by describing the nature of imperfect data, and giving an overview of the various models that have been proposed. Fuzzy sets theory is shown to be an extension of classical set theory, and as such has a proeminent role or modelling imperfect data. The mathematic of fuzzy sets theory is detailled, in particular the role of the triangular norms. The use of fuzzy sets theory in fuzzy logic and possibility theory,the nature of the generalized modus ponens and of the implication operator for approximate reasoning are analysed. The use of fuzzy logic is detailled for application oriented towards process control and database problems.
Rahonis, George
The theory of fuzzy recognizable languages over bounded distributive lattices is presented as a paradigm of recognizable formal power series. Due to the idempotency properties of bounded distributive lattices, the equality of fuzzy recognizable languages is decidable, the determinization of multi-valued automata is effective, and a pumping lemma exists. Fuzzy recognizable languages over finite and infinite words are expressively equivalent to sentences of the multi-valued monadic second-order logic. Fuzzy recognizability over bounded ℓ-monoids and residuated lattices is briefly reported. The chapter concludes with two applications of fuzzy recognizable languages to real world problems in medicine.
Relational Demonic Fuzzy Refinement
Fairouz Tchier
2014-01-01
Full Text Available We use relational algebra to define a refinement fuzzy order called demonic fuzzy refinement and also the associated fuzzy operators which are fuzzy demonic join (⊔fuz, fuzzy demonic meet (⊓fuz, and fuzzy demonic composition (□fuz. Our definitions and properties are illustrated by some examples using mathematica software (fuzzy logic.
Lu, Quan; Henderson, Eric
2000-01-01
G-DNA is a four-stranded DNA structure with diverse putative biological roles. We have previously purified and cloned a novel G-DNA-binding protein TGP1 from the ciliate Tetrahymena thermophila. Here we report the molecular cloning of TGP3, an additional G-DNA-binding protein from the same organism. The TGP3 cDNA encodes a 365 amino acid protein that is homologous to TGP1 (34% identity and 44% similarity). The proteins share a sequence pattern that contains two novel repetitive and homologous...
Abdul Hameed Q. A. Al-Tai
2011-01-01
Full Text Available The aim of this paper is to introduce and study the fuzzy neighborhood, the limit fuzzy number, the convergent fuzzy sequence, the bounded fuzzy sequence, and the Cauchy fuzzy sequence on the base which is adopted by Abdul Hameed (every real number r is replaced by a fuzzy number r¯ (either triangular fuzzy number or singleton fuzzy set (fuzzy point. And then, we will consider that some results respect effect of the upper sequence on the convergent fuzzy sequence, the bounded fuzzy sequence, and the Cauchy fuzzy sequence.
Juels, Ari
The purpose of this chapter is to introduce fuzzy commitment, one of the earliest and simplest constructions geared toward cryptography over noisy data. The chapter also explores applications of fuzzy commitment to two problems in data security: (1) secure management of biometrics, with a focus on iriscodes, and (2) use of knowledge-based authentication (i.e., personal questions) for password recovery.
Wu, R R; Couchman, J R
1997-01-01
Basement membranes contain several proteoglycans, and those bearing heparan sulfate glycosaminoglycans such as perlecan and agrin usually predominate. Most mammalian basement membranes also contain chondroitin sulfate, and a core protein, bamacan, has been partially characterized. We have now....... The protein sequence has low overall homology, apart from very small NH2- and COOH-terminal motifs. At the junctions between the distal globular domains and the coiled-coil regions lie glycosylation sites, with up to three N-linked oligosaccharides and probably three chondroitin chains. Three other Ser...
CompariMotif: quick and easy comparisons of sequence motifs.
Edwards, Richard J; Davey, Norman E; Shields, Denis C
2008-05-15
CompariMotif is a novel tool for making motif-motif comparisons, identifying and describing similarities between regular expression motifs. CompariMotif can identify a number of different relationships between motifs, including exact matches, variants of degenerate motifs and complex overlapping motifs. Motif relationships are scored using shared information content, allowing the best matches to be easily identified in large comparisons. Many input and search options are available, enabling a list of motifs to be compared to itself (to identify recurring motifs) or to datasets of known motifs. CompariMotif can be run online at http://bioware.ucd.ie/ and is freely available for academic use as a set of open source Python modules under a GNU General Public License from http://bioinformatics.ucd.ie/shields/software/comparimotif/
Breslin, Claire; Mani, Rajam S; Fanta, Mesfin; Hoch, Nicolas; Weinfeld, Michael; Caldecott, Keith W
2017-09-29
The scaffold protein X-ray repair cross-complementing 1 (XRCC1) interacts with multiple enzymes involved in DNA base excision repair and single-strand break repair (SSBR) and is important for genetic integrity and normal neurological function. One of the most important interactions of XRCC1 is that with polynucleotide kinase/phosphatase (PNKP), a dual-function DNA kinase/phosphatase that processes damaged DNA termini and that, if mutated, results in ataxia with oculomotor apraxia 4 (AOA4) and microcephaly with early-onset seizures and developmental delay (MCSZ). XRCC1 and PNKP interact via a high-affinity phosphorylation-dependent interaction site in XRCC1 and a forkhead-associated domain in PNKP. Here, we identified using biochemical and biophysical approaches a second PNKP interaction site in XRCC1 that binds PNKP with lower affinity and independently of XRCC1 phosphorylation. However, this interaction nevertheless stimulated PNKP activity and promoted SSBR and cell survival. The low-affinity interaction site required the highly conserved Rev1-interacting region (RIR) motif in XRCC1 and included three critical and evolutionarily invariant phenylalanine residues. We propose a bipartite interaction model in which the previously identified high-affinity interaction acts as a molecular tether, holding XRCC1 and PNKP together and thereby promoting the low-affinity interaction identified here, which then stimulates PNKP directly. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
Anker, Thomas Boysen; Kappel, Klemens; Eadie, Douglas
2012-01-01
as narrative material to communicate self-identity. Finally, (c) we propose that brands deliver fuzzy experiential promises through effectively motivating consumers to adopt and play a social role implicitly suggested and facilitated by the brand. A promise is an inherently ethical concept and the article...... concludes with an in-depth discussion of fuzzy brand promises as two-way ethical commitments that put requirements on both brands and consumers....
Large-scale discovery of promoter motifs in Drosophila melanogaster.
Thomas A Down
2007-01-01
Full Text Available A key step in understanding gene regulation is to identify the repertoire of transcription factor binding motifs (TFBMs that form the building blocks of promoters and other regulatory elements. Identifying these experimentally is very laborious, and the number of TFBMs discovered remains relatively small, especially when compared with the hundreds of transcription factor genes predicted in metazoan genomes. We have used a recently developed statistical motif discovery approach, NestedMICA, to detect candidate TFBMs from a large set of Drosophila melanogaster promoter regions. Of the 120 motifs inferred in our initial analysis, 25 were statistically significant matches to previously reported motifs, while 87 appeared to be novel. Analysis of sequence conservation and motif positioning suggested that the great majority of these discovered motifs are predictive of functional elements in the genome. Many motifs showed associations with specific patterns of gene expression in the D. melanogaster embryo, and we were able to obtain confident annotation of expression patterns for 25 of our motifs, including eight of the novel motifs. The motifs are available through Tiffin, a new database of DNA sequence motifs. We have discovered many new motifs that are overrepresented in D. melanogaster promoter regions, and offer several independent lines of evidence that these are novel TFBMs. Our motif dictionary provides a solid foundation for further investigation of regulatory elements in Drosophila, and demonstrates techniques that should be applicable in other species. We suggest that further improvements in computational motif discovery should narrow the gap between the set of known motifs and the total number of transcription factors in metazoan genomes.
Panopoulos, Athanasia D; Smith, Erin N; Arias, Angelo D; Shepard, Peter J; Hishida, Yuriko; Modesto, Veronica; Diffenderfer, Kenneth E; Conner, Clay; Biggs, William; Sandoval, Efren; D'Antonio-Chronowska, Agnieszka; Berggren, W Travis; Izpisua Belmonte, Juan Carlos; Frazer, Kelly A
2017-04-06
Induced pluripotent stem cells (iPSCs) show variable methylation patterns between lines, some of which reflect aberrant differences relative to embryonic stem cells (ESCs). To examine whether this aberrant methylation results from genetic variation or non-genetic mechanisms, we generated human iPSCs from monozygotic twins to investigate how genetic background, clone, and passage number contribute. We found that aberrantly methylated CpGs are enriched in regulatory regions associated with MYC protein motifs and affect gene expression. We classified differentially methylated CpGs as being associated with genetic and/or non-genetic factors (clone and passage), and we found that aberrant methylation preferentially occurs at CpGs associated with clone-specific effects. We further found that clone-specific effects play a strong role in recurrent aberrant methylation at specific CpG sites across different studies. Our results argue that a non-genetic biological mechanism underlies aberrant methylation in iPSCs and that it is likely based on a probabilistic process involving MYC that takes place during or shortly after reprogramming. Published by Elsevier Inc.
Harrit, Niels; Behrens, Carsten; Nielsen, P. E.
2001-01-01
The synthesis of a new versatile "Hoechst 33258-like" Boc-protected amino acid building block for peptide synthesis is described. It is demonstrated that this new ligand is an effective mimic of Hoechst 33258 in terms of DNA affinity and sequence specificity. Furthermore, this minor groove binder...
Zelenka, Jaroslav; Alán, Lukáš; Jabůrek, Martin; Ježek, Petr
2014-04-01
Based on the matrix-addressing sequence of mitochondrial ribosomal 5S-rRNA (termed MAM), which is naturally imported into mitochondria, we have constructed an import system for in vivo targeting of mitochondrial DNA (mtDNA) or mt-mRNA, in order to provide fluorescence hybridization of the desired sequences. Thus DNA oligonucleotides were constructed, containing the 5'-flanked T7 RNA polymerase promoter. After in vitro transcription and fluorescent labeling with Alexa Fluor(®) 488 or 647 dye, we obtained the fluorescent "L-ND5 probe" containing MAM and exemplar cargo, i.e., annealing sequence to a short portion of ND5 mRNA and to the light-strand mtDNA complementary to the heavy strand nd5 mt gene (5'-end 21 base pair sequence). For mitochondrial in vivo fluorescent hybridization, HepG2 cells were treated with dequalinium micelles, containing the fluorescent probes, bringing the probes proximally to the mitochondrial outer membrane and to the natural import system. A verification of import into the mitochondrial matrix of cultured HepG2 cells was provided by confocal microscopy colocalizations. Transfections using lipofectamine or probes without 5S-rRNA addressing MAM sequence or with MAM only were ineffective. Alternatively, the same DNA oligonucleotides with 5'-CACC overhang (substituting T7 promoter) were transcribed from the tetracycline-inducible pENTRH1/TO vector in human embryonic kidney T-REx®-293 cells, while mitochondrial matrix localization after import of the resulting unlabeled RNA was detected by PCR. The MAM-containing probe was then enriched by three-order of magnitude over the natural ND5 mRNA in the mitochondrial matrix. In conclusion, we present a proof-of-principle for mitochondrial in vivo hybridization and mitochondrial nucleic acid import.
Berks, G.; Keyserlingk, Diedrich Graf von; Jantzen, Jan
2000-01-01
A symptom is a condition indicating the presence of a disease, especially, when regarded as an aid in diagnosis.Symptoms are the smallest units indicating the existence of a disease. A syndrome on the other hand is an aggregate, set or cluster of concurrent symptoms which together indicate...... and clustering are the basic concerns in medicine. Classification depends on definitions of the classes and their required degree of participant of the elements in the cases' symptoms. In medicine imprecise conditions are the rule and therefore fuzzy methods are much more suitable than crisp ones. Fuzzy c......-mean clustering is an easy and well improved tool, which has been applied in many medical fields. We used c-mean fuzzy clustering after feature extraction from an aphasia database. Factor analysis was applied on a correlation matrix of 26 symptoms of language disorders and led to five factors. The factors...
T. Pathinathan
2015-01-01
Full Text Available In this paper we define diamond fuzzy number with the help of triangular fuzzy number. We include basic arithmetic operations like addition, subtraction of diamond fuzzy numbers with examples. We define diamond fuzzy matrix with some matrix properties. We have defined Nested diamond fuzzy number and Linked diamond fuzzy number. We have further classified Right Linked Diamond Fuzzy number and Left Linked Diamond Fuzzy number. Finally we have verified the arithmetic operations for the above mentioned types of Diamond Fuzzy Numbers.
Christensen, Line Hjorth
"Fuzzy stuff". Exploring the displacement of the design sketch. What kind of knowledge can historical sketches reveal when they have outplayed their primary instrumental function in the design process and are moved into a museum collection? What are the rational benefits of ‘archival displacement...
Rapin, Nicolas Philippe Jean-Pierre; Hoof, Ilka; Lund, Ole
2008-01-01
. Algorithms that predict which peptides MHC molecules bind have recently been developed and cover many different alleles, but the utility of these algorithms is hampered by the lack of tools for browsing and comparing the specificity of these molecules. We have, therefore, developed a web server, MHC motif....... A special viewing feature, MHC fight, allows for display of the specificity of two different MHC molecules side by side. We show how the web server can be used to discover and display surprising similarities as well as differences between MHC molecules within and between different species. The MHC motif...
Relational Demonic Fuzzy Refinement
Tchier, Fairouz
2014-01-01
We use relational algebra to define a refinement fuzzy order called demonic fuzzy refinement and also the associated fuzzy operators which are fuzzy demonic join $({\\bigsqcup }_{\\mathrm{\\text{f}}\\mathrm{\\text{u}}\\mathrm{\\text{z}}})$ , fuzzy demonic meet $({\\sqcap }_{\\mathrm{\\text{f}}\\mathrm{\\text{u}}\\mathrm{\\text{z}}})$ , and fuzzy demonic composition $({\\square }_{\\mathrm{\\text{f}}\\mathrm{\\text{u}}\\mathrm{\\text{z}}})$ . Our definitions and properties are illustrated by some examples using ma...
Gerevich, József
2015-01-01
One of the basic questions of the art psychology is whether a personal motif is to be found behind works of art and if so, how openly or indirectly it appears in the work itself. Analysis of examples and documents from the fine arts and literature allow us to conclude that the personal motif that can be identified by the viewer through symbols, at times easily at others with more difficulty, gives an emotional plus to the artistic product. The personal motif may be found in traumatic experiences, in communication to the model or with other emotionally important persons (mourning, disappointment, revenge, hatred, rivalry, revolt etc.), in self-searching, or self-analysis. The emotions are expressed in artistic activity either directly or indirectly. The intention nourished by the artist's identity (Kunstwollen) may stand in the way of spontaneous self-expression, channelling it into hidden paths. Under the influence of certain circumstances, the artist may arouse in the viewer, consciously or unconsciously, an illusionary, misleading image of himself. An examination of the personal motif is one of the important research areas of art therapy.
Edgardo Sepulveda
2017-11-01
Full Text Available The CrbS/R system is a two-component signal transduction system that regulates acetate utilization in Vibrio cholerae, P. aeruginosa, and P. entomophila. CrbS is a hybrid histidine kinase that belongs to a recently identified family, in which the signaling domain is fused to an SLC5 solute symporter domain through aSTAC domain. Upon activation by CrbS, CrbR activates transcription of the acs gene, which encodes an acetyl-CoA synthase (ACS, and the actP gene, which encodes an acetate/solute symporter. In this work, we characterized the CrbS/R system in Pseudomonas fluorescens SBW25. Through the quantitative proteome analysis of different mutants, we were able to identify a new set of genes under its control, which play an important role during growth on acetate. These results led us to the identification of a conserved DNA motif in the putative promoter region of acetate-utilization genes in the Gammaproteobacteria that is essential for the CrbR-mediated transcriptional activation of genes under acetate-utilizing conditions. Finally, we took advantage of the existence of a second SLC5-containing two-component signal transduction system in P. fluorescens, CbrA/B, to demonstrate that the activation of the response regulator by the histidine kinase is not dependent on substrate transport through the SLC5 domain.
Trbusek, Martin; Smardova, Jana; Malcikova, Jitka; Sebejova, Ludmila; Dobes, Petr; Svitakova, Miluse; Vranova, Vladimira; Mraz, Marek; Francova, Hana Skuhrova; Doubek, Michael; Brychtova, Yvona; Kuglik, Petr; Pospisilova, Sarka; Mayer, Jiri
2011-07-01
There is a distinct connection between TP53 defects and poor prognosis in chronic lymphocytic leukemia (CLL). It remains unclear whether patients harboring TP53 mutations represent a homogenous prognostic group. We evaluated the survival of patients with CLL and p53 defects identified at our institution by p53 yeast functional assay and complementary interphase fluorescence in situ hybridization analysis detecting del(17p) from 2003 to 2010. A defect of the TP53 gene was identified in 100 of 550 patients. p53 mutations were strongly associated with the deletion of 17p and the unmutated IgVH locus (both P DBMs), structurally well-defined parts of the DNA-binding domain, manifested a clearly shorter median survival (12 months) compared with patients having missense mutations outside DBMs (41 months; P = .002) or nonmissense alterations (36 months; P = .005). The difference in survival was similar in the analysis limited to patients harboring mutation accompanied by del(17p) and was also confirmed in a subgroup harboring TP53 defect at diagnosis. The patients with p53 DBMs mutation (at diagnosis) also manifested a short median time to first therapy (TTFT; 1 month). The substantially worse survival and the short TTFT suggest a strong mutated p53 gain-of-function phenotype in patients with CLL with DBMs mutations. The impact of p53 DBMs mutations on prognosis and response to therapy should be analyzed in investigative clinical trials.
Huang, Yong-Heng; Jankowski, Aleksander; Cheah, Kathryn S E; Prabhakar, Shyam; Jauch, Ralf
2015-05-27
The SOXE transcription factors SOX8, SOX9 and SOX10 are master regulators of mammalian development directing sex determination, gliogenesis, pancreas specification and neural crest development. We identified a set of palindromic SOX binding sites specifically enriched in regulatory regions of melanoma cells. SOXE proteins homodimerize on these sequences with high cooperativity. In contrast to other transcription factor dimers, which are typically rigidly spaced, SOXE group proteins can bind cooperatively at a wide range of dimer spacings. Using truncated forms of SOXE proteins, we show that a single dimerization (DIM) domain, that precedes the DNA binding high mobility group (HMG) domain, is sufficient for dimer formation, suggesting that DIM : HMG rather than DIM:DIM interactions mediate the dimerization. All SOXE members can also heterodimerize in this fashion, whereas SOXE heterodimers with SOX2, SOX4, SOX6 and SOX18 are not supported. We propose a structural model where SOXE-specific intramolecular DIM:HMG interactions are allosterically communicated to the HMG of juxtaposed molecules. Collectively, SOXE factors evolved a unique mode to combinatorially regulate their target genes that relies on a multifaceted interplay between the HMG and DIM domains. This property potentially extends further the diversity of target genes and cell-specific functions that are regulated by SOXE proteins.
Huang, Yong-Heng; Jankowski, Aleksander; Cheah, Kathryn S. E.; Prabhakar, Shyam; Jauch, Ralf
2015-01-01
The SOXE transcription factors SOX8, SOX9 and SOX10 are master regulators of mammalian development directing sex determination, gliogenesis, pancreas specification and neural crest development. We identified a set of palindromic SOX binding sites specifically enriched in regulatory regions of melanoma cells. SOXE proteins homodimerize on these sequences with high cooperativity. In contrast to other transcription factor dimers, which are typically rigidly spaced, SOXE group proteins can bind cooperatively at a wide range of dimer spacings. Using truncated forms of SOXE proteins, we show that a single dimerization (DIM) domain, that precedes the DNA binding high mobility group (HMG) domain, is sufficient for dimer formation, suggesting that DIM : HMG rather than DIM:DIM interactions mediate the dimerization. All SOXE members can also heterodimerize in this fashion, whereas SOXE heterodimers with SOX2, SOX4, SOX6 and SOX18 are not supported. We propose a structural model where SOXE-specific intramolecular DIM:HMG interactions are allosterically communicated to the HMG of juxtaposed molecules. Collectively, SOXE factors evolved a unique mode to combinatorially regulate their target genes that relies on a multifaceted interplay between the HMG and DIM domains. This property potentially extends further the diversity of target genes and cell-specific functions that are regulated by SOXE proteins. PMID:26013289
Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters
Farré Domènec
2007-12-01
Full Text Available Abstract Background The arrangement of regulatory motifs in gene promoters, or promoter architecture, is the result of mutation and selection processes that have operated over many millions of years. In mammals, tissue-specific transcriptional regulation is related to the presence of specific protein-interacting DNA motifs in gene promoters. However, little is known about the relative location and spacing of these motifs. To fill this gap, we have performed a systematic search for motifs that show significant bias at specific promoter locations in a large collection of housekeeping and tissue-specific genes. Results We observe that promoters driving housekeeping gene expression are enriched in particular motifs with strong positional bias, such as YY1, which are of little relevance in promoters driving tissue-specific expression. We also identify a large number of motifs that show positional bias in genes expressed in a highly tissue-specific manner. They include well-known tissue-specific motifs, such as HNF1 and HNF4 motifs in liver, kidney and small intestine, or RFX motifs in testis, as well as many potentially novel regulatory motifs. Based on this analysis, we provide predictions for 559 tissue-specific motifs in mouse gene promoters. Conclusion The study shows that motif positional bias is an important feature of mammalian proximal promoters and that it affects both general and tissue-specific motifs. Motif positional constraints define very distinct promoter architectures depending on breadth of expression and type of tissue.
Chen, Guanrong
2005-01-01
Introduction to Fuzzy Systems provides students with a self-contained introduction that requires no preliminary knowledge of fuzzy mathematics and fuzzy control systems theory. Simplified and readily accessible, it encourages both classroom and self-directed learners to build a solid foundation in fuzzy systems. After introducing the subject, the authors move directly into presenting real-world applications of fuzzy logic, revealing its practical flavor. This practicality is then followed by basic fuzzy systems theory. The book also offers a tutorial on fuzzy control theory, based mainly on th
Intuitionistic supra fuzzy topological spaces
Abbas, S.E.
2004-01-01
In this paper, We introduce an intuitionistic supra fuzzy closure space and investigate the relationship between intuitionistic supra fuzzy topological spaces and intuitionistic supra fuzzy closure spaces. Moreover, we can obtain intuitionistic supra fuzzy topological space induced by an intuitionistic fuzzy bitopological space. We study the relationship between intuitionistic supra fuzzy closure space and the intuitionistic supra fuzzy topological space induced by an intuitionistic fuzzy bitopological space
Xu, Zeshui
2014-01-01
This book provides the readers with a thorough and systematic introduction to hesitant fuzzy theory. It presents the most recent research results and advanced methods in the field. These includes: hesitant fuzzy aggregation techniques, hesitant fuzzy preference relations, hesitant fuzzy measures, hesitant fuzzy clustering algorithms and hesitant fuzzy multi-attribute decision making methods. Since its introduction by Torra and Narukawa in 2009, hesitant fuzzy sets have become more and more popular and have been used for a wide range of applications, from decision-making problems to cluster analysis, from medical diagnosis to personnel appraisal and information retrieval. This book offers a comprehensive report on the state-of-the-art in hesitant fuzzy sets theory and applications, aiming at becoming a reference guide for both researchers and practitioners in the area of fuzzy mathematics and other applied research fields (e.g. operations research, information science, management science and engineering) chara...
Carlsson, Christer; Fullér, Robert
2004-01-01
Fuzzy Logic in Management demonstrates that difficult problems and changes in the management environment can be more easily handled by bringing fuzzy logic into the practice of management. This explicit theme is developed through the book as follows: Chapter 1, "Management and Intelligent Support Technologies", is a short survey of management leadership and what can be gained from support technologies. Chapter 2, "Fuzzy Sets and Fuzzy Logic", provides a short introduction to fuzzy sets, fuzzy relations, the extension principle, fuzzy implications and linguistic variables. Chapter 3, "Group Decision Support Systems", deals with group decision making, and discusses methods for supporting the consensus reaching processes. Chapter 4, "Fuzzy Real Options for Strategic Planning", summarizes research where the fuzzy real options theory was implemented as a series of models. These models were thoroughly tested on a number of real life investments, and validated in 2001. Chapter 5, "Soft Computing Methods for Reducing...
Parallel motif extraction from very long sequences
Sahli, Majed
2013-01-01
Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern applications require mining of motifs in one very long sequence (i.e., in the order of several gigabytes). For this case, there exist statistical approaches that are fast but inaccurate; or combinatorial methods that are sound and complete. Unfortunately, existing combinatorial methods are serial and very slow. Consequently, they are limited to very short sequences (i.e., a few megabytes), small alphabets (typically 4 symbols for DNA sequences), and restricted types of motifs. This paper presents ACME, a combinatorial method for extracting motifs from a single very long sequence. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution. It also decomposes the search space in a smart way that allows scalability to thousands of processors with more than 90% speedup. ACME is the only method that: (i) scales to gigabyte-long sequences; (ii) handles large alphabets; (iii) supports interesting types of motifs with minimal additional cost; and (iv) is optimized for a variety of architectures such as multi-core systems, clusters in the cloud, and supercomputers. ACME reduces the extraction time for an exact-length query from 4 hours to 7 minutes on a typical workstation; handles 3 orders of magnitude longer sequences; and scales up to 16, 384 cores on a supercomputer. Copyright is held by the owner/author(s).
Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated
Down Thomas A
2010-09-01
Full Text Available Abstract Background DNA methylation can regulate gene expression by modulating the interaction between DNA and proteins or protein complexes. Conserved consensus motifs exist across the human genome ("predicted transcription factor binding sites": "predicted TFBS" but the large majority of these are proven by chromatin immunoprecipitation and high throughput sequencing (ChIP-seq not to be biological transcription factor binding sites ("empirical TFBS". We hypothesize that DNA methylation at conserved consensus motifs prevents promiscuous or disorderly transcription factor binding. Results Using genome-wide methylation maps of the human heart and sperm, we found that all conserved consensus motifs as well as the subset of those that reside outside CpG islands have an aggregate profile of hyper-methylation. In contrast, empirical TFBS with conserved consensus motifs have a profile of hypo-methylation. 40% of empirical TFBS with conserved consensus motifs resided in CpG islands whereas only 7% of all conserved consensus motifs were in CpG islands. Finally we further identified a minority subset of TF whose profiles are either hypo-methylated or neutral at their respective conserved consensus motifs implicating that these TF may be responsible for establishing or maintaining an un-methylated DNA state, or whose binding is not regulated by DNA methylation. Conclusions Our analysis supports the hypothesis that at least for a subset of TF, empirical binding to conserved consensus motifs genome-wide may be controlled by DNA methylation.
Why fuzzy controllers should be fuzzy
Nowe, A.
1996-01-01
Fuzzy controllers are usually looked at as crisp valued mappings especially when artificial intelligence learning techniques are used to build up the controller. By doing so the semantics of a fuzzy conclusion being a fuzzy restriction on the viable control actions is non-existing. In this paper the authors criticise from an approximation point of view using a fuzzy controller to express a crisp mapping does not seem the right way to go. Secondly it is illustrated that interesting information is contained in a fuzzy conclusion when indeed this conclusion is considered as a fuzzy restriction. This information turns out to be very valuable when viability problems are concerned, i.e. problems where the objective is to keep a system within predefined boundaries
Fuzzy Neuroidal Nets and Recurrent Fuzzy Computations
Wiedermann, Jiří
2001-01-01
Roč. 11, č. 6 (2001), s. 675-686 ISSN 1210-0552. [SOFSEM 2001 Workshop on Soft Computing. Piešťany, 29.11.2001-30.11.2001] R&D Projects: GA ČR GA201/00/1489; GA AV ČR KSK1019101 Institutional research plan: AV0Z1030915 Keywords : fuzzy computing * fuzzy neural nets * fuzzy Turing machines * non-uniform computational complexity Subject RIV: BA - General Mathematics
RNA motif search with data-driven element ordering.
Rampášek, Ladislav; Jimenez, Randi M; Lupták, Andrej; Vinař, Tomáš; Brejová, Broňa
2016-05-18
In this paper, we study the problem of RNA motif search in long genomic sequences. This approach uses a combination of sequence and structure constraints to uncover new distant homologs of known functional RNAs. The problem is NP-hard and is traditionally solved by backtracking algorithms. We have designed a new algorithm for RNA motif search and implemented a new motif search tool RNArobo. The tool enhances the RNAbob descriptor language, allowing insertions in helices, which enables better characterization of ribozymes and aptamers. A typical RNA motif consists of multiple elements and the running time of the algorithm is highly dependent on their ordering. By approaching the element ordering problem in a principled way, we demonstrate more than 100-fold speedup of the search for complex motifs compared to previously published tools. We have developed a new method for RNA motif search that allows for a significant speedup of the search of complex motifs that include pseudoknots. Such speed improvements are crucial at a time when the rate of DNA sequencing outpaces growth in computing. RNArobo is available at http://compbio.fmph.uniba.sk/rnarobo .
Fuzzy Itand#244; Integral Driven by a Fuzzy Brownian Motion
Didier Kumwimba Seya
2015-11-01
Full Text Available In this paper we take into account the fuzzy stochastic integral driven by fuzzy Brownian motion. To define the metric between two fuzzy numbers and to take into account the limit of a sequence of fuzzy numbers, we invoke the Hausdorff metric. First this fuzzy stochastic integral is constructed for fuzzy simple stochastic functions, then the construction is done for fuzzy stochastic integrable functions.
Rodríguez, J. Tinguaro; Franco de los Ríos, Camilo; Gómez, Daniel
2015-01-01
In this paper we want to stress the relevance of paired fuzzy sets, as already proposed in previous works of the authors, as a family of fuzzy sets that offers a unifying view for different models based upon the opposition of two fuzzy sets, simply allowing the existence of different types...
Mesiar, Radko
2005-01-01
Roč. 28, č. 156 (2005), s. 365-370 ISSN 0165-0114 R&D Projects: GA ČR(CZ) GA402/04/1026 Institutional research plan: CEZ:AV0Z10750506 Keywords : fuzzy measures * fuzzy integral * regular fuzzy integral Subject RIV: BA - General Mathematics Impact factor: 1.039, year: 2005
Fuzzy Graph Language Recognizability
Kalampakas , Antonios; Spartalis , Stefanos; Iliadis , Lazaros
2012-01-01
Part 5: Fuzzy Logic; International audience; Fuzzy graph language recognizability is introduced along the lines of the established theory of syntactic graph language recognizability by virtue of the algebraic structure of magmoids. The main closure properties of the corresponding class are investigated and several interesting examples of fuzzy graph languages are examined.
Intuitionistic Fuzzy Subbialgebras and Duality
Wenjuan Chen
2014-01-01
Full Text Available We investigate connections between bialgebras and Atanassov’s intuitionistic fuzzy sets. Firstly we define an intuitionistic fuzzy subbialgebra of a bialgebra with an intuitionistic fuzzy subalgebra structure and also with an intuitionistic fuzzy subcoalgebra structure. Secondly we investigate the related properties of intuitionistic fuzzy subbialgebras. Finally we prove that the dual of an intuitionistic fuzzy strong subbialgebra is an intuitionistic fuzzy strong subbialgebra.
A speedup technique for (l, d-motif finding algorithms
Dinh Hieu
2011-03-01
Full Text Available Abstract Background The discovery of patterns in DNA, RNA, and protein sequences has led to the solution of many vital biological problems. For instance, the identification of patterns in nucleic acid sequences has resulted in the determination of open reading frames, identification of promoter elements of genes, identification of intron/exon splicing sites, identification of SH RNAs, location of RNA degradation signals, identification of alternative splicing sites, etc. In protein sequences, patterns have proven to be extremely helpful in domain identification, location of protease cleavage sites, identification of signal peptides, protein interactions, determination of protein degradation elements, identification of protein trafficking elements, etc. Motifs are important patterns that are helpful in finding transcriptional regulatory elements, transcription factor binding sites, functional genomics, drug design, etc. As a result, numerous papers have been written to solve the motif search problem. Results Three versions of the motif search problem have been proposed in the literature: Simple Motif Search (SMS, (l, d-motif search (or Planted Motif Search (PMS, and Edit-distance-based Motif Search (EMS. In this paper we focus on PMS. Two kinds of algorithms can be found in the literature for solving the PMS problem: exact and approximate. An exact algorithm identifies the motifs always and an approximate algorithm may fail to identify some or all of the motifs. The exact version of PMS problem has been shown to be NP-hard. Exact algorithms proposed in the literature for PMS take time that is exponential in some of the underlying parameters. In this paper we propose a generic technique that can be used to speedup PMS algorithms. Conclusions We present a speedup technique that can be used on any PMS algorithm. We have tested our speedup technique on a number of algorithms. These experimental results show that our speedup technique is indeed very
Probabilistic fuzzy systems as additive fuzzy systems
Almeida, R.J.; Verbeek, N.; Kaymak, U.; Costa Sousa, da J.M.; Laurent, A.; Strauss, O.; Bouchon-Meunier, B.; Yager, R.
2014-01-01
Probabilistic fuzzy systems combine a linguistic description of the system behaviour with statistical properties of data. It was originally derived based on Zadeh’s concept of probability of a fuzzy event. Two possible and equivalent additive reasoning schemes were proposed, that lead to the
Optimality Conditions for Fuzzy Number Quadratic Programming with Fuzzy Coefficients
Xue-Gang Zhou
2014-01-01
Full Text Available The purpose of the present paper is to investigate optimality conditions and duality theory in fuzzy number quadratic programming (FNQP in which the objective function is fuzzy quadratic function with fuzzy number coefficients and the constraint set is fuzzy linear functions with fuzzy number coefficients. Firstly, the equivalent quadratic programming of FNQP is presented by utilizing a linear ranking function and the dual of fuzzy number quadratic programming primal problems is introduced. Secondly, we present optimality conditions for fuzzy number quadratic programming. We then prove several duality results for fuzzy number quadratic programming problems with fuzzy coefficients.
Countable Fuzzy Topological Space and Countable Fuzzy Topological Vector Space
Apu Kumar Saha
2015-06-01
Full Text Available This paper deals with countable fuzzy topological spaces, a generalization of the notion of fuzzy topological spaces. A collection of fuzzy sets F on a universe X forms a countable fuzzy topology if in the definition of a fuzzy topology, the condition of arbitrary supremum is relaxed to countable supremum. In this generalized fuzzy structure, the continuity of fuzzy functions and some other related properties are studied. Also the class of countable fuzzy topological vector spaces as a generalization of the class of fuzzy topological vector spaces has been introduced and investigated.
Recurrent fuzzy ranking methods
Hajjari, Tayebeh
2012-11-01
With the increasing development of fuzzy set theory in various scientific fields and the need to compare fuzzy numbers in different areas. Therefore, Ranking of fuzzy numbers plays a very important role in linguistic decision-making, engineering, business and some other fuzzy application systems. Several strategies have been proposed for ranking of fuzzy numbers. Each of these techniques has been shown to produce non-intuitive results in certain case. In this paper, we reviewed some recent ranking methods, which will be useful for the researchers who are interested in this area.
B Gibilisco, Michael; E Albert, Karen; N Mordeson, John; J Wierman, Mark; D Clark, Terry
2014-01-01
This book offers a comprehensive analysis of the social choice literature and shows, by applying fuzzy sets, how the use of fuzzy preferences, rather than that of strict ones, may affect the social choice theorems. To do this, the book explores the presupposition of rationality within the fuzzy framework and shows that the two conditions for rationality, completeness and transitivity, do exist with fuzzy preferences. Specifically, this book examines: the conditions under which a maximal set exists; the Arrow’s theorem; the Gibbard-Satterthwaite theorem; and the median voter theorem. After showing that a non-empty maximal set does exists for fuzzy preference relations, this book goes on to demonstrating the existence of a fuzzy aggregation rule satisfying all five Arrowian conditions, including non-dictatorship. While the Gibbard-Satterthwaite theorem only considers individual fuzzy preferences, this work shows that both individuals and groups can choose alternatives to various degrees, resulting in a so...
SSTRAP: A computational model for genomic motif discovery ...
Computational methods can potentially provide high-quality prediction of biological molecules such as DNA binding sites and Transcription factors and therefore reduce the time needed for experimental verification and challenges associated with experimental methods. These biological molecules or motifs have significant ...
Efficient motif finding algorithms for large-alphabet inputs
Pavlovic Vladimir
2010-10-01
Full Text Available Abstract Background We consider the problem of identifying motifs, recurring or conserved patterns, in the biological sequence data sets. To solve this task, we present a new deterministic algorithm for finding patterns that are embedded as exact or inexact instances in all or most of the input strings. Results The proposed algorithm (1 improves search efficiency compared to existing algorithms, and (2 scales well with the size of alphabet. On a synthetic planted DNA motif finding problem our algorithm is over 10× more efficient than MITRA, PMSPrune, and RISOTTO for long motifs. Improvements are orders of magnitude higher in the same setting with large alphabets. On benchmark TF-binding site problems (FNP, CRP, LexA we observed reduction in running time of over 12×, with high detection accuracy. The algorithm was also successful in rapidly identifying protein motifs in Lipocalin, Zinc metallopeptidase, and supersecondary structure motifs for Cadherin and Immunoglobin families. Conclusions Our algorithm reduces computational complexity of the current motif finding algorithms and demonstrate strong running time improvements over existing exact algorithms, especially in important and difficult cases of large-alphabet sequences.
Discovering Motifs in Biological Sequences Using the Micron Automata Processor.
Roy, Indranil; Aluru, Srinivas
2016-01-01
Finding approximately conserved sequences, called motifs, across multiple DNA or protein sequences is an important problem in computational biology. In this paper, we consider the (l, d) motif search problem of identifying one or more motifs of length l present in at least q of the n given sequences, with each occurrence differing from the motif in at most d substitutions. The problem is known to be NP-complete, and the largest solved instance reported to date is (26,11). We propose a novel algorithm for the (l,d) motif search problem using streaming execution over a large set of non-deterministic finite automata (NFA). This solution is designed to take advantage of the micron automata processor, a new technology close to deployment that can simultaneously execute multiple NFA in parallel. We demonstrate the capability for solving much larger instances of the (l, d) motif search problem using the resources available within a single automata processor board, by estimating run-times for problem instances (39,18) and (40,17). The paper serves as a useful guide to solving problems using this new accelerator technology.
Solving fully fuzzy transportation problem using pentagonal fuzzy numbers
Maheswari, P. Uma; Ganesan, K.
2018-04-01
In this paper, we propose a simple approach for the solution of fuzzy transportation problem under fuzzy environment in which the transportation costs, supplies at sources and demands at destinations are represented by pentagonal fuzzy numbers. The fuzzy transportation problem is solved without converting to its equivalent crisp form using a robust ranking technique and a new fuzzy arithmetic on pentagonal fuzzy numbers. To illustrate the proposed approach a numerical example is provided.
Introduction to Fuzzy Set Theory
Kosko, Bart
1990-01-01
An introduction to fuzzy set theory is described. Topics covered include: neural networks and fuzzy systems; the dynamical systems approach to machine intelligence; intelligent behavior as adaptive model-free estimation; fuzziness versus probability; fuzzy sets; the entropy-subsethood theorem; adaptive fuzzy systems for backing up a truck-and-trailer; product-space clustering with differential competitive learning; and adaptive fuzzy system for target tracking.
Decomposition of fuzzy continuity and fuzzy ideal continuity via fuzzy idealization
Zahran, A.M.; Abbas, S.E.; Abd El-baki, S.A.; Saber, Y.M.
2009-01-01
Recently, El-Naschie has shown that the notion of fuzzy topology may be relevant to quantum paretical physics in connection with string theory and E-infinity space time theory. In this paper, we study the concepts of r-fuzzy semi-I-open, r-fuzzy pre-I-open, r-fuzzy α-I-open and r-fuzzy β-I-open sets, which is properly placed between r-fuzzy openness and r-fuzzy α-I-openness (r-fuzzy pre-I-openness) sets regardless the fuzzy ideal topological space in Sostak sense. Moreover, we give a decomposition of fuzzy continuity, fuzzy ideal continuity and fuzzy ideal α-continuity, and obtain several characterization and some properties of these functions. Also, we investigate their relationship with other types of function.
Markowski, Adam S.; Mannan, M. Sam
2008-01-01
A risk matrix is a mechanism to characterize and rank process risks that are typically identified through one or more multifunctional reviews (e.g., process hazard analysis, audits, or incident investigation). This paper describes a procedure for developing a fuzzy risk matrix that may be used for emerging fuzzy logic applications in different safety analyses (e.g., LOPA). The fuzzification of frequency and severity of the consequences of the incident scenario are described which are basic inputs for fuzzy risk matrix. Subsequently using different design of risk matrix, fuzzy rules are established enabling the development of fuzzy risk matrices. Three types of fuzzy risk matrix have been developed (low-cost, standard, and high-cost), and using a distillation column case study, the effect of the design on final defuzzified risk index is demonstrated
Jantzen, Jan
The objective of this textbook is to acquire an understanding of the behaviour of fuzzy logic controllers. Under certain conditions a fuzzy controller is equivalent to a proportional-integral-derivative (PID) controller. Using that equivalence as a link, the book applies analysis methods from...... linear and nonlinear control theory. In the linear domain, PID tuning methods and stability analyses are transferred to linear fuzzy controllers. The Nyquist plot shows the robustness of different settings of the fuzzy gain parameters. As a result, a fuzzy controller is guaranteed to perform as well...... as any PID controller. In the nonlinear domain, the stability of four standard control surfaces is analysed by means of describing functions and Nyquist plots. The self-organizing controller (SOC) is shown to be a model reference adaptive controller. There is a possibility that a nonlinear fuzzy PID...
Lei, Qian
2017-01-01
This book offers a comprehensive and systematic review of the latest research findings in the area of intuitionistic fuzzy calculus. After introducing the intuitionistic fuzzy numbers’ operational laws and their geometrical and algebraic properties, the book defines the concept of intuitionistic fuzzy functions and presents the research on the derivative, differential, indefinite integral and definite integral of intuitionistic fuzzy functions. It also discusses some of the methods that have been successfully used to deal with continuous intuitionistic fuzzy information or data, which are different from the previous aggregation operators focusing on discrete information or data. Mainly intended for engineers and researchers in the fields of fuzzy mathematics, operations research, information science and management science, this book is also a valuable textbook for postgraduate and advanced undergraduate students alike.
FUZZY RINGS AND ITS PROPERTIES
Karyati Karyati
2017-01-01
One of algebraic structure that involves a binary operation is a group that is defined an un empty set (classical with an associative binary operation, it has identity elements and each element has an inverse. In the structure of the group known as the term subgroup, normal subgroup, subgroup and factor group homomorphism and its properties. Classical algebraic structure is developed to algebraic structure fuzzy by the researchers as an example semi group fuzzy and fuzzy group after fuzzy sets is introduced by L. A. Zadeh at 1965. It is inspired of writing about semi group fuzzy and group of fuzzy, a research on the algebraic structure of the ring is held with reviewing ring fuzzy, ideal ring fuzzy, homomorphism ring fuzzy and quotient ring fuzzy with its properties. The results of this study are obtained fuzzy properties of the ring, ring ideal properties fuzzy, properties of fuzzy ring homomorphism and properties of fuzzy quotient ring by utilizing a subset of a subset level and strong level as well as image and pre-image homomorphism fuzzy ring. Keywords: fuzzy ring, subset level, homomorphism fuzzy ring, fuzzy quotient ring
Metamathematics of fuzzy logic
Hájek, Petr
1998-01-01
This book presents a systematic treatment of deductive aspects and structures of fuzzy logic understood as many valued logic sui generis. Some important systems of real-valued propositional and predicate calculus are defined and investigated. The aim is to show that fuzzy logic as a logic of imprecise (vague) propositions does have well-developed formal foundations and that most things usually named `fuzzy inference' can be naturally understood as logical deduction.
Dotoli, M.; Jantzen, Jan
1999-01-01
The tutorial concerns automatic control of an inverted pendulum, especially rule based control by means of fuzzy logic. A ball balancer, implemented in a software simulator in Matlab, is used as a practical case study. The objectives of the tutorial are to teach the basics of fuzzy control......, and to show how to apply fuzzy logic in automatic control. The tutorial is distance learning, where students interact one-to-one with the teacher using e-mail....
T Atanassov, Krassimir
2017-01-01
The book offers a comprehensive survey of intuitionistic fuzzy logics. By reporting on both the author’s research and others’ findings, it provides readers with a complete overview of the field and highlights key issues and open problems, thus suggesting new research directions. Starting with an introduction to the basic elements of intuitionistic fuzzy propositional calculus, it then provides a guide to the use of intuitionistic fuzzy operators and quantifiers, and lastly presents state-of-the-art applications of intuitionistic fuzzy sets. The book is a valuable reference resource for graduate students and researchers alike.
Fuzzy control and identification
Lilly, John H
2010-01-01
This book gives an introduction to basic fuzzy logic and Mamdani and Takagi-Sugeno fuzzy systems. The text shows how these can be used to control complex nonlinear engineering systems, while also also suggesting several approaches to modeling of complex engineering systems with unknown models. Finally, fuzzy modeling and control methods are combined in the book, to create adaptive fuzzy controllers, ending with an example of an obstacle-avoidance controller for an autonomous vehicle using modus ponendo tollens logic.
Relations Among Some Fuzzy Entropy Formulae
卿铭
2004-01-01
Fuzzy entropy has been widely used to analyze and design fuzzy systems, and many fuzzy entropy formulae have been proposed. For further in-deepth analysis of fuzzy entropy, the axioms and some important formulae of fuzzy entropy are introduced. Some equivalence results among these fuzzy entropy formulae are proved, and it is shown that fuzzy entropy is a special distance measurement.
On Intuitionistic Fuzzy Filters of Intuitionistic Fuzzy Coframes
Rajesh K. Thumbakara
2013-01-01
Full Text Available Frame theory is the study of topology based on its open set lattice, and it was studied extensively by various authors. In this paper, we study quotients of intuitionistic fuzzy filters of an intuitionistic fuzzy coframe. The quotients of intuitionistic fuzzy filters are shown to be filters of the given intuitionistic fuzzy coframe. It is shown that the collection of all intuitionistic fuzzy filters of a coframe and the collection of all intutionistic fuzzy quotient filters of an intuitionistic fuzzy filter are coframes.
POWRS: position-sensitive motif discovery.
Ian W Davis
Full Text Available Transcription factors and the short, often degenerate DNA sequences they recognize are central regulators of gene expression, but their regulatory code is challenging to dissect experimentally. Thus, computational approaches have long been used to identify putative regulatory elements from the patterns in promoter sequences. Here we present a new algorithm "POWRS" (POsition-sensitive WoRd Set for identifying regulatory sequence motifs, specifically developed to address two common shortcomings of existing algorithms. First, POWRS uses the position-specific enrichment of regulatory elements near transcription start sites to significantly increase sensitivity, while providing new information about the preferred localization of those elements. Second, POWRS forgoes position weight matrices for a discrete motif representation that appears more resistant to over-generalization. We apply this algorithm to discover sequences related to constitutive, high-level gene expression in the model plant Arabidopsis thaliana, and then experimentally validate the importance of those elements by systematically mutating two endogenous promoters and measuring the effect on gene expression levels. This provides a foundation for future efforts to rationally engineer gene expression in plants, a problem of great importance in developing biotech crop varieties.BSD-licensed Python code at http://grassrootsbio.com/papers/powrs/.
Promoter Motifs in NCLDVs: An Evolutionary Perspective
Oliveira, Graziele Pereira; Andrade, Ana Cláudia dos Santos Pereira; Rodrigues, Rodrigo Araújo Lima; Arantes, Thalita Souza; Boratto, Paulo Victor Miranda; Silva, Ludmila Karen dos Santos; Dornas, Fábio Pio; Trindade, Giliane de Souza; Drumond, Betânia Paiva; La Scola, Bernard; Kroon, Erna Geessien; Abrahão, Jônatas Santos
2017-01-01
For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV), raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’) that could be evolved gradually by nucleotides’ gain and loss and point mutations. PMID:28117683
Promoter Motifs in NCLDVs: An Evolutionary Perspective
Graziele Pereira Oliveira
2017-01-01
Full Text Available For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV, raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’ that could be evolved gradually by nucleotides’ gain and loss and point mutations.
Uncovering transcriptional interactions via an adaptive fuzzy logic approach
Chen Chung-Ming
2009-12-01
Full Text Available Abstract Background To date, only a limited number of transcriptional regulatory interactions have been uncovered. In a pilot study integrating sequence data with microarray data, a position weight matrix (PWM performed poorly in inferring transcriptional interactions (TIs, which represent physical interactions between transcription factors (TF and upstream sequences of target genes. Inferring a TI means that the promoter sequence of a target is inferred to match the consensus sequence motifs of a potential TF, and their interaction type such as AT or RT is also predicted. Thus, a robust PWM (rPWM was developed to search for consensus sequence motifs. In addition to rPWM, one feature extracted from ChIP-chip data was incorporated to identify potential TIs under specific conditions. An interaction type classifier was assembled to predict activation/repression of potential TIs using microarray data. This approach, combining an adaptive (learning fuzzy inference system and an interaction type classifier to predict transcriptional regulatory networks, was named AdaFuzzy. Results AdaFuzzy was applied to predict TIs using real genomics data from Saccharomyces cerevisiae. Following one of the latest advances in predicting TIs, constrained probabilistic sparse matrix factorization (cPSMF, and using 19 transcription factors (TFs, we compared AdaFuzzy to four well-known approaches using over-representation analysis and gene set enrichment analysis. AdaFuzzy outperformed these four algorithms. Furthermore, AdaFuzzy was shown to perform comparably to 'ChIP-experimental method' in inferring TIs identified by two sets of large scale ChIP-chip data, respectively. AdaFuzzy was also able to classify all predicted TIs into one or more of the four promoter architectures. The results coincided with known promoter architectures in yeast and provided insights into transcriptional regulatory mechanisms. Conclusion AdaFuzzy successfully integrates multiple types of
Shawkat Alkhazaleh
2011-01-01
Full Text Available We introduce the concept of possibility fuzzy soft set and its operation and study some of its properties. We give applications of this theory in solving a decision-making problem. We also introduce a similarity measure of two possibility fuzzy soft sets and discuss their application in a medical diagnosis problem.
Properties of Bipolar Fuzzy Hypergraphs
Akram, M.; Dudek, W. A.; Sarwar, S.
2013-01-01
In this article, we apply the concept of bipolar fuzzy sets to hypergraphs and investigate some properties of bipolar fuzzy hypergraphs. We introduce the notion of $A-$ tempered bipolar fuzzy hypergraphs and present some of their properties. We also present application examples of bipolar fuzzy hypergraphs.
Regulation of TCF ETS-domain transcription factors by helix-loop-helix motifs.
Stinson, Julie; Inoue, Toshiaki; Yates, Paula; Clancy, Anne; Norton, John D; Sharrocks, Andrew D
2003-08-15
DNA binding by the ternary complex factor (TCF) subfamily of ETS-domain transcription factors is tightly regulated by intramolecular and intermolecular interactions. The helix-loop-helix (HLH)-containing Id proteins are trans-acting negative regulators of DNA binding by the TCFs. In the TCF, SAP-2/Net/ERP, intramolecular inhibition of DNA binding is promoted by the cis-acting NID region that also contains an HLH-like motif. The NID also acts as a transcriptional repression domain. Here, we have studied the role of HLH motifs in regulating DNA binding and transcription by the TCF protein SAP-1 and how Cdk-mediated phosphorylation affects the inhibitory activity of the Id proteins towards the TCFs. We demonstrate that the NID region of SAP-1 is an autoinhibitory motif that acts to inhibit DNA binding and also functions as a transcription repression domain. This region can be functionally replaced by fusion of Id proteins to SAP-1, whereby the Id moiety then acts to repress DNA binding in cis. Phosphorylation of the Ids by cyclin-Cdk complexes results in reduction in protein-protein interactions between the Ids and TCFs and relief of their DNA-binding inhibitory activity. In revealing distinct mechanisms through which HLH motifs modulate the activity of TCFs, our results therefore provide further insight into the role of HLH motifs in regulating TCF function and how the inhibitory properties of the trans-acting Id HLH proteins are themselves regulated by phosphorylation.
DNA nanotechnology: On-command molecular Trojans
Niemeyer, Christof M.
2017-12-01
Lipid-motif-decorated DNA nanocapsules filled with photoresponsive polymers are capable of delivering signalling molecules into target organisms for biological perturbations at high spatiotemporal resolution.
Statistical Methods for Fuzzy Data
Viertl, Reinhard
2011-01-01
Statistical data are not always precise numbers, or vectors, or categories. Real data are frequently what is called fuzzy. Examples where this fuzziness is obvious are quality of life data, environmental, biological, medical, sociological and economics data. Also the results of measurements can be best described by using fuzzy numbers and fuzzy vectors respectively. Statistical analysis methods have to be adapted for the analysis of fuzzy data. In this book, the foundations of the description of fuzzy data are explained, including methods on how to obtain the characterizing function of fuzzy m
Michael, Sushama; Travé, Gilles; Ramu, Chenna; Chica, Claudia; Gibson, Toby J
2008-02-15
KEN-box-mediated target selection is one of the mechanisms used in the proteasomal destruction of mitotic cell cycle proteins via the APC/C complex. While annotating the Eukaryotic Linear Motif resource (ELM, http://elm.eu.org/), we found that KEN motifs were significantly enriched in human protein entries with cell cycle keywords in the UniProt/Swiss-Prot database-implying that KEN-boxes might be more common than reported. Matches to short linear motifs in protein database searches are not, per se, significant. KEN-box enrichment with cell cycle Gene Ontology terms suggests that collectively these motifs are functional but does not prove that any given instance is so. Candidates were surveyed for native disorder prediction using GlobPlot and IUPred and for motif conservation in homologues. Among >25 strong new candidates, the most notable are human HIPK2, CHFR, CDC27, Dab2, Upf2, kinesin Eg5, DNA Topoisomerase 1 and yeast Cdc5 and Swi5. A similar number of weaker candidates were present. These proteins have yet to be tested for APC/C targeted destruction, providing potential new avenues of research.
Motif signatures of transcribed enhancers
Kleftogiannis, Dimitrios
2017-09-14
In mammalian cells, transcribed enhancers (TrEn) play important roles in the initiation of gene expression and maintenance of gene expression levels in spatiotemporal manner. One of the most challenging questions in biology today is how the genomic characteristics of enhancers relate to enhancer activities. This is particularly critical, as several recent studies have linked enhancer sequence motifs to specific functional roles. To date, only a limited number of enhancer sequence characteristics have been investigated, leaving space for exploring the enhancers genomic code in a more systematic way. To address this problem, we developed a novel computational method, TELS, aimed at identifying predictive cell type/tissue specific motif signatures. We used TELS to compile a comprehensive catalog of motif signatures for all known TrEn identified by the FANTOM5 consortium across 112 human primary cells and tissues. Our results confirm that distinct cell type/tissue specific motif signatures characterize TrEn. These signatures allow discriminating successfully a) TrEn from random controls, proxy of non-enhancer activity, and b) cell type/tissue specific TrEn from enhancers expressed and transcribed in different cell types/tissues. TELS codes and datasets are publicly available at http://www.cbrc.kaust.edu.sa/TELS.
Construction of fuzzy automata by fuzzy experiments
Mironov, A.
1994-01-01
The solving the problem of canonical realization of partial reaction morphisms (PRM) for automata in toposes and fuzzy automata is addressed. This problem extends the optimal construction problem for finite deterministic automata by experiments. In the present paper the conception of canonical realization of PRM for automata in toposes is introduced and the sufficient conditions for the existence of canonical realizations for PRM in toposes are presented. As a consequence of this result the existence of canonical realizations for PRM in the category of fuzzy sets over arbitrary complete chain is proven
Construction of fuzzy automata by fuzzy experiments
Mironov, A [Moscow Univ. (Russian Federation). Dept. of Mathematics and Computer Science
1994-12-31
The solving the problem of canonical realization of partial reaction morphisms (PRM) for automata in toposes and fuzzy automata is addressed. This problem extends the optimal construction problem for finite deterministic automata by experiments. In the present paper the conception of canonical realization of PRM for automata in toposes is introduced and the sufficient conditions for the existence of canonical realizations for PRM in toposes are presented. As a consequence of this result the existence of canonical realizations for PRM in the category of fuzzy sets over arbitrary complete chain is proven.
Creating Clinical Fuzzy Automata with Fuzzy Arden Syntax.
de Bruin, Jeroen S; Steltzer, Heinz; Rappelsberger, Andrea; Adlassnig, Klaus-Peter
2017-01-01
Formal constructs for fuzzy sets and fuzzy logic are incorporated into Arden Syntax version 2.9 (Fuzzy Arden Syntax). With fuzzy sets, the relationships between measured or observed data and linguistic terms are expressed as degrees of compatibility that model the unsharpness of the boundaries of linguistic terms. Propositional uncertainty due to incomplete knowledge of relationships between clinical linguistic concepts is modeled with fuzzy logic. Fuzzy Arden Syntax also supports the construction of fuzzy state monitors. The latter are defined as monitors that employ fuzzy automata to observe gradual transitions between different stages of disease. As a use case, we re-implemented FuzzyARDS, a previously published clinical monitoring system for patients suffering from acute respiratory distress syndrome (ARDS). Using the re-implementation as an example, we show how key concepts of fuzzy automata, i.e., fuzzy states and parallel fuzzy state transitions, can be implemented in Fuzzy Arden Syntax. The results showed that fuzzy state monitors can be implemented in a straightforward manner.
TRStalker: an efficient heuristic for finding fuzzy tandem repeats.
Pellegrini, Marco; Renda, M Elena; Vecchio, Alessio
2010-06-15
Genomes in higher eukaryotic organisms contain a substantial amount of repeated sequences. Tandem Repeats (TRs) constitute a large class of repetitive sequences that are originated via phenomena such as replication slippage and are characterized by close spatial contiguity. They play an important role in several molecular regulatory mechanisms, and also in several diseases (e.g. in the group of trinucleotide repeat disorders). While for TRs with a low or medium level of divergence the current methods are rather effective, the problem of detecting TRs with higher divergence (fuzzy TRs) is still open. The detection of fuzzy TRs is propaedeutic to enriching our view of their role in regulatory mechanisms and diseases. Fuzzy TRs are also important as tools to shed light on the evolutionary history of the genome, where higher divergence correlates with more remote duplication events. We have developed an algorithm (christened TRStalker) with the aim of detecting efficiently TRs that are hard to detect because of their inherent fuzziness, due to high levels of base substitutions, insertions and deletions. To attain this goal, we developed heuristics to solve a Steiner version of the problem for which the fuzziness is measured with respect to a motif string not necessarily present in the input string. This problem is akin to the 'generalized median string' that is known to be an NP-hard problem. Experiments with both synthetic and biological sequences demonstrate that our method performs better than current state of the art for fuzzy TRs and that the fuzzy TRs of the type we detect are indeed present in important biological sequences. TRStalker will be integrated in the web-based TRs Discovery Service (TReaDS) at bioalgo.iit.cnr.it. Supplementary data are available at Bioinformatics online.
Model predictive control using fuzzy decision functions
Kaymak, U.; Costa Sousa, da J.M.
2001-01-01
Fuzzy predictive control integrates conventional model predictive control with techniques from fuzzy multicriteria decision making, translating the goals and the constraints to predictive control in a transparent way. The information regarding the (fuzzy) goals and the (fuzzy) constraints of the
Approximations of Fuzzy Systems
Vinai K. Singh
2013-03-01
Full Text Available A fuzzy system can uniformly approximate any real continuous function on a compact domain to any degree of accuracy. Such results can be viewed as an existence of optimal fuzzy systems. Li-Xin Wang discussed a similar problem using Gaussian membership function and Stone-Weierstrass Theorem. He established that fuzzy systems, with product inference, centroid defuzzification and Gaussian functions are capable of approximating any real continuous function on a compact set to arbitrary accuracy. In this paper we study a similar approximation problem by using exponential membership functions
Govindarajan, T R; Padmanabhan, Pramod; Shreecharan, T
2010-01-01
We study polynomial deformations of the fuzzy sphere, specifically given by the cubic or the Higgs algebra. We derive the Higgs algebra by quantizing the Poisson structure on a surface in R 3 . We find that several surfaces, differing by constants, are described by the Higgs algebra at the fuzzy level. Some of these surfaces have a singularity and we overcome this by quantizing this manifold using coherent states for this nonlinear algebra. This is seen in the measure constructed from these coherent states. We also find the star product for this non-commutative algebra as a first step in constructing field theories on such fuzzy spaces.
REASONING IN THE FUZZY FRONT END OF INNOVATION:
Haase, Louise Møller; Laursen, Linda Nhu
2018-01-01
in the fuzzy front end is the reasoning process: innovation teams are faced with open-ended, ill-defined problems, where they need to make decisions about an unknown future but have only incomplete, ambiguous and contradicting insights available. We study the reasoning of experts, how they frame to make sense...... of all the insights and create a basis for decision-making in relation to a new project. Based on case studies of five innovative products from various industries, we propose a Product DNA model for understanding the reasoning in the fuzzy front end of innovation. The Product DNA Model explains how...... experts reason and what direct their reasoning....
Selection against spurious promoter motifs correlates withtranslational efficiency across bacteria
Froula, Jeffrey L.; Francino, M. Pilar
2007-05-01
Because binding of RNAP to misplaced sites could compromise the efficiency of transcription, natural selection for the optimization of gene expression should regulate the distribution of DNA motifs capable of RNAP-binding across the genome. Here we analyze the distribution of the -10 promoter motifs that bind the {sigma}{sup 70} subunit of RNAP in 42 bacterial genomes. We show that selection on these motifs operates across the genome, maintaining an over-representation of -10 motifs in regulatory sequences while eliminating them from the nonfunctional and, in most cases, from the protein coding regions. In some genomes, however, -10 sites are over-represented in the coding sequences; these sites could induce pauses effecting regulatory roles throughout the length of a transcriptional unit. For nonfunctional sequences, the extent of motif under-representation varies across genomes in a manner that broadly correlates with the number of tRNA genes, a good indicator of translational speed and growth rate. This suggests that minimizing the time invested in gene transcription is an important selective pressure against spurious binding. However, selection against spurious binding is detectable in the reduced genomes of host-restricted bacteria that grow at slow rates, indicating that components of efficiency other than speed may also be important. Minimizing the number of RNAP molecules per cell required for transcription, and the corresponding energetic expense, may be most relevant in slow growers. These results indicate that genome-level properties affecting the efficiency of transcription and translation can respond in an integrated manner to optimize gene expression. The detection of selection against promoter motifs in nonfunctional regions also implies that no sequence may evolve free of selective constraints, at least in the relatively small and unstructured genomes of bacteria.
Fuzzy Rough Ring and Its Prop erties
REN Bi-jun; FU Yan-ling
2013-01-01
This paper is devoted to the theories of fuzzy rough ring and its properties. The fuzzy approximation space generated by fuzzy ideals and the fuzzy rough approximation operators were proposed in the frame of fuzzy rough set model. The basic properties of fuzzy rough approximation operators were analyzed and the consistency between approximation operators and the binary operation of ring was discussed.
Bandemer, Hans
1992-01-01
Fuzzy data such as marks, scores, verbal evaluations, imprecise observations, experts' opinions and grey tone pictures, are quite common. In Fuzzy Data Analysis the authors collect their recent results providing the reader with ideas, approaches and methods for processing such data when looking for sub-structures in knowledge bases for an evaluation of functional relationship, e.g. in order to specify diagnostic or control systems. The modelling presented uses ideas from fuzzy set theory and the suggested methods solve problems usually tackled by data analysis if the data are real numbers. Fuzzy Data Analysis is self-contained and is addressed to mathematicians oriented towards applications and to practitioners in any field of application who have some background in mathematics and statistics.
Fuzzy stochastic multiobjective programming
Sakawa, Masatoshi; Katagiri, Hideki
2011-01-01
With a stress on interactive decision-making, this work breaks new ground by covering both the random nature of events related to environments, and the fuzziness of human judgements. The text runs from mathematical preliminaries to future research directions.
Klaus-Dietrich Kramer
2016-05-01
Full Text Available Many degree courses at technical universities include the subject of control systems engineering. As an addition to conventional approaches Fuzzy Control can be used to easily find control solutions for systems, even if they include nonlinearities. To support further educational training, models which represent a technical system to be controlled are required. These models have to represent the system in a transparent and easy cognizable manner. Furthermore, a programming tool is required that supports an easy Fuzzy Control development process, including the option to verify the results and tune the system behavior. In order to support the development process a graphical user interface is needed to display the fuzzy terms under real time conditions, especially with a debug system and trace functionality. The experiences with such a programming tool, the Fuzzy Control Design Tool (FHFCE Tool, and four fuzzy teaching models will be presented in this paper. The methodical and didactical objective in the utilization of these teaching models is to develop solution strategies using Computational Intelligence (CI applications for Fuzzy Controllers in order to analyze different algorithms of inference or defuzzyfication and to verify and tune those systems efficiently.
Fuzzy forecasting based on fuzzy-trend logical relationship groups.
Chen, Shyi-Ming; Wang, Nai-Yi
2010-10-01
In this paper, we present a new method to predict the Taiwan Stock Exchange Capitalization Weighted Stock Index (TAIEX) based on fuzzy-trend logical relationship groups (FTLRGs). The proposed method divides fuzzy logical relationships into FTLRGs based on the trend of adjacent fuzzy sets appearing in the antecedents of fuzzy logical relationships. First, we apply an automatic clustering algorithm to cluster the historical data into intervals of different lengths. Then, we define fuzzy sets based on these intervals of different lengths. Then, the historical data are fuzzified into fuzzy sets to derive fuzzy logical relationships. Then, we divide the fuzzy logical relationships into FTLRGs for forecasting the TAIEX. Moreover, we also apply the proposed method to forecast the enrollments and the inventory demand, respectively. The experimental results show that the proposed method gets higher average forecasting accuracy rates than the existing methods.
The Verrucomicrobia LexA-binding Motif: Insights into the Evolutionary Dynamics of the SOS Response
Ivan Erill
2016-07-01
Full Text Available The SOS response is the primary bacterial mechanism to address DNA damage, coordinating multiple cellular processes that include DNA repair, cell division and translesion synthesis. In contrast to other regulatory systems, the composition of the SOS genetic network and the binding motif of its transcriptional repressor, LexA, have been shown to vary greatly across bacterial clades, making it an ideal system to study the co-evolution of transcription factors and their regulons. Leveraging comparative genomics approaches and prior knowledge on the core SOS regulon, here we define the binding motif of the Verrucomicrobia, a recently described phylum of emerging interest due to its association with eukaryotic hosts. Site directed mutagenesis of the Verrucomicrobium spinosum recA promoter confirms that LexA binds a 14 bp palindromic motif with consensus sequence TGTTC-N4-GAACA. Computational analyses suggest that recognition of this novel motif is determined primarily by changes in base-contacting residues of the third alpha helix of the LexA helix-turn-helix DNA binding motif. In conjunction with comparative genomics analysis of the LexA regulon in the Verrucomicrobia phylum, electrophoretic shift assays reveal that LexA binds to operators in the promoter region of DNA repair genes and a mutagenesis cassette in this organism, and identify previously unreported components of the SOS response. The identification of tandem LexA-binding sites generating instances of other LexA-binding motifs in the lexA gene promoter of Verrucomicrobia species leads us to postulate a novel mechanism for LexA-binding motif evolution. This model, based on gene duplication, successfully addresses outstanding questions in the intricate co-evolution of the LexA protein, its binding motif and the regulatory network it controls.
The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response.
Erill, Ivan; Campoy, Susana; Kılıç, Sefa; Barbé, Jordi
2016-01-01
The SOS response is the primary bacterial mechanism to address DNA damage, coordinating multiple cellular processes that include DNA repair, cell division, and translesion synthesis. In contrast to other regulatory systems, the composition of the SOS genetic network and the binding motif of its transcriptional repressor, LexA, have been shown to vary greatly across bacterial clades, making it an ideal system to study the co-evolution of transcription factors and their regulons. Leveraging comparative genomics approaches and prior knowledge on the core SOS regulon, here we define the binding motif of the Verrucomicrobia, a recently described phylum of emerging interest due to its association with eukaryotic hosts. Site directed mutagenesis of the Verrucomicrobium spinosum recA promoter confirms that LexA binds a 14 bp palindromic motif with consensus sequence TGTTC-N4-GAACA. Computational analyses suggest that recognition of this novel motif is determined primarily by changes in base-contacting residues of the third alpha helix of the LexA helix-turn-helix DNA binding motif. In conjunction with comparative genomics analysis of the LexA regulon in the Verrucomicrobia phylum, electrophoretic shift assays reveal that LexA binds to operators in the promoter region of DNA repair genes and a mutagenesis cassette in this organism, and identify previously unreported components of the SOS response. The identification of tandem LexA-binding sites generating instances of other LexA-binding motifs in the lexA gene promoter of Verrucomicrobia species leads us to postulate a novel mechanism for LexA-binding motif evolution. This model, based on gene duplication, successfully addresses outstanding questions in the intricate co-evolution of the LexA protein, its binding motif and the regulatory network it controls.
Kopi dan Kakao dalam Kreasi Motif Batik Khas Jember
Irfa'ina Rohana Salma
2015-06-01
Full Text Available ABSTRAK Batik Jember selama ini identik dengan motif daun tembakau. Visualisasi daun tembakau dalam motif Batik Jember cukup lemah, yaitu kurang berkarakter karena motif yang muncul adalah seperti gambar daun pada umumnya. Oleh karena itu perlu diciptakan desain motif batik khas Jember yang sumber inspirasinya digali dari kekayaan alam lainnya dari Jember yang mempunyai bentuk spesifik dan karakteristik sehingga identitas motif bisa didapatkan dengan lebih kuat. Hasil alam khas Jember tersebut adalah kopi dan kakao. Tujuan penciptaan seni ini adalah untuk menghasilkan motif batik baru yang mempunyai ciri khas Jember. Metode yang digunakan yaitu pengumpulan data, pengamatan mendalam terhadap objek penciptaan, pengkajian sumber inspirasi, pembuatan desain motif, dan perwujudan menjadi batik. Dari penciptaan seni ini berhasil dikreasikan 6 (enam motif batik yaitu: (1 Motif Uwoh Kopi; (2 Motif Godong Kopi; (3 Motif Ceplok Kakao; (4 Motif Kakao Raja; (5 Motif Kakao Biru; dan (6 Motif Wiji Mukti. Berdasarkan hasil penilaian “Selera Estetika” diketahui bahwa motif yang paling banyak disukai adalah Motif Uwoh Kopi dan Motif Kakao Raja. Kata kunci: Motif Woh Kopi, Motif Godong Kopi, Motif Ceplok Kakao, Motif Kakao Raja, Motif Kakao Biru, Motif Wiji Mukti ABSTRACTBatik Jember is synonymous with tobacco leaf motif. Tobacco leaf shape is quite weak in the visual appearance characterized as that motif emerges like a picture of leaves in general. Therefore, it is necessary to create a distinctive design motif extracted from other natural resources of Jember that have specific shapes and characteristics that can be obtained as the stronger motif identity. The typical natural resources from Jember are coffee and cocoa. The purpose of the creation of this art is to produce the unique, creative and innovative batik and have specific characteristics of Jember. The method used are data collection, observation of the object, reviewing inspiration sources
Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium
Lynch Michael
2010-05-01
Full Text Available Abstract Background In protozoa, the identification of preserved motifs by comparative genomics is often impeded by difficulties to generate reliable alignments for non-coding sequences. Moreover, the evolutionary dynamics of regulatory elements in 3' untranslated regions (both in protozoa and metazoa remains a virtually unexplored issue. Results By screening Paramecium tetraurelia's 3' untranslated regions for 8-mers that were previously found to be preserved in mammalian 3' UTRs, we detect and characterize a motif that is distinctly conserved in the ribosomal genes of this ciliate. The motif appears to be conserved across Paramecium aurelia species but is absent from the ribosomal genes of four additional non-Paramecium species surveyed, including another ciliate, Tetrahymena thermophila. Motif-free ribosomal genes retain fewer paralogs in the genome and appear to be lost more rapidly relative to motif-containing genes. Features associated with the discovered preserved motif are consistent with this 8-mer playing a role in post-transcriptional regulation. Conclusions Our observations 1 shed light on the evolution of a putative regulatory motif across large phylogenetic distances; 2 are expected to facilitate the understanding of the modulation of ribosomal genes expression in Paramecium; and 3 reveal a largely unexplored--and presumably not restricted to Paramecium--association between the presence/absence of a DNA motif and the evolutionary fate of its host genes.
Catania, Francesco; Lynch, Michael
2010-05-04
In protozoa, the identification of preserved motifs by comparative genomics is often impeded by difficulties to generate reliable alignments for non-coding sequences. Moreover, the evolutionary dynamics of regulatory elements in 3' untranslated regions (both in protozoa and metazoa) remains a virtually unexplored issue. By screening Paramecium tetraurelia's 3' untranslated regions for 8-mers that were previously found to be preserved in mammalian 3' UTRs, we detect and characterize a motif that is distinctly conserved in the ribosomal genes of this ciliate. The motif appears to be conserved across Paramecium aurelia species but is absent from the ribosomal genes of four additional non-Paramecium species surveyed, including another ciliate, Tetrahymena thermophila. Motif-free ribosomal genes retain fewer paralogs in the genome and appear to be lost more rapidly relative to motif-containing genes. Features associated with the discovered preserved motif are consistent with this 8-mer playing a role in post-transcriptional regulation. Our observations 1) shed light on the evolution of a putative regulatory motif across large phylogenetic distances; 2) are expected to facilitate the understanding of the modulation of ribosomal genes expression in Paramecium; and 3) reveal a largely unexplored--and presumably not restricted to Paramecium--association between the presence/absence of a DNA motif and the evolutionary fate of its host genes.
Shapley's value for fuzzy games
Raúl Alvarado Sibaja
2009-02-01
Full Text Available This is the continuation of a previous article titled "Fuzzy Games", where I defined a new type of games based on the Multilinear extensions f, of characteristic functions and most of standard theorems for cooperative games also hold for this new type of games: The fuzzy games. Now we give some other properties and the extension of the definition of Shapley¨s Value for Fuzzy Games Keywords: game theory, fuzzy sets, multiattribute decisions.
Codon based co-occurrence network motifs in human mitochondria
Pramod Shinde
2017-10-01
Full Text Available The nucleotide polymorphism in human mitochondrial genome (mtDNA tolled by codon position bias plays an indispensable role in human population dispersion and expansion. Herein, we constructed genome-wide nucleotide co-occurrence networks using a massive data consisting of five different geographical regions and around 3000 samples for each region. We developed a powerful network model to describe complex mitochondrial evolutionary patterns between codon and non-codon positions. It was interesting to report a different evolution of Asian genomes than those of the rest which is divulged by network motifs. We found evidence that mtDNA undergoes substantial amounts of adaptive evolution, a finding which was supported by a number of previous studies. The dominance of higher order motifs indicated the importance of long-range nucleotide co-occurrence in genomic diversity. Most notably, codon motifs apparently underpinned the preferences among codon positions for co-evolution which is probably highly biased during the origin of the genetic code. Our analyses manifested that codon position co-evolution is very well conserved across human sub-populations and independently maintained within human sub-populations implying the selective role of evolutionary processes on codon position co-evolution. Ergo, this study provided a framework to investigate cooperative genomic interactions which are critical in underlying complex mitochondrial evolution.
Statistical tests to compare motif count exceptionalities
Vandewalle Vincent
2007-03-01
Full Text Available Abstract Background Finding over- or under-represented motifs in biological sequences is now a common task in genomics. Thanks to p-value calculation for motif counts, exceptional motifs are identified and represent candidate functional motifs. The present work addresses the related question of comparing the exceptionality of one motif in two different sequences. Just comparing the motif count p-values in each sequence is indeed not sufficient to decide if this motif is significantly more exceptional in one sequence compared to the other one. A statistical test is required. Results We develop and analyze two statistical tests, an exact binomial one and an asymptotic likelihood ratio test, to decide whether the exceptionality of a given motif is equivalent or significantly different in two sequences of interest. For that purpose, motif occurrences are modeled by Poisson processes, with a special care for overlapping motifs. Both tests can take the sequence compositions into account. As an illustration, we compare the octamer exceptionalities in the Escherichia coli K-12 backbone versus variable strain-specific loops. Conclusion The exact binomial test is particularly adapted for small counts. For large counts, we advise to use the likelihood ratio test which is asymptotic but strongly correlated with the exact binomial test and very simple to use.
CHARACTERIZATIONS OF FUZZY SOFT PRE SEPARATION AXIOMS
El-Latif, Alaa Mohamed Abd
2015-01-01
− The notions of fuzzy pre open soft sets and fuzzy pre closed soft sets were introducedby Abd El-latif et al. [2]. In this paper, we continue the study on fuzzy soft topological spaces andinvestigate the properties of fuzzy pre open soft sets, fuzzy pre closed soft sets and study variousproperties and notions related to these structures. In particular, we study the relationship betweenfuzzy pre soft interior fuzzy pre soft closure. Moreover, we study the properties of fuzzy soft pre regulars...
Wiese, Claudia; Hinz, John M; Tebbs, Robert S; Nham, Peter B; Urbin, Salustra S; Collins, David W; Thompson, Larry H; Schild, David
2006-01-01
In vertebrates, homologous recombinational repair (HRR) requires RAD51 and five RAD51 paralogs (XRCC2, XRCC3, RAD51B, RAD51C and RAD51D) that all contain conserved Walker A and B ATPase motifs. In human RAD51D we examined the requirement for these motifs in interactions with XRCC2 and RAD51C, and for survival of cells in response to DNA interstrand crosslinks (ICLs). Ectopic expression of wild-type human RAD51D or mutants having a non-functional A or B motif was used to test for complementation of a rad51d knockout hamster CHO cell line. Although A-motif mutants complement very efficiently, B-motif mutants do not. Consistent with these results, experiments using the yeast two- and three-hybrid systems show that the interactions between RAD51D and its XRCC2 and RAD51C partners also require a functional RAD51D B motif, but not motif A. Similarly, hamster Xrcc2 is unable to bind to the non-complementing human RAD51D B-motif mutants in co-immunoprecipitation assays. We conclude that a functional Walker B motif, but not A motif, is necessary for RAD51D's interactions with other paralogs and for efficient HRR. We present a model in which ATPase sites are formed in a bipartite manner between RAD51D and other RAD51 paralogs.
Wiese, Claudia; Hinz, John M.; Tebbs, Robert S.; Nham, Peter B.; Urbin, Salustra S.; Collins, David W.; Thompson, Larry H.; Schild, David
2006-04-21
In vertebrates, homologous recombinational repair (HRR) requires RAD51 and five RAD51 paralogs (XRCC2, XRCC3, RAD51B, RAD51C, and RAD51D) that all contain conserved Walker A and B ATPase motifs. In human RAD51D we examined the requirement for these motifs in interactions with XRCC2 and RAD51C, and for survival of cells in response to DNA interstrand crosslinks. Ectopic expression of wild type human RAD51D or mutants having a non-functional A or B motif was used to test for complementation of a rad51d knockout hamster CHO cell line. Although A-motif mutants complement very efficiently, B-motif mutants do not. Consistent with these results, experiments using the yeast two- and three-hybrid systems show that the interactions between RAD51D and its XRCC2 and RAD51C partners also require a functional RAD51D B motif, but not motif A. Similarly, hamster Xrcc2 is unable to bind to the non-complementing human RAD51D B-motif mutants in co-immunoprecipitation assays. We conclude that a functional Walker B motif, but not A motif, is necessary for RAD51D's interactions with other paralogs and for efficient HRR. We present a model in which ATPase sites are formed in a bipartite manner between RAD51D and other RAD51 paralogs.
A neural fuzzy controller learning by fuzzy error propagation
Nauck, Detlef; Kruse, Rudolf
1992-01-01
In this paper, we describe a procedure to integrate techniques for the adaptation of membership functions in a linguistic variable based fuzzy control environment by using neural network learning principles. This is an extension to our work. We solve this problem by defining a fuzzy error that is propagated back through the architecture of our fuzzy controller. According to this fuzzy error and the strength of its antecedent each fuzzy rule determines its amount of error. Depending on the current state of the controlled system and the control action derived from the conclusion, each rule tunes the membership functions of its antecedent and its conclusion. By this we get an unsupervised learning technique that enables a fuzzy controller to adapt to a control task by knowing just about the global state and the fuzzy error.
The foundations of fuzzy control
Lewis, Harold W
1997-01-01
Harold Lewis applied a cross-disciplinary approach in his highly accessible discussion of fuzzy control concepts. With the aid of fifty-seven illustrations, he thoroughly presents a unique mathematical formalism to explain the workings of the fuzzy inference engine and a novel test plant used in the research. Additionally, the text posits a new viewpoint on why fuzzy control is more popular in some countries than in others. A direct and original view of Japanese thinking on fuzzy control methods, based on the author's personal knowledge of - and association with - Japanese fuzzy research, is also included.
Abbas Parchami
2016-09-01
Full Text Available Such as other statistical problems, we may confront with uncertain and fuzzy concepts in quality control. One particular case in process capability analysis is a situation in which specification limits are two fuzzy sets. In such a uncertain and vague environment, the produced product is not qualified with a two-valued Boolean view, but to some degree depending on the decision-maker strictness and the quality level of the produced product. This matter can be cause to a rational decision-making on the quality of the production line. First, a comprehensive approach is presented in this paper for modeling the fuzzy quality concept. Then, motivations and advantages of applying this flexible approach instead of using classical quality are mentioned.
BayesMotif: de novo protein sorting motif discovery from impure datasets.
Hu, Jianjun; Zhang, Fan
2010-01-18
Protein sorting is the process that newly synthesized proteins are transported to their target locations within or outside of the cell. This process is precisely regulated by protein sorting signals in different forms. A major category of sorting signals are amino acid sub-sequences usually located at the N-terminals or C-terminals of protein sequences. Genome-wide experimental identification of protein sorting signals is extremely time-consuming and costly. Effective computational algorithms for de novo discovery of protein sorting signals is needed to improve the understanding of protein sorting mechanisms. We formulated the protein sorting motif discovery problem as a classification problem and proposed a Bayesian classifier based algorithm (BayesMotif) for de novo identification of a common type of protein sorting motifs in which a highly conserved anchor is present along with a less conserved motif regions. A false positive removal procedure is developed to iteratively remove sequences that are unlikely to contain true motifs so that the algorithm can identify motifs from impure input sequences. Experiments on both implanted motif datasets and real-world datasets showed that the enhanced BayesMotif algorithm can identify anchored sorting motifs from pure or impure protein sequence dataset. It also shows that the false positive removal procedure can help to identify true motifs even when there is only 20% of the input sequences containing true motif instances. We proposed BayesMotif, a novel Bayesian classification based algorithm for de novo discovery of a special category of anchored protein sorting motifs from impure datasets. Compared to conventional motif discovery algorithms such as MEME, our algorithm can find less-conserved motifs with short highly conserved anchors. Our algorithm also has the advantage of easy incorporation of additional meta-sequence features such as hydrophobicity or charge of the motifs which may help to overcome the limitations of
Fitness for synchronization of network motifs
Vega, Y.M.; Vázquez-Prada, M.; Pacheco, A.F.
2004-01-01
We study the synchronization of Kuramoto's oscillators in small parts of networks known as motifs. We first report on the system dynamics for the case of a scale-free network and show the existence of a non-trivial critical point. We compute the probability that network motifs synchronize, and fi...... that the fitness for synchronization correlates well with motifs interconnectedness and structural complexity. Possible implications for present debates about network evolution in biological and other systems are discussed....
Fu-Gui Shi
2010-01-01
Full Text Available The notion of (L,M-fuzzy σ-algebras is introduced in the lattice value fuzzy set theory. It is a generalization of Klement's fuzzy σ-algebras. In our definition of (L,M-fuzzy σ-algebras, each L-fuzzy subset can be regarded as an L-measurable set to some degree.
The first order fuzzy predicate logic (I)
Sheng, Y.M.
1986-01-01
Some analysis tools of fuzzy measures, Sugeno's integrals, etc. are introduced into the semantic of the first order predicate logic to explain the concept of fuzzy quantifiers. The truth value of a fuzzy quantification proposition is represented by Sugeno's integral. With this framework, several important notions of formation rules, fuzzy valutions and fuzzy validity are discussed
Seeman, Nadrian C.; Sleiman, Hanadi F.
2018-01-01
DNA is the molecule that stores and transmits genetic information in biological systems. The field of DNA nanotechnology takes this molecule out of its biological context and uses its information to assemble structural motifs and then to connect them together. This field has had a remarkable impact on nanoscience and nanotechnology, and has been revolutionary in our ability to control molecular self-assembly. In this Review, we summarize the approaches used to assemble DNA nanostructures and examine their emerging applications in areas such as biophysics, diagnostics, nanoparticle and protein assembly, biomolecule structure determination, drug delivery and synthetic biology. The introduction of orthogonal interactions into DNA nanostructures is discussed, and finally, a perspective on the future directions of this field is presented.
A Novel Protein Interaction between Nucleotide Binding Domain of Hsp70 and p53 Motif
Asita Elengoe
2015-01-01
Full Text Available Currently, protein interaction of Homo sapiens nucleotide binding domain (NBD of heat shock 70 kDa protein (PDB: 1HJO with p53 motif remains to be elucidated. The NBD-p53 motif complex enhances the p53 stabilization, thereby increasing the tumor suppression activity in cancer treatment. Therefore, we identified the interaction between NBD and p53 using STRING version 9.1 program. Then, we modeled the three-dimensional structure of p53 motif through homology modeling and determined the binding affinity and stability of NBD-p53 motif complex structure via molecular docking and dynamics (MD simulation. Human DNA binding domain of p53 motif (SCMGGMNR retrieved from UniProt (UniProtKB: P04637 was docked with the NBD protein, using the Autodock version 4.2 program. The binding energy and intermolecular energy for the NBD-p53 motif complex were −0.44 Kcal/mol and −9.90 Kcal/mol, respectively. Moreover, RMSD, RMSF, hydrogen bonds, salt bridge, and secondary structure analyses revealed that the NBD protein had a strong bond with p53 motif and the protein-ligand complex was stable. Thus, the current data would be highly encouraging for designing Hsp70 structure based drug in cancer therapy.
A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data.
Tran, Ngoc Tam L; Huang, Chun-Hsi
2014-02-20
ChIP-Seq (chromatin immunoprecipitation sequencing) has provided the advantage for finding motifs as ChIP-Seq experiments narrow down the motif finding to binding site locations. Recent motif finding tools facilitate the motif detection by providing user-friendly Web interface. In this work, we reviewed nine motif finding Web tools that are capable for detecting binding site motifs in ChIP-Seq data. We showed each motif finding Web tool has its own advantages for detecting motifs that other tools may not discover. We recommended the users to use multiple motif finding Web tools that implement different algorithms for obtaining significant motifs, overlapping resemble motifs, and non-overlapping motifs. Finally, we provided our suggestions for future development of motif finding Web tool that better assists researchers for finding motifs in ChIP-Seq data.
MSDmotif: exploring protein sites and motifs
Henrick Kim
2008-07-01
Full Text Available Abstract Background Protein structures have conserved features – motifs, which have a sufficient influence on the protein function. These motifs can be found in sequence as well as in 3D space. Understanding of these fragments is essential for 3D structure prediction, modelling and drug-design. The Protein Data Bank (PDB is the source of this information however present search tools have limited 3D options to integrate protein sequence with its 3D structure. Results We describe here a web application for querying the PDB for ligands, binding sites, small 3D structural and sequence motifs and the underlying database. Novel algorithms for chemical fragments, 3D motifs, ϕ/ψ sequences, super-secondary structure motifs and for small 3D structural motif associations searches are incorporated. The interface provides functionality for visualization, search criteria creation, sequence and 3D multiple alignment options. MSDmotif is an integrated system where a results page is also a search form. A set of motif statistics is available for analysis. This set includes molecule and motif binding statistics, distribution of motif sequences, occurrence of an amino-acid within a motif, correlation of amino-acids side-chain charges within a motif and Ramachandran plots for each residue. The binding statistics are presented in association with properties that include a ligand fragment library. Access is also provided through the distributed Annotation System (DAS protocol. An additional entry point facilitates XML requests with XML responses. Conclusion MSDmotif is unique by combining chemical, sequence and 3D data in a single search engine with a range of search and visualisation options. It provides multiple views of data found in the PDB archive for exploring protein structures.
Chilton, Scott S; Falbel, Tanya G; Hromada, Susan; Burton, Briana M
2017-08-01
Genetic competence is a process in which cells are able to take up DNA from their environment, resulting in horizontal gene transfer, a major mechanism for generating diversity in bacteria. Many bacteria carry homologs of the central DNA uptake machinery that has been well characterized in Bacillus subtilis It has been postulated that the B. subtilis competence helicase ComFA belongs to the DEAD box family of helicases/translocases. Here, we made a series of mutants to analyze conserved amino acid motifs in several regions of B. subtilis ComFA. First, we confirmed that ComFA activity requires amino acid residues conserved among the DEAD box helicases, and second, we show that a zinc finger-like motif consisting of four cysteines is required for efficient transformation. Each cysteine in the motif is important, and mutation of at least two of the cysteines dramatically reduces transformation efficiency. Further, combining multiple cysteine mutations with the helicase mutations shows an additive phenotype. Our results suggest that the helicase and metal binding functions are two distinct activities important for ComFA function during transformation. IMPORTANCE ComFA is a highly conserved protein that has a role in DNA uptake during natural competence, a mechanism for horizontal gene transfer observed in many bacteria. Investigation of the details of the DNA uptake mechanism is important for understanding the ways in which bacteria gain new traits from their environment, such as drug resistance. To dissect the role of ComFA in the DNA uptake machinery, we introduced point mutations into several motifs in the protein sequence. We demonstrate that several amino acid motifs conserved among ComFA proteins are important for efficient transformation. This report is the first to demonstrate the functional requirement of an amino-terminal cysteine motif in ComFA. Copyright © 2017 American Society for Microbiology.
Fuzzy efficiency without convexity
Hougaard, Jens Leth; Balezentis, Tomas
2014-01-01
approach builds directly upon the definition of Farrell's indexes of technical efficiency used in crisp FDH. Therefore we do not require the use of fuzzy programming techniques but only utilize ranking probabilities of intervals as well as a related definition of dominance between pairs of intervals. We...
Neuro-fuzzy system modeling based on automatic fuzzy clustering
Yuangang TANG; Fuchun SUN; Zengqi SUN
2005-01-01
A neuro-fuzzy system model based on automatic fuzzy clustering is proposed.A hybrid model identification algorithm is also developed to decide the model structure and model parameters.The algorithm mainly includes three parts:1) Automatic fuzzy C-means (AFCM),which is applied to generate fuzzy rules automatically,and then fix on the size of the neuro-fuzzy network,by which the complexity of system design is reducesd greatly at the price of the fitting capability;2) Recursive least square estimation (RLSE).It is used to update the parameters of Takagi-Sugeno model,which is employed to describe the behavior of the system;3) Gradient descent algorithm is also proposed for the fuzzy values according to the back propagation algorithm of neural network.Finally,modeling the dynamical equation of the two-link manipulator with the proposed approach is illustrated to validate the feasibility of the method.
Hierarchical type-2 fuzzy aggregation of fuzzy controllers
Cervantes, Leticia
2016-01-01
This book focuses on the fields of fuzzy logic, granular computing and also considering the control area. These areas can work together to solve various control problems, the idea is that this combination of areas would enable even more complex problem solving and better results. In this book we test the proposed method using two benchmark problems: the total flight control and the problem of water level control for a 3 tank system. When fuzzy logic is used it make it easy to performed the simulations, these fuzzy systems help to model the behavior of a real systems, using the fuzzy systems fuzzy rules are generated and with this can generate the behavior of any variable depending on the inputs and linguistic value. For this reason this work considers the proposed architecture using fuzzy systems and with this improve the behavior of the complex control problems.
Immune Genetic Learning of Fuzzy Cognitive Map
LIN Chun-mei; HE Yue; TANG Bing-yong
2006-01-01
This paper presents a hybrid methodology of automatically constructing fuzzy cognitive map (FCM). The method uses immune genetic algorithm to learn the connection matrix of FCM. In the algorithm, the DNA coding method is used and an immune operator based on immune mechanism is constructed. The characteristics of the system and the experts' knowledge are abstracted as vaccine for restraining the degenerative phenomena during evolution so as to improve the algorithmic efficiency. Finally, an illustrative example is provided, and its results suggest that the method is capable of automatically generating FCM model.
Temporal motifs in time-dependent networks
Kovanen, Lauri; Karsai, Márton; Kaski, Kimmo; Kertész, János; Saramäki, Jari
2011-01-01
Temporal networks are commonly used to represent systems where connections between elements are active only for restricted periods of time, such as telecommunication, neural signal processing, biochemical reaction and human social interaction networks. We introduce the framework of temporal motifs to study the mesoscale topological–temporal structure of temporal networks in which the events of nodes do not overlap in time. Temporal motifs are classes of similar event sequences, where the similarity refers not only to topology but also to the temporal order of the events. We provide a mapping from event sequences to coloured directed graphs that enables an efficient algorithm for identifying temporal motifs. We discuss some aspects of temporal motifs, including causality and null models, and present basic statistics of temporal motifs in a large mobile call network
Motif discovery in ranked lists of sequences
Nielsen, Morten Muhlig; Tataru, Paula; Madsen, Tobias
2016-01-01
Motif analysis has long been an important method to characterize biological functionality and the current growth of sequencing-based genomics experiments further extends its potential. These diverse experiments often generate sequence lists ranked by some functional property. There is therefore...... advantage of the regular expression feature, including enrichments for combinations of different microRNA seed sites. The method is implemented and made publicly available as an R package and supports high parallelization on multi-core machinery....... a growing need for motif analysis methods that can exploit this coupled data structure and be tailored for specific biological questions. Here, we present an exploratory motif analysis tool, Regmex (REGular expression Motif EXplorer), which offers several methods to evaluate the correlation of motifs...
iFORM: Incorporating Find Occurrence of Regulatory Motifs.
Ren, Chao; Chen, Hebing; Yang, Bite; Liu, Feng; Ouyang, Zhangyi; Bo, Xiaochen; Shu, Wenjie
2016-01-01
Accurately identifying the binding sites of transcription factors (TFs) is crucial to understanding the mechanisms of transcriptional regulation and human disease. We present incorporating Find Occurrence of Regulatory Motifs (iFORM), an easy-to-use and efficient tool for scanning DNA sequences with TF motifs described as position weight matrices (PWMs). Both performance assessment with a receiver operating characteristic (ROC) curve and a correlation-based approach demonstrated that iFORM achieves higher accuracy and sensitivity by integrating five classical motif discovery programs using Fisher's combined probability test. We have used iFORM to provide accurate results on a variety of data in the ENCODE Project and the NIH Roadmap Epigenomics Project, and the tool has demonstrated its utility in further elucidating individual roles of functional elements. Both the source and binary codes for iFORM can be freely accessed at https://github.com/wenjiegroup/iFORM. The identified TF binding sites across human cell and tissue types using iFORM have been deposited in the Gene Expression Omnibus under the accession ID GSE53962.
Word Similarity from Dictionaries: Inferring Fuzzy Measures from Fuzzy Graphs
Vicenc Torra
2008-01-01
Full Text Available WORD SIMILARITY FROM DICTIONARIES: INFERRING FUZZY MEASURES FROM FUZZY GRAPHS The computation of similarities between words is a basic element of information retrieval systems, when retrieval is not solely based on word matching. In this work we consider a measure between words based on dictionaries. This is achieved assuming that a dictionary is formalized as a fuzzy graph. We show that the approach permits to compute measures not only for pairs of words but for sets of them.
MotifNet: a web-server for network motif analysis.
Smoly, Ilan Y; Lerman, Eugene; Ziv-Ukelson, Michal; Yeger-Lotem, Esti
2017-06-15
Network motifs are small topological patterns that recur in a network significantly more often than expected by chance. Their identification emerged as a powerful approach for uncovering the design principles underlying complex networks. However, available tools for network motif analysis typically require download and execution of computationally intensive software on a local computer. We present MotifNet, the first open-access web-server for network motif analysis. MotifNet allows researchers to analyze integrated networks, where nodes and edges may be labeled, and to search for motifs of up to eight nodes. The output motifs are presented graphically and the user can interactively filter them by their significance, number of instances, node and edge labels, and node identities, and view their instances. MotifNet also allows the user to distinguish between motifs that are centered on specific nodes and motifs that recur in distinct parts of the network. MotifNet is freely available at http://netbio.bgu.ac.il/motifnet . The website was implemented using ReactJs and supports all major browsers. The server interface was implemented in Python with data stored on a MySQL database. estiyl@bgu.ac.il or michaluz@cs.bgu.ac.il. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com
Fuzzy control. Fundamentals, stability and design of fuzzy controllers
Michels, K. [Fichtner GmbH und Co. KG, Stuttgart (Germany); Klawonn, F. [Fachhochschule Braunschweig/Wolfenbuettel (Germany). Fachbereich Informatik; Kruse, R. [Magdeburg Univ. (Germany). Fakultaet Informatik, Abt. Wiss.- und Sprachverarbeitung; Nuernberger, A. (eds.) [California Univ., Berkeley, CA (United States). Computer Science Division
2006-07-01
The book provides a critical discussion of fuzzy controllers from the perspective of classical control theory. Special emphases are placed on topics that are of importance for industrial applications, like (self-) tuning of fuzzy controllers, optimisation and stability analysis. The book is written as a textbook for graduate students as well as a comprehensive reference book about fuzzy control for researchers and application engineers. Starting with a detailed introduction to fuzzy systems and control theory the reader is guided to up-to-date research results. (orig.)
Fuzzy pharmacology: theory and applications.
Sproule, Beth A; Naranjo, Claudio A; Türksen, I Burhan
2002-09-01
Fuzzy pharmacology is a term coined to represent the application of fuzzy logic and fuzzy set theory to pharmacological problems. Fuzzy logic is the science of reasoning, thinking and inference that recognizes and uses the real world phenomenon that everything is a matter of degree. It is an extension of binary logic that is able to deal with complex systems because it does not require crisp definitions and distinctions for the system components. In pharmacology, fuzzy modeling has been used for the mechanical control of drug delivery in surgical settings, and work has begun evaluating its use in other pharmacokinetic and pharmacodynamic applications. Fuzzy pharmacology is an emerging field that, based on these initial explorations, warrants further investigation.
Efficient sequential and parallel algorithms for planted motif search.
Nicolae, Marius; Rajasekaran, Sanguthevar
2014-01-31
Motif searching is an important step in the detection of rare events occurring in a set of DNA or protein sequences. One formulation of the problem is known as (l,d)-motif search or Planted Motif Search (PMS). In PMS we are given two integers l and d and n biological sequences. We want to find all sequences of length l that appear in each of the input sequences with at most d mismatches. The PMS problem is NP-complete. PMS algorithms are typically evaluated on certain instances considered challenging. Despite ample research in the area, a considerable performance gap exists because many state of the art algorithms have large runtimes even for moderately challenging instances. This paper presents a fast exact parallel PMS algorithm called PMS8. PMS8 is the first algorithm to solve the challenging (l,d) instances (25,10) and (26,11). PMS8 is also efficient on instances with larger l and d such as (50,21). We include a comparison of PMS8 with several state of the art algorithms on multiple problem instances. This paper also presents necessary and sufficient conditions for 3 l-mers to have a common d-neighbor. The program is freely available at http://engr.uconn.edu/~man09004/PMS8/. We present PMS8, an efficient exact algorithm for Planted Motif Search. PMS8 introduces novel ideas for generating common neighborhoods. We have also implemented a parallel version for this algorithm. PMS8 can solve instances not solved by any previous algorithms.
Stochastic Optimal Estimation with Fuzzy Random Variables and Fuzzy Kalman Filtering
FENG Yu-hu
2005-01-01
By constructing a mean-square performance index in the case of fuzzy random variable, the optimal estimation theorem for unknown fuzzy state using the fuzzy observation data are given. The state and output of linear discrete-time dynamic fuzzy system with Gaussian noise are Gaussian fuzzy random variable sequences. An approach to fuzzy Kalman filtering is discussed. Fuzzy Kalman filtering contains two parts: a real-valued non-random recurrence equation and the standard Kalman filtering.
Intuitionistic fuzzy aggregation and clustering
Xu, Zeshui
2012-01-01
This book offers a systematic introduction to the clustering algorithms for intuitionistic fuzzy values, the latest research results in intuitionistic fuzzy aggregation techniques, the extended results in interval-valued intuitionistic fuzzy environments, and their applications in multi-attribute decision making, such as supply chain management, military system performance evaluation, project management, venture capital, information system selection, building materials classification, and operational plan assessment, etc.
On the mathematics of fuzziness
Chulichkov, A.I.; Chulichkova, N.M.; Pyt`ev, Y. P.; Smolnik, L.
1994-12-31
The problem of the minimax linear interpretation of stochastic measurements with fuzzy conditions on values of the object`s parameters is considered. The result of a measurement interpretation is the fuzzy element (u, h, alpha, mu(.,.,.)), where u is the object`s parameter estimation, h is the estimation accuracy and alpha is the reliability of interpretation, mu is the characteristic function of a fuzzy element. Reliability is the characteristic of the agreement between fuzzy a priori information and measuring data. The information on the values of the parameters of an object under investigation is interactively submitted to the computer.
Pasternak, Anna; Wengel, Jesper
2011-01-01
The influence of acyclic RNA derivatives, UNA (unlocked nucleic acid) monomers, on i-DNA thermodynamic stability has been investigated. The 22 nt human telomeric fragment was chosen as the model sequence for stability studies. UNA monomers modulate i-motif stability in a position-depending manner...
Kurihara, Hiroyuki; Shinkai, Masashige; Nagamune, Teruyuki
2004-01-01
We developed a novel method for creating repetitive DNA libraries using overlap elongation PCR, and prepared a DNA library encoding repetitive Arg-Gly-Asp (RGD) cell adhesive motifs. We obtained various length DNAs encoding repetitive RGD from a short monomer DNA (18 bp) after a thermal cyclic reaction without a DNA template for amplification, and isolated DNAs encoding 2, 21, and 43 repeats of the RGD motif. We cloned these DNAs into a protein expression vector and overexpressed them as thioredoxin fusion proteins: RGD2, RGD21, and RGD43, respectively. The solubility of RGD43 in water was low and it formed a fibrous precipitate in water. Scanning electron microscopy revealed that RGD43 formed a branched 3D-network structure in the solid state. To evaluate the function of the cell adhesive motifs in RGD43, mouse fibroblast cells were cultivated on the RGD43 scaffold. The fibroblast cells adhered to the RGD43 scaffold and extended long filopodia
Sequence-specific high mobility group box factors recognize 10-12-base pair minor groove motifs
van Beest, M; Dooijes, D; van De Wetering, M
2000-01-01
Sequence-specific high mobility group (HMG) box factors bind and bend DNA via interactions in the minor groove. Three-dimensional NMR analyses have provided the structural basis for this interaction. The cognate HMG domain DNA motif is generally believed to span 6-8 bases. However, alignment...
Baron, Jorge H.; Rivera, S.S.
2000-01-01
The so-called vulnerability matrix is used in the evaluation part of the probabilistic safety assessment for a nuclear power plant, during the containment event trees calculations. This matrix is established from what is knows as Numerical Categories for Engineering Judgement. This matrix is usually established with numerical values obtained with traditional arithmetic using the set theory. The representation of this matrix with fuzzy numbers is much more adequate, due to the fact that the Numerical Categories for Engineering Judgement are better represented with linguistic variables, such as 'highly probable', 'probable', 'impossible', etc. In the present paper a methodology to obtain a Fuzzy Vulnerability Matrix is presented, starting from the recommendations on the Numerical Categories for Engineering Judgement. (author)
Berenstein, David; Dzienkowski, Eric; Lashof-Regas, Robin
2015-01-01
We construct various exact analytical solutions of the SO(3) BMN matrix model that correspond to rotating fuzzy spheres and rotating fuzzy tori. These are also solutions of Yang Mills theory compactified on a sphere times time and they are also translationally invariant solutions of the N=1"∗ field theory with a non-trivial charge density. The solutions we construct have a ℤ_N symmetry, where N is the rank of the matrices. After an appropriate ansatz, we reduce the problem to solving a set of polynomial equations in 2N real variables. These equations have a discrete set of solutions for each value of the angular momentum. We study the phase structure of the solutions for various values of N. Also the continuum limit where N→∞, where the problem reduces to finding periodic solutions of a set of coupled differential equations. We also study the topology change transition from the sphere to the torus.
Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas
Petrov, Anton I.; Zirbel, Craig L.; Leontis, Neocles B.
2013-01-01
The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. PMID:23970545
Coufal, David
2017-01-01
Roč. 319, 15 July (2017), s. 1-27 ISSN 0165-0114 R&D Projects: GA MŠk(CZ) LD13002 Institutional support: RVO:67985807 Keywords : fuzzy systems * radial functions * coherence Subject RIV: BA - General Mathematics OBOR OECD: Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8) Impact factor: 2.718, year: 2016
Andrej Preložnik
2013-07-01
Full Text Available Situla art developed as an echo of the toreutic style which had spread from the Near East through the Phoenicians, Greeks and Etruscans as far as the Veneti, Raeti, Histri, and their eastern neighbours in the region of Dolenjska (Lower Carniola. An Early Iron Age phenomenon (c. 600—300 BC, it rep- resents the major and most arresting form of the contemporary visual arts in an area stretching from the foot of the Apennines in the south to the Drava and Sava rivers in the east. Indeed, individual pieces have found their way across the Alpine passes and all the way north to the Danube. In the world and art of the situlae, a prominent role is accorded to ani- mals. They are displayed in numerous representations of human activities on artefacts crafted in the classic situla style – that is, between the late 6th and early 5th centuries BC – as passive participants (e.g. in pageants or in harness or as an active element of the situla narrative. The most typical example of the latter is the hunting scene. Today we know at least four objects decorat- ed exclusively with hunting themes, and a number of situlae and other larger vessels where hunting scenes are embedded in composite narratives. All this suggests a popularity unparallelled by any other genre. Clearly recognisable are various hunting techniques and weapons, each associated with a particu- lar type of game (Fig. 1. The chase of a stag with javelin, horse and hound is depicted on the long- familiar and repeatedly published fibula of Zagorje (Fig. 2. It displays a hound mauling the stag’s back and a hunter on horseback pursuing a hind, her neck already pierced by the javelin. To judge by the (so far unnoticed shaft end un- der the stag’s muzzle, the hunter would have been brandishing a second jave- lin as well, like the warrior of the Vače fibula or the rider of the Nesactium situla, presumably himself a hunter. Many parallels to his motif are known from Greece, Etruria, and
Fuzzy Clustering Methods and their Application to Fuzzy Modeling
Kroszynski, Uri; Zhou, Jianjun
1999-01-01
Fuzzy modeling techniques based upon the analysis of measured input/output data sets result in a set of rules that allow to predict system outputs from given inputs. Fuzzy clustering methods for system modeling and identification result in relatively small rule-bases, allowing fast, yet accurate....... An illustrative synthetic example is analyzed, and prediction accuracy measures are compared between the different variants...
GPUmotif: an ultra-fast and energy-efficient motif analysis program using graphics processing units.
Zandevakili, Pooya; Hu, Ming; Qin, Zhaohui
2012-01-01
Computational detection of TF binding patterns has become an indispensable tool in functional genomics research. With the rapid advance of new sequencing technologies, large amounts of protein-DNA interaction data have been produced. Analyzing this data can provide substantial insight into the mechanisms of transcriptional regulation. However, the massive amount of sequence data presents daunting challenges. In our previous work, we have developed a novel algorithm called Hybrid Motif Sampler (HMS) that enables more scalable and accurate motif analysis. Despite much improvement, HMS is still time-consuming due to the requirement to calculate matching probabilities position-by-position. Using the NVIDIA CUDA toolkit, we developed a graphics processing unit (GPU)-accelerated motif analysis program named GPUmotif. We proposed a "fragmentation" technique to hide data transfer time between memories. Performance comparison studies showed that commonly-used model-based motif scan and de novo motif finding procedures such as HMS can be dramatically accelerated when running GPUmotif on NVIDIA graphics cards. As a result, energy consumption can also be greatly reduced when running motif analysis using GPUmotif. The GPUmotif program is freely available at http://sourceforge.net/projects/gpumotif/
GPUmotif: an ultra-fast and energy-efficient motif analysis program using graphics processing units.
Pooya Zandevakili
Full Text Available Computational detection of TF binding patterns has become an indispensable tool in functional genomics research. With the rapid advance of new sequencing technologies, large amounts of protein-DNA interaction data have been produced. Analyzing this data can provide substantial insight into the mechanisms of transcriptional regulation. However, the massive amount of sequence data presents daunting challenges. In our previous work, we have developed a novel algorithm called Hybrid Motif Sampler (HMS that enables more scalable and accurate motif analysis. Despite much improvement, HMS is still time-consuming due to the requirement to calculate matching probabilities position-by-position. Using the NVIDIA CUDA toolkit, we developed a graphics processing unit (GPU-accelerated motif analysis program named GPUmotif. We proposed a "fragmentation" technique to hide data transfer time between memories. Performance comparison studies showed that commonly-used model-based motif scan and de novo motif finding procedures such as HMS can be dramatically accelerated when running GPUmotif on NVIDIA graphics cards. As a result, energy consumption can also be greatly reduced when running motif analysis using GPUmotif. The GPUmotif program is freely available at http://sourceforge.net/projects/gpumotif/
Improved i-motif thermal stability by insertion of anthraquinone monomers
Gouda, Alaa S; Amine, Mahasen S.; Pedersen, Erik Bjerregaard
2017-01-01
In order to gain insight into how to improve thermal stability of i-motifs when used in the context of biomedical and nanotechnological applications, novel anthraquinone-modified i-motifs were synthesized by insertion of 1,8-, 1,4-, 1,5- and 2,6-disubstituted anthraquinone monomers into the TAA...... loops of a 22mer cytosine-rich human telomeric DNA sequence. The influence of the four anthraquinone linkers on the i-motif thermal stability was investigated at 295 nm and pH 5.5. Anthraquinone monomers modulate the i-motif stability in a position-depending manner and the modulation also depends...... unlocked nucleic acid monomers or twisted intercalating nucleic acid. The 2,6-disubstituted anthraquinone linker replacing T10 enabled a significant increase of i-motif thermal melting by 8.2 °C. A substantial increase of 5.0 °C in i-motif thermal melting was recorded when both A6 and T16 were modified...
AN IMPROVED FUZZY CLUSTERING ALGORITHM FOR MICROARRAY IMAGE SPOTS SEGMENTATION
V.G. Biju
2015-11-01
Full Text Available An automatic cDNA microarray image processing using an improved fuzzy clustering algorithm is presented in this paper. The spot segmentation algorithm proposed uses the gridding technique developed by the authors earlier, for finding the co-ordinates of each spot in an image. Automatic cropping of spots from microarray image is done using these co-ordinates. The present paper proposes an improved fuzzy clustering algorithm Possibility fuzzy local information c means (PFLICM to segment the spot foreground (FG from background (BG. The PFLICM improves fuzzy local information c means (FLICM algorithm by incorporating typicality of a pixel along with gray level information and local spatial information. The performance of the algorithm is validated using a set of simulated cDNA microarray images added with different levels of AWGN noise. The strength of the algorithm is tested by computing the parameters such as the Segmentation matching factor (SMF, Probability of error (pe, Discrepancy distance (D and Normal mean square error (NMSE. SMF value obtained for PFLICM algorithm shows an improvement of 0.9 % and 0.7 % for high noise and low noise microarray images respectively compared to FLICM algorithm. The PFLICM algorithm is also applied on real microarray images and gene expression values are computed.
Parallel motif extraction from very long sequences
Sahli, Majed; Mansour, Essam; Kalnis, Panos
2013-01-01
Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern
Deciphering functional glycosaminoglycan motifs in development.
Townley, Robert A; Bülow, Hannes E
2018-03-23
Glycosaminoglycans (GAGs) such as heparan sulfate, chondroitin/dermatan sulfate, and keratan sulfate are linear glycans, which when attached to protein backbones form proteoglycans. GAGs are essential components of the extracellular space in metazoans. Extensive modifications of the glycans such as sulfation, deacetylation and epimerization create structural GAG motifs. These motifs regulate protein-protein interactions and are thereby repsonsible for many of the essential functions of GAGs. This review focusses on recent genetic approaches to characterize GAG motifs and their function in defined signaling pathways during development. We discuss a coding approach for GAGs that would enable computational analyses of GAG sequences such as alignments and the computation of position weight matrices to describe GAG motifs. Copyright © 2018 Elsevier Ltd. All rights reserved.
Bayesian centroid estimation for motif discovery.
Carvalho, Luis
2013-01-01
Biological sequences may contain patterns that signal important biomolecular functions; a classical example is regulation of gene expression by transcription factors that bind to specific patterns in genomic promoter regions. In motif discovery we are given a set of sequences that share a common motif and aim to identify not only the motif composition, but also the binding sites in each sequence of the set. We propose a new centroid estimator that arises from a refined and meaningful loss function for binding site inference. We discuss the main advantages of centroid estimation for motif discovery, including computational convenience, and how its principled derivation offers further insights about the posterior distribution of binding site configurations. We also illustrate, using simulated and real datasets, that the centroid estimator can differ from the traditional maximum a posteriori or maximum likelihood estimators.
Bayesian centroid estimation for motif discovery.
Luis Carvalho
Full Text Available Biological sequences may contain patterns that signal important biomolecular functions; a classical example is regulation of gene expression by transcription factors that bind to specific patterns in genomic promoter regions. In motif discovery we are given a set of sequences that share a common motif and aim to identify not only the motif composition, but also the binding sites in each sequence of the set. We propose a new centroid estimator that arises from a refined and meaningful loss function for binding site inference. We discuss the main advantages of centroid estimation for motif discovery, including computational convenience, and how its principled derivation offers further insights about the posterior distribution of binding site configurations. We also illustrate, using simulated and real datasets, that the centroid estimator can differ from the traditional maximum a posteriori or maximum likelihood estimators.
Fuzzy linguistic model for interpolation
Abbasbandy, S.; Adabitabar Firozja, M.
2007-01-01
In this paper, a fuzzy method for interpolating of smooth curves was represented. We present a novel approach to interpolate real data by applying the universal approximation method. In proposed method, fuzzy linguistic model (FLM) applied as universal approximation for any nonlinear continuous function. Finally, we give some numerical examples and compare the proposed method with spline method
Fuzzy Logic in Medicine and Bioinformatics
Angela Torres
2006-01-01
Full Text Available The purpose of this paper is to present a general view of the current applications of fuzzy logic in medicine and bioinformatics. We particularly review the medical literature using fuzzy logic. We then recall the geometrical interpretation of fuzzy sets as points in a fuzzy hypercube and present two concrete illustrations in medicine (drug addictions and in bioinformatics (comparison of genomes.
Algebraic Aspects of Families of Fuzzy Languages
Asveld, P.R.J.; Heylen, Dirk K.J.; Nijholt, Antinus; Scollo, Giuseppe
2000-01-01
We study operations on fuzzy languages such as union, concatenation,Kleene $\\star$, intersection with regular fuzzy languages, and several kinds of (iterated) fuzzy substitution. Then we consider families of fuzzy languages, closed under a fixed collection of these operations, which results in the
Fuzzy control in environmental engineering
Chmielowski, Wojciech Z
2016-01-01
This book is intended for engineers, technicians and people who plan to use fuzzy control in more or less developed and advanced control systems for manufacturing processes, or directly for executive equipment. Assuming that the reader possesses elementary knowledge regarding fuzzy sets and fuzzy control, by way of a reminder, the first parts of the book contain a reminder of the theoretical foundations as well as a description of the tools to be found in the Matlab/Simulink environment in the form of a toolbox. The major part of the book presents applications for fuzzy controllers in control systems for various manufacturing and engineering processes. It presents seven processes and problems which have been programmed using fuzzy controllers. The issues discussed concern the field of Environmental Engineering. Examples are the control of a flood wave passing through a hypothetical, and then the real Dobczyce reservoir in the Raba River, which is located in the upper Vistula River basin in Southern Poland, th...
Design of interpretable fuzzy systems
Cpałka, Krzysztof
2017-01-01
This book shows that the term “interpretability” goes far beyond the concept of readability of a fuzzy set and fuzzy rules. It focuses on novel and precise operators of aggregation, inference, and defuzzification leading to flexible Mamdani-type and logical-type systems that can achieve the required accuracy using a less complex rule base. The individual chapters describe various aspects of interpretability, including appropriate selection of the structure of a fuzzy system, focusing on improving the interpretability of fuzzy systems designed using both gradient-learning and evolutionary algorithms. It also demonstrates how to eliminate various system components, such as inputs, rules and fuzzy sets, whose reduction does not adversely affect system accuracy. It illustrates the performance of the developed algorithms and methods with commonly used benchmarks. The book provides valuable tools for possible applications in many fields including expert systems, automatic control and robotics.
On Intuitionistic Fuzzy Sets Theory
Atanassov, Krassimir T
2012-01-01
This book aims to be a comprehensive and accurate survey of state-of-art research on intuitionistic fuzzy sets theory and could be considered a continuation and extension of the author´s previous book on Intuitionistic Fuzzy Sets, published by Springer in 1999 (Atanassov, Krassimir T., Intuitionistic Fuzzy Sets, Studies in Fuzziness and soft computing, ISBN 978-3-7908-1228-2, 1999). Since the aforementioned book has appeared, the research activity of the author within the area of intuitionistic fuzzy sets has been expanding into many directions. The results of the author´s most recent work covering the past 12 years as well as the newest general ideas and open problems in this field have been therefore collected in this new book.
Safety critical application of fuzzy control
Schildt, G.H.
1995-01-01
After an introduction into safety terms a short description of fuzzy logic will be given. Especially, for safety critical applications of fuzzy controllers a possible controller structure will be described. The following items will be discussed: Configuration of fuzzy controllers, design aspects like fuzzfiication, inference strategies, defuzzification and types of membership functions. As an example a typical fuzzy rule set will be presented. Especially, real-time behaviour a fuzzy controllers is mentioned. An example of fuzzy controlling for temperature control purpose within a nuclear reactor together with membership functions and inference strategy of such a fuzzy controller will be presented. (author). 4 refs, 17 figs
Image matching navigation based on fuzzy information
田玉龙; 吴伟仁; 田金文; 柳健
2003-01-01
In conventional image matching methods, the image matching process is mostly based on image statistic information. One aspect neglected by all these methods is that there is much fuzzy information contained in these images. A new fuzzy matching algorithm based on fuzzy similarity for navigation is presented in this paper. Because the fuzzy theory is of the ability of making good description of the fuzzy information contained in images, the image matching method based on fuzzy similarity would look forward to producing good performance results. Experimental results using matching algorithm based on fuzzy information also demonstrate its reliability and practicability.
Radiation protection and fuzzy set theory
Nishiwaki, Y.
1993-01-01
In radiation protection we encounter a variety of sources of uncertainties which are due to fuzziness in our cognition or perception of objects. For systematic treatment of this type of uncertainty, the concepts of fuzzy sets or fuzzy measures could be applied to construct system models, which may take into consideration both subjective or intrinsic fuzziness and objective or extrinsic fuzziness. The theory of fuzzy sets and fuzzy measures is still in a developing stage, but its concept may be applied to various problems of subjective perception of risk, nuclear safety, radiation protection and also to the problems of man-machine interface and human factor engineering or ergonomic
DNA regulatory motif selection based on support vector machine ...
Administrator
2011-10-19
Oct 19, 2011 ... ... gene expression values of controls and i x i y. 1 i y = 1 i y = −. 1. 2. { , ,..., , } i i i im i g. x x. x y. = 1. 2. 1. 2. , ,..., ,. , ,..., k i i i im. x x x. x x x x x. = =.
Native characterization of nucleic acid motif thermodynamics via non-covalent catalysis
Wang, Chunyan; Bae, Jin H.; Zhang, David Yu
2016-01-01
DNA hybridization thermodynamics is critical for accurate design of oligonucleotides for biotechnology and nanotechnology applications, but parameters currently in use are inaccurately extrapolated based on limited quantitative understanding of thermal behaviours. Here, we present a method to measure the ΔG° of DNA motifs at temperatures and buffer conditions of interest, with significantly better accuracy (6- to 14-fold lower s.e.) than prior methods. The equilibrium constant of a reaction with thermodynamics closely approximating that of a desired motif is numerically calculated from directly observed reactant and product equilibrium concentrations; a DNA catalyst is designed to accelerate equilibration. We measured the ΔG° of terminal fluorophores, single-nucleotide dangles and multinucleotide dangles, in temperatures ranging from 10 to 45 °C. PMID:26782977
Chiu, Yi-Yuan; Lin, Chun-Yu; Lin, Chih-Ta; Hsu, Kai-Cheng; Chang, Li-Zen; Yang, Jinn-Moon
2012-01-01
To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions. We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/. SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery.
Fuzzy portfolio model with fuzzy-input return rates and fuzzy-output proportions
Tsaur, Ruey-Chyn
2015-02-01
In the finance market, a short-term investment strategy is usually applied in portfolio selection in order to reduce investment risk; however, the economy is uncertain and the investment period is short. Further, an investor has incomplete information for selecting a portfolio with crisp proportions for each chosen security. In this paper we present a new method of constructing fuzzy portfolio model for the parameters of fuzzy-input return rates and fuzzy-output proportions, based on possibilistic mean-standard deviation models. Furthermore, we consider both excess or shortage of investment in different economic periods by using fuzzy constraint for the sum of the fuzzy proportions, and we also refer to risks of securities investment and vagueness of incomplete information during the period of depression economics for the portfolio selection. Finally, we present a numerical example of a portfolio selection problem to illustrate the proposed model and a sensitivity analysis is realised based on the results.
Improvement of Fuzzy Image Contrast Enhancement Using Simulated Ergodic Fuzzy Markov Chains
Behrouz Fathi-Vajargah
2014-01-01
Full Text Available This paper presents a novel fuzzy enhancement technique using simulated ergodic fuzzy Markov chains for low contrast brain magnetic resonance imaging (MRI. The fuzzy image contrast enhancement is proposed by weighted fuzzy expected value. The membership values are then modified to enhance the image using ergodic fuzzy Markov chains. The qualitative performance of the proposed method is compared to another method in which ergodic fuzzy Markov chains are not considered. The proposed method produces better quality image.
The World of Combinatorial Fuzzy Problems and the Efficiency of Fuzzy Approximation Algorithms
Yamakami, Tomoyuki
2015-01-01
We re-examine a practical aspect of combinatorial fuzzy problems of various types, including search, counting, optimization, and decision problems. We are focused only on those fuzzy problems that take series of fuzzy input objects and produce fuzzy values. To solve such problems efficiently, we design fast fuzzy algorithms, which are modeled by polynomial-time deterministic fuzzy Turing machines equipped with read-only auxiliary tapes and write-only output tapes and also modeled by polynomia...
Sergio eTofanelli
2014-11-01
Full Text Available Several authors have proposed haplotype motifs based on site variants at the mitochondrial genome (mtDNA and the non-recombining portion of the Y chromosome (NRY to trace the genealogies of Jewish people. Here, we analyzed their main approaches and test the feasibility of adopting motifs as ancestry markers through construction of a large database of mtDNA and NRY haplotypes from public genetic genealogical repositories. We verified the reliability of Jewish ancestry prediction based on the Cohen and Levite Modal Haplotypes in their classical 6 STR marker format or in the extended 12 STR format, as well as four founder mtDNA lineages (HVS-I segments accounting for about 40% of the current population of Ashkenazi Jews. For this purpose we compared haplotype composition in individuals of self-reported Jewish ancestry with the rest of European, African or Middle Eastern samples, to test for non-random association of ethno-geographic groups and haplotypes. Overall, NRY and mtDNA based motifs, previously reported to differentiate between groups, were found to be more represented in Jewish compared to non-Jewish groups. However, this seems to stem from common ancestors of Jewish lineages being rather recent respect to ancestors of non-Jewish lineages with the same haplotype signatures. Moreover, the polyphyly of haplotypes which contain the proposed motifs and the misuse of constant mutation rates heavily affected previous attempts to correctly dating the origin of common ancestries. Accordingly, our results stress the limitations of using the above haplotype motifs as reliable Jewish ancestry predictors and show its inadequacy for forensic or genealogical purposes.
The MHC motif viewer: a visualization tool for MHC binding motifs
Rapin, Nicolas; Hoof, Ilka; Lund, Ole
2010-01-01
is hampered by the lack of tools for browsing and comparing specificity of these molecules. We have developed a Web server, MHC Motif Viewer, which allows the display of the binding motif for MHC class I proteins for human, chimpanzee, rhesus monkey, mouse, and swine, as well as HLA-DR protein sequences...
Analisis Unsur Matematika pada Motif Sulam Usus
Fredi Ganda Putra
2017-12-01
Full Text Available Based on interviews with researchers sources said that the beginning of the intestine embroidery is an art of genuine crafts. Called the intestine embroidery because this technique is a technique of combining a strand of cloth resembling the intestine formed according to the pattern by means of embroidered using a thread. Intestinal embroidery techniques were originally used to create a cover of the women's customary wardrobe of Lampung or often referred to as bebe. But not many people in Lampung, especially people who live in Lampung are still many who do not know and recognize the intestine embroidery because most only know tapis only characteristic of Lampung, besides that there are other cultural results that is embroidered intestine. There are still many who do not know that the intestine motif there is a knowledge of mathematics. The researcher's problem formulation is whether there are mathematical elements contained in the intestine embroidery motif based on the concept of geometry. The purpose of this study is to determine whether there are elements of mathematics contained in the intestine motif based on the concept of geometry. Subjects in this study consisted of 4 people obtained by purposive sampling technique. From the results of data analysis conducted by using descriptive analysis and discussion as follows: (1 Intestinal embroidery motif contains the meaning of mathematics and culture or often called Etnomatematika. On the meaning of culture there is a link between the embroidery intestine with a culture that has been there before as the existence of cultural linkage between Hindu belief Buddhism and there are similarities of motifs and decorative patterns contained in the motif embroidery intestine with ornamental variety in Indonesia. (2 The relationship between the intestine with mathematical motifs there are elements of mathematics such as geometry elements in the form of geometry of dimension one and dimension two, and the
Sanchez, Mauricio A; Castro, Juan R
2017-01-01
In this book, a series of granular algorithms are proposed. A nature inspired granular algorithm based on Newtonian gravitational forces is proposed. A series of methods for the formation of higher-type information granules represented by Interval Type-2 Fuzzy Sets are also shown, via multiple approaches, such as Coefficient of Variation, principle of justifiable granularity, uncertainty-based information concept, and numerical evidence based. And a fuzzy granular application comparison is given as to demonstrate the differences in how uncertainty affects the performance of fuzzy information granules.
Fuzzy resource optimization for safeguards
Zardecki, A.; Markin, J.T.
1991-01-01
Authorization, enforcement, and verification -- three key functions of safeguards systems -- form the basis of a hierarchical description of the system risk. When formulated in terms of linguistic rather than numeric attributes, the risk can be computed through an algorithm based on the notion of fuzzy sets. Similarly, this formulation allows one to analyze the optimal resource allocation by maximizing the overall detection probability, regarded as a linguistic variable. After summarizing the necessary elements of the fuzzy sets theory, we outline the basic algorithm. This is followed by a sample computation of the fuzzy optimization. 10 refs., 1 tab
Hudec Miroslav
2011-01-01
Full Text Available Structured Query Language (SQL is used to obtain data from relational databases. Fuzzy improvement of SQL queries has advantages in cases when the user cannot unambiguously define selection criteria or when the user wants to examine data that almost meet the given criteria. In this paper we examine a realization of the fuzzy querying concept. For this purposes the fuzzy generalized logical condition for the WHERE part of the SQL is created. It allows users to create queries by linguistic terms. The proposed model is an extension of the SQL so that no modification inside databases has to be undertaken.
Fuzzy expert systems using CLIPS
Le, Thach C.
1994-01-01
This paper describes a CLIPS-based fuzzy expert system development environment called FCLIPS and illustrates its application to the simulated cart-pole balancing problem. FCLIPS is a straightforward extension of CLIPS without any alteration to the CLIPS internal structures. It makes use of the object-oriented and module features in CLIPS version 6.0 for the implementation of fuzzy logic concepts. Systems of varying degrees of mixed Boolean and fuzzy rules can be implemented in CLIPS. Design and implementation issues of FCLIPS will also be discussed.
Integrating Fuzzy AHP and Fuzzy ARAS for evaluating financial performance
Abdolhamid Safaei Ghadikolaei
2014-09-01
Full Text Available Multi Criteria Decision Making (MCDM is an advanced field of Operation Research; recently MCDM methods are efficient and common tools for performance evaluation in many areas such as finance and economy. The aim of this study is to show one of applications of mathematics in real word. This study with considering value based measures and accounting based measures simultaneously, provided a hybrid approach of MCDM methods in fuzzy environment for financial performance evaluation of automotive and parts manufacturing industry of Tehran stock exchange (TSE.for this purpose Fuzzy analytic hierarchy process (FAHP is applied to determine the relative important of each criterion, then The companies are ranked according their financial performance by using fuzzy additive ratio assessment (Fuzzy ARAS method. The finding of this study showed effective of this approach in evaluating financial performance.
Armadillo motifs involved in vesicular transport.
Harald Striegl
Full Text Available Armadillo (ARM repeat proteins function in various cellular processes including vesicular transport and membrane tethering. They contain an imperfect repeating sequence motif that forms a conserved three-dimensional structure. Recently, structural and functional insight into tethering mediated by the ARM-repeat protein p115 has been provided. Here we describe the p115 ARM-motifs for reasons of clarity and nomenclature and show that both sequence and structure are highly conserved among ARM-repeat proteins. We argue that there is no need to invoke repeat types other than ARM repeats for a proper description of the structure of the p115 globular head region. Additionally, we propose to define a new subfamily of ARM-like proteins and show lack of evidence that the ARM motifs found in p115 are present in other long coiled-coil tethering factors of the golgin family.
Comprehensive human transcription factor binding site map for combinatory binding motifs discovery.
Arnoldo J Müller-Molina
Full Text Available To know the map between transcription factors (TFs and their binding sites is essential to reverse engineer the regulation process. Only about 10%-20% of the transcription factor binding motifs (TFBMs have been reported. This lack of data hinders understanding gene regulation. To address this drawback, we propose a computational method that exploits never used TF properties to discover the missing TFBMs and their sites in all human gene promoters. The method starts by predicting a dictionary of regulatory "DNA words." From this dictionary, it distills 4098 novel predictions. To disclose the crosstalk between motifs, an additional algorithm extracts TF combinatorial binding patterns creating a collection of TF regulatory syntactic rules. Using these rules, we narrowed down a list of 504 novel motifs that appear frequently in syntax patterns. We tested the predictions against 509 known motifs confirming that our system can reliably predict ab initio motifs with an accuracy of 81%-far higher than previous approaches. We found that on average, 90% of the discovered combinatorial binding patterns target at least 10 genes, suggesting that to control in an independent manner smaller gene sets, supplementary regulatory mechanisms are required. Additionally, we discovered that the new TFBMs and their combinatorial patterns convey biological meaning, targeting TFs and genes related to developmental functions. Thus, among all the possible available targets in the genome, the TFs tend to regulate other TFs and genes involved in developmental functions. We provide a comprehensive resource for regulation analysis that includes a dictionary of "DNA words," newly predicted motifs and their corresponding combinatorial patterns. Combinatorial patterns are a useful filter to discover TFBMs that play a major role in orchestrating other factors and thus, are likely to lock/unlock cellular functional clusters.
The BsaHI restriction-modification system: Cloning, sequencing and analysis of conserved motifs
Roberts Richard J
2008-05-01
Full Text Available Abstract Background Restriction and modification enzymes typically recognise short DNA sequences of between two and eight bases in length. Understanding the mechanism of this recognition represents a significant challenge that we begin to address for the BsaHI restriction-modification system, which recognises the six base sequence GRCGYC. Results The DNA sequences of the genes for the BsaHI methyltransferase, bsaHIM, and restriction endonuclease, bsaHIR, have been determined (GenBank accession #EU386360, cloned and expressed in E. coli. Both the restriction endonuclease and methyltransferase enzymes share significant similarity with a group of 6 other enzymes comprising the restriction-modification systems HgiDI and HgiGI and the putative HindVP, NlaCORFDP, NpuORFC228P and SplZORFNP restriction-modification systems. A sequence alignment of these homologues shows that their amino acid sequences are largely conserved and highlights several motifs of interest. We target one such conserved motif, reading SPERRFD, at the C-terminal end of the bsaHIR gene. A mutational analysis of these amino acids indicates that the motif is crucial for enzymatic activity. Sequence alignment of the methyltransferase gene reveals a short motif within the target recognition domain that is conserved among enzymes recognising the same sequences. Thus, this motif may be used as a diagnostic tool to define the recognition sequences of the cytosine C5 methyltransferases. Conclusion We have cloned and sequenced the BsaHI restriction and modification enzymes. We have identified a region of the R. BsaHI enzyme that is crucial for its activity. Analysis of the amino acid sequence of the BsaHI methyltransferase enzyme led us to propose two new motifs that can be used in the diagnosis of the recognition sequence of the cytosine C5-methyltransferases.
Pemodelan Sistem Fuzzy Dengan Menggunakan Matlab
Afan Galih Salman
2010-12-01
Full Text Available Fuzzy logic is a method in soft computing category, a method that could process uncertain, inaccurate, and less cost implemented data. Some methods in soft computing category besides fuzzy logic are artificial network nerve, probabilistic reasoning, and evolutionary computing. Fuzzy logic has the ability to develop fuzzy system that is intelligent system in uncertain environment. Some stages in fuzzy system formation process is input and output analysis, determining input and output variable, defining each fuzzy set member function, determining rules based on experience or knowledge of an expert in his field, and implementing fuzzy system. Overall, fuzzy logic uses simple mathematical concept, understandable, detectable uncertain and accurate data. Fuzzy system could create and apply expert experiences directly without exercise process and effort to decode the knowledge into a computer until becoming a modeling system that could be relied on decision making.
Implementation of Steiner point of fuzzy set.
Liang, Jiuzhen; Wang, Dejiang
2014-01-01
This paper deals with the implementation of Steiner point of fuzzy set. Some definitions and properties of Steiner point are investigated and extended to fuzzy set. This paper focuses on establishing efficient methods to compute Steiner point of fuzzy set. Two strategies of computing Steiner point of fuzzy set are proposed. One is called linear combination of Steiner points computed by a series of crisp α-cut sets of the fuzzy set. The other is an approximate method, which is trying to find the optimal α-cut set approaching the fuzzy set. Stability analysis of Steiner point of fuzzy set is also studied. Some experiments on image processing are given, in which the two methods are applied for implementing Steiner point of fuzzy image, and both strategies show their own advantages in computing Steiner point of fuzzy set.
Fuzzy histogram for internal and external fuzzy directional relations
Salamat , Nadeem; Zahzah , El-Hadi
2009-01-01
5 Pages; Spatial relations have key point importance in image analysis and computer vision. Numerous technics have been developed to study these relations especially directional relations. Modern digital computers give rise to quantitative methods and among them fuzzy methods have core importance due to handling imprecise knowledge information and vagueness. In most fuzzy methods external directional relations are considered which are useful for small scale space image analysis but in large s...
Solution of Fuzzy Differential Equations Using Fuzzy Sumudu Transforms
Raheleh Jafari
2018-01-01
Full Text Available The uncertain nonlinear systems can be modeled with fuzzy differential equations (FDEs and the solutions of these equations are applied to analyze many engineering problems. However, it is very difficult to obtain solutions of FDEs. In this paper, the solutions of FDEs are approximated by utilizing the fuzzy Sumudu transform (FST method. Significant theorems are suggested in order to explain the properties of FST. The proposed method is validated with three real examples.
Direct AUC optimization of regulatory motifs.
Zhu, Lin; Zhang, Hong-Bo; Huang, De-Shuang
2017-07-15
The discovery of transcription factor binding site (TFBS) motifs is essential for untangling the complex mechanism of genetic variation under different developmental and environmental conditions. Among the huge amount of computational approaches for de novo identification of TFBS motifs, discriminative motif learning (DML) methods have been proven to be promising for harnessing the discovery power of accumulated huge amount of high-throughput binding data. However, they have to sacrifice accuracy for speed and could fail to fully utilize the information of the input sequences. We propose a novel algorithm called CDAUC for optimizing DML-learned motifs based on the area under the receiver-operating characteristic curve (AUC) criterion, which has been widely used in the literature to evaluate the significance of extracted motifs. We show that when the considered AUC loss function is optimized in a coordinate-wise manner, the cost function of each resultant sub-problem is a piece-wise constant function, whose optimal value can be found exactly and efficiently. Further, a key step of each iteration of CDAUC can be efficiently solved as a computational geometry problem. Experimental results on real world high-throughput datasets illustrate that CDAUC outperforms competing methods for refining DML motifs, while being one order of magnitude faster. Meanwhile, preliminary results also show that CDAUC may also be useful for improving the interpretability of convolutional kernels generated by the emerging deep learning approaches for predicting TF sequences specificities. CDAUC is available at: https://drive.google.com/drive/folders/0BxOW5MtIZbJjNFpCeHlBVWJHeW8 . dshuang@tongji.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com
Overlapping ETS and CRE Motifs (G/CCGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins
Chatterjee, Raghunath; Zhao, Jianfei; He, Ximiao; Shlyakhtenko, Andrey; Mann, Ishminder; Waterfall, Joshua J.; Meltzer, Paul; Sathyanarayana, B. K.; FitzGerald, Peter C.; Vinson, Charles
2012-01-01
Previously, we identified 8-bps long DNA sequences (8-mers) that localize in human proximal promoters and grouped them into known transcription factor binding sites (TFBS). We now examine split 8-mers consisting of two 4-mers separated by 1-bp to 30-bps (X4-N1-30-X4) to identify pairs of TFBS that localize in proximal promoters at a precise distance. These include two overlapping TFBS: the ETS⇔ETS motif (C/GCCGGAAGCGGAA) and the ETS⇔CRE motif (C/GCGGAAGTGACGTCAC). The nucleotides in bold are part of both TFBS. Molecular modeling shows that the ETS⇔CRE motif can be bound simultaneously by both the ETS and the B-ZIP domains without protein-protein clashes. The electrophoretic mobility shift assay (EMSA) shows that the ETS protein GABPα and the B-ZIP protein CREB preferentially bind to the ETS⇔CRE motif only when the two TFBS overlap precisely. In contrast, the ETS domain of ETV5 and CREB interfere with each other for binding the ETS⇔CRE. The 11-mer (CGGAAGTGACG), the conserved part of the ETS⇔CRE motif, occurs 226 times in the human genome and 83% are in known regulatory regions. In vivo GABPα and CREB ChIP-seq peaks identified the ETS⇔CRE as the most enriched motif occurring in promoters of genes involved in mRNA processing, cellular catabolic processes, and stress response, suggesting that a specific class of genes is regulated by this composite motif. PMID:23050235
Memetic algorithms for de novo motif-finding in biomedical sequences.
Bi, Chengpeng
2012-09-01
The objectives of this study are to design and implement a new memetic algorithm for de novo motif discovery, which is then applied to detect important signals hidden in various biomedical molecular sequences. In this paper, memetic algorithms are developed and tested in de novo motif-finding problems. Several strategies in the algorithm design are employed that are to not only efficiently explore the multiple sequence local alignment space, but also effectively uncover the molecular signals. As a result, there are a number of key features in the implementation of the memetic motif-finding algorithm (MaMotif), including a chromosome replacement operator, a chromosome alteration-aware local search operator, a truncated local search strategy, and a stochastic operation of local search imposed on individual learning. To test the new algorithm, we compare MaMotif with a few of other similar algorithms using simulated and experimental data including genomic DNA, primary microRNA sequences (let-7 family), and transmembrane protein sequences. The new memetic motif-finding algorithm is successfully implemented in C++, and exhaustively tested with various simulated and real biological sequences. In the simulation, it shows that MaMotif is the most time-efficient algorithm compared with others, that is, it runs 2 times faster than the expectation maximization (EM) method and 16 times faster than the genetic algorithm-based EM hybrid. In both simulated and experimental testing, results show that the new algorithm is compared favorably or superior to other algorithms. Notably, MaMotif is able to successfully discover the transcription factors' binding sites in the chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) data, correctly uncover the RNA splicing signals in gene expression, and precisely find the highly conserved helix motif in the transmembrane protein sequences, as well as rightly detect the palindromic segments in the primary micro
Theta-Generalized closed sets in fuzzy topological spaces
El-Shafei, M.E.; Zakari, A.
2006-01-01
In this paper we introduce the concepts of theta-generalized closed fuzzy sets and generalized fuzzy sets in topological spaces. Furthermore, generalized fuzzy sets are extended to theta-generalized fuzzy sets. Also, we introduce the concepts of fuzzy theta-generalized continuous and fuzzy theta-generalized irresolute mappings. (author)
Yaron Orenstein
Full Text Available The new technology of protein binding microarrays (PBMs allows simultaneous measurement of the binding intensities of a transcription factor to tens of thousands of synthetic double-stranded DNA probes, covering all possible 10-mers. A key computational challenge is inferring the binding motif from these data. We present a systematic comparison of four methods developed specifically for reconstructing a binding site motif represented as a positional weight matrix from PBM data. The reconstructed motifs were evaluated in terms of three criteria: concordance with reference motifs from the literature and ability to predict in vivo and in vitro bindings. The evaluation encompassed over 200 transcription factors and some 300 assays. The results show a tradeoff between how the methods perform according to the different criteria, and a dichotomy of method types. Algorithms that construct motifs with low information content predict PBM probe ranking more faithfully, while methods that produce highly informative motifs match reference motifs better. Interestingly, in predicting high-affinity binding, all methods give far poorer results for in vivo assays compared to in vitro assays.
Basem Mohamed Elomda
2013-07-01
Full Text Available This paper presents a new extension to Fuzzy Decision Maps (FDMs by allowing use of fuzzy linguistic values to represent relative importance among criteria in the preference matrix as well as representing relative influence among criteria for computing the steady-state matrix in the stage of Fuzzy Cognitive Map (FCM. The proposed model is called the Linguistic Fuzzy Decision Networks (LFDNs. The proposed LFDN provides considerable flexibility to decision makers when solving real world Multi-Criteria Decision-Making (MCDM problems. The performance of the proposed LFDN model is compared with the original FDM using a previously published case study. The result of comparison ensures the ability to draw the same decisions with a more realistic decision environment.
FUZZY LOGIC IN LEGAL EDUCATION
Z. Gonul BALKIR
2011-04-01
Full Text Available The necessity of examination of every case within its peculiar conditions in social sciences requires different approaches complying with the spirit and nature of social sciences. Multiple realities require different and various perceptual interpretations. In modern world and social sciences, interpretation of perception of valued and multi-valued have been started to be understood by the principles of fuzziness and fuzzy logic. Having the verbally expressible degrees of truthness such as true, very true, rather true, etc. fuzzy logic provides the opportunity for the interpretation of especially complex and rather vague set of information by flexibility or equivalence of the variables’ of fuzzy limitations. The methods and principles of fuzzy logic can be benefited in examination of the methodological problems of law, especially in the applications of filling the legal loopholes arising from the ambiguities and interpretation problems in order to understand the legal rules in a more comprehensible and applicable way and the efficiency of legal implications. On the other hand, fuzzy logic can be used as a technical legal method in legal education and especially in legal case studies and legal practice applications in order to provide the perception of law as a value and the more comprehensive and more quality perception and interpretation of value of justice, which is the core value of law. In the perception of what happened as it has happened in legal relationships and formations, the understanding of social reality and sociological legal rules with multi valued sense perspective and the their applications in accordance with the fuzzy logic’s methods could create more equivalent and just results. It can be useful for the young lawyers and law students as a facilitating legal method especially in the materialization of the perception and interpretation of multi valued and variables. Using methods and principles of fuzzy logic in legal
On the mathematics of fuzziness
Kerre, E. [Ghent Univ. (Belgium)
1994-12-31
During the past twenty-five years, the scientific community has been working very extensively on the development of reliable models for the representation and manipulation of impreciseness and uncertainty that pervade the real world. Fuzzy set theory is one of the most popular theories able to treat incomplete information. In this paper, the basic mathematical principles underlying fuzzy set theory are outlined. Special attention is paid to the way that set theory has influenced the development of mathematics in a positive way.
On the mathematics of fuzziness
Kerre, E.
1994-01-01
During the past twenty-five years, the scientific community has been working very extensively on the development of reliable models for the representation and manipulation of impreciseness and uncertainty that pervade the real world. Fuzzy set theory is one of the most popular theories able to treat incomplete information. In this paper, the basic mathematical principles underlying fuzzy set theory are outlined. Special attention is paid to the way that set theory has influenced the development of mathematics in a positive way
Liu, X.; Fang, K.
1986-01-01
A theoretical study in fuzzy reasoning on Horn Set is presented in this paper. The authors first introduce the concepts of λ-Horn Set of clauses and λ-Input Half Lock deduction. They then use the λ-resolution method to discuss fuzzy reasoning on λ-Horn set of clauses. It is proved that the proposed λ-Input Half Lock resolution method is complete with the rules in certain format
A Fuzzy Query Mechanism for Human Resource Websites
Lai, Lien-Fu; Wu, Chao-Chin; Huang, Liang-Tsung; Kuo, Jung-Chih
Users' preferences often contain imprecision and uncertainty that are difficult for traditional human resource websites to deal with. In this paper, we apply the fuzzy logic theory to develop a fuzzy query mechanism for human resource websites. First, a storing mechanism is proposed to store fuzzy data into conventional database management systems without modifying DBMS models. Second, a fuzzy query language is proposed for users to make fuzzy queries on fuzzy databases. User's fuzzy requirement can be expressed by a fuzzy query which consists of a set of fuzzy conditions. Third, each fuzzy condition associates with a fuzzy importance to differentiate between fuzzy conditions according to their degrees of importance. Fourth, the fuzzy weighted average is utilized to aggregate all fuzzy conditions based on their degrees of importance and degrees of matching. Through the mutual compensation of all fuzzy conditions, the ordering of query results can be obtained according to user's preference.
Sutera, V A; Han, E S; Rajman, L A; Lovett, S T
1999-10-01
The recJ gene, identified in Escherichia coli, encodes a Mg(+2)-dependent 5'-to-3' exonuclease with high specificity for single-strand DNA. Genetic and biochemical experiments implicate RecJ exonuclease in homologous recombination, base excision, and methyl-directed mismatch repair. Genes encoding proteins with strong similarities to RecJ have been found in every eubacterial genome sequenced to date, with the exception of Mycoplasma and Mycobacterium tuberculosis. Multiple genes encoding proteins similar to RecJ are found in some eubacteria, including Bacillus and Helicobacter, and in the archaea. Among this divergent set of sequences, seven conserved motifs emerge. We demonstrate here that amino acids within six of these motifs are essential for both the biochemical and genetic functions of E. coli RecJ. These motifs may define interactions with Mg(2+) ions or substrate DNA. A large family of proteins more distantly related to RecJ is present in archaea, eubacteria, and eukaryotes, including a hypothetical protein in the MgPa adhesin operon of Mycoplasma, a domain of putative polyA polymerases in Synechocystis and Aquifex, PRUNE of Drosophila, and an exopolyphosphatase (PPX1) of Saccharomyces cereviseae. Because these six RecJ motifs are shared between exonucleases and exopolyphosphatases, they may constitute an ancient phosphoesterase domain now found in all kingdoms of life.
Fuzzy support vector machine for microarray imbalanced data classification
Ladayya, Faroh; Purnami, Santi Wulan; Irhamah
2017-11-01
DNA microarrays are data containing gene expression with small sample sizes and high number of features. Furthermore, imbalanced classes is a common problem in microarray data. This occurs when a dataset is dominated by a class which have significantly more instances than the other minority classes. Therefore, it is needed a classification method that solve the problem of high dimensional and imbalanced data. Support Vector Machine (SVM) is one of the classification methods that is capable of handling large or small samples, nonlinear, high dimensional, over learning and local minimum issues. SVM has been widely applied to DNA microarray data classification and it has been shown that SVM provides the best performance among other machine learning methods. However, imbalanced data will be a problem because SVM treats all samples in the same importance thus the results is bias for minority class. To overcome the imbalanced data, Fuzzy SVM (FSVM) is proposed. This method apply a fuzzy membership to each input point and reformulate the SVM such that different input points provide different contributions to the classifier. The minority classes have large fuzzy membership so FSVM can pay more attention to the samples with larger fuzzy membership. Given DNA microarray data is a high dimensional data with a very large number of features, it is necessary to do feature selection first using Fast Correlation based Filter (FCBF). In this study will be analyzed by SVM, FSVM and both methods by applying FCBF and get the classification performance of them. Based on the overall results, FSVM on selected features has the best classification performance compared to SVM.
Piasecki, E.
2009-01-01
Heavy-ion collisions often produce a fusion barrier distribution with structures displaying a fingerprint of couplings to highly collective excitations [1]. Basically the same distribution can be obtained from large-angle quasi-elastic scattering, though here the role of the many weak direct-reaction channels is unclear. For 2 0N e + 9 0Z r we have observed the barrier structures expected for the highly deformed neon projectile, but for 2 0N e + 9 2Z r we find completely smooth distribution (see Fig.1). We find that transfer channels in these systems are of similar strength but single particle excitations are significantly stronger in the latter case. They apparently reduce the 'resolving power' of the quasi-elastic channel, what leads to smeared out, or 'fuzzy' barrier distribution. This is the first case when such a phenomenon has been observed.(author)
Highly scalable Ab initio genomic motif identification
Marchand, Benoit; Bajic, Vladimir B.; Kaushik, Dinesh
2011-01-01
We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.
On Fuzzy β-I-open sets and Fuzzy β-I-continuous functions
Keskin, Aynur
2009-01-01
In this paper, first of all we obtain some properties and characterizations of fuzzy β-I-open sets. After that, we also define the notion of β-I-closed sets and obtain some properties. Lastly, we introduce the notions of fuzzy β-I-continuity with the help of fuzzy β-I-open sets to obtain decomposition of fuzzy continuity.
On Fuzzy {beta}-I-open sets and Fuzzy {beta}-I-continuous functions
Keskin, Aynur [Department of Mathematics, Faculty of Science and Arts, Selcuk University, Campus, 42075 Konya (Turkey)], E-mail: akeskin@selcuk.edu.tr
2009-11-15
In this paper, first of all we obtain some properties and characterizations of fuzzy {beta}-I-open sets. After that, we also define the notion of {beta}-I-closed sets and obtain some properties. Lastly, we introduce the notions of fuzzy {beta}-I-continuity with the help of fuzzy {beta}-I-open sets to obtain decomposition of fuzzy continuity.
Supply chain management under fuzziness recent developments and techniques
Öztayşi, Başar
2014-01-01
Supply Chain Management Under Fuzziness presents recently developed fuzzy models and techniques for supply chain management. These include: fuzzy PROMETHEE, fuzzy AHP, fuzzy ANP, fuzzy VIKOR, fuzzy DEMATEL, fuzzy clustering, fuzzy linear programming, and fuzzy inference systems. The book covers both practical applications and new developments concerning these methods. This book offers an excellent resource for researchers and practitioners in supply chain management and logistics, and will provide them with new suggestions and directions for future research. Moreover, it will support graduate students in their university courses, such as specialized courses on supply chains and logistics, as well as related courses in the fields of industrial engineering, engineering management and business administration.
Target motifs affecting natural immunity by a constitutive CRISPR-Cas system in Escherichia coli.
Cristóbal Almendros
Full Text Available Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR and CRISPR associated (cas genes conform the CRISPR-Cas systems of various bacteria and archaea and produce degradation of invading nucleic acids containing sequences (protospacers that are complementary to repeat intervening spacers. It has been demonstrated that the base sequence identity of a protospacer with the cognate spacer and the presence of a protospacer adjacent motif (PAM influence CRISPR-mediated interference efficiency. By using an original transformation assay with plasmids targeted by a resident spacer here we show that natural CRISPR-mediated immunity against invading DNA occurs in wild type Escherichia coli. Unexpectedly, the strongest activity is observed with protospacer adjoining nucleotides (interference motifs that differ from the PAM both in sequence and location. Hence, our results document for the first time native CRISPR activity in E. coli and demonstrate that positions next to the PAM in invading DNA influence their recognition and degradation by these prokaryotic immune systems.
Stability Analysis of Interconnected Fuzzy Systems Using the Fuzzy Lyapunov Method
Ken Yeh
2010-01-01
Full Text Available The fuzzy Lyapunov method is investigated for use with a class of interconnected fuzzy systems. The interconnected fuzzy systems consist of J interconnected fuzzy subsystems, and the stability analysis is based on Lyapunov functions. Based on traditional Lyapunov stability theory, we further propose a fuzzy Lyapunov method for the stability analysis of interconnected fuzzy systems. The fuzzy Lyapunov function is defined in fuzzy blending quadratic Lyapunov functions. Some stability conditions are derived through the use of fuzzy Lyapunov functions to ensure that the interconnected fuzzy systems are asymptotically stable. Common solutions can be obtained by solving a set of linear matrix inequalities (LMIs that are numerically feasible. Finally, simulations are performed in order to verify the effectiveness of the proposed stability conditions in this paper.
CombiMotif: A new algorithm for network motifs discovery in protein-protein interaction networks
Luo, Jiawei; Li, Guanghui; Song, Dan; Liang, Cheng
2014-12-01
Discovering motifs in protein-protein interaction networks is becoming a current major challenge in computational biology, since the distribution of the number of network motifs can reveal significant systemic differences among species. However, this task can be computationally expensive because of the involvement of graph isomorphic detection. In this paper, we present a new algorithm (CombiMotif) that incorporates combinatorial techniques to count non-induced occurrences of subgraph topologies in the form of trees. The efficiency of our algorithm is demonstrated by comparing the obtained results with the current state-of-the art subgraph counting algorithms. We also show major differences between unicellular and multicellular organisms. The datasets and source code of CombiMotif are freely available upon request.
Fuzzy relational calculus theory, applications and software
Peeva, Ketty
2004-01-01
This book examines fuzzy relational calculus theory with applications in various engineering subjects. The scope of the text covers unified and exact methods with algorithms for direct and inverse problem resolution in fuzzy relational calculus. Extensive engineering applications of fuzzy relation compositions and fuzzy linear systems (linear, relational and intuitionistic) are discussed. Some examples of such applications include solutions of equivalence, reduction and minimization problems in fuzzy machines, pattern recognition in fuzzy languages, optimization and inference engines in textile and chemical engineering, etc. A comprehensive overview of the authors' original work in fuzzy relational calculus is also provided in each chapter. The attached CD-Rom contains a toolbox with many functions for fuzzy calculations, together with an original algorithm for inverse problem resolution in MATLAB. This book is also suitable for use as a textbook in related courses at advanced undergraduate and graduate level...
Compound Option Pricing under Fuzzy Environment
Xiandong Wang
2014-01-01
Full Text Available Considering the uncertainty of a financial market includes two aspects: risk and vagueness; in this paper, fuzzy sets theory is applied to model the imprecise input parameters (interest rate and volatility. We present the fuzzy price of compound option by fuzzing the interest and volatility in Geske’s compound option pricing formula. For each α, the α-level set of fuzzy prices is obtained according to the fuzzy arithmetics and the definition of fuzzy-valued function. We apply a defuzzification method based on crisp possibilistic mean values of the fuzzy interest rate and fuzzy volatility to obtain the crisp possibilistic mean value of compound option price. Finally, we present a numerical analysis to illustrate the compound option pricing under fuzzy environment.
Fuzzy Arden Syntax: A fuzzy programming language for medicine.
Vetterlein, Thomas; Mandl, Harald; Adlassnig, Klaus-Peter
2010-05-01
The programming language Arden Syntax has been optimised for use in clinical decision support systems. We describe an extension of this language named Fuzzy Arden Syntax, whose original version was introduced in S. Tiffe's dissertation on "Fuzzy Arden Syntax: Representation and Interpretation of Vague Medical Knowledge by Fuzzified Arden Syntax" (Vienna University of Technology, 2003). The primary aim is to provide an easy means of processing vague or uncertain data, which frequently appears in medicine. For both propositional and number data types, fuzzy equivalents have been added to Arden Syntax. The Boolean data type was generalised to represent any truth degree between the two extremes 0 (falsity) and 1 (truth); fuzzy data types were introduced to represent fuzzy sets. The operations on truth values and real numbers were generalised accordingly. As the conditions to decide whether a certain programme unit is executed or not may be indeterminate, a Fuzzy Arden Syntax programme may split. The data in the different branches may be optionally aggregated subsequently. Fuzzy Arden Syntax offers the possibility to formulate conveniently Medical Logic Modules (MLMs) based on the principle of a continuously graded applicability of statements. Furthermore, ad hoc decisions about sharp value boundaries can be avoided. As an illustrative example shows, an MLM making use of the features of Fuzzy Arden Syntax is not significantly more complex than its Arden Syntax equivalent; in the ideal case, a programme handling crisp data remains practically unchanged when compared to its fuzzified version. In the latter case, the output data, which can be a set of weighted alternatives, typically depends continuously from the input data. In typical applications an Arden Syntax MLM can produce a different output after only slight changes of the input; discontinuities are in fact unavoidable when the input varies continuously but the output is taken from a discrete set of possibilities
Dhruba Das; Hemanta K. Baruah
2015-01-01
In this article, based on Zadeh’s extension principle we have apply the parametric programming approach to construct the membership functions of the performance measures when the interarrival time and the service time are fuzzy numbers based on the Baruah’s Randomness- Fuzziness Consistency Principle. The Randomness-Fuzziness Consistency Principle leads to defining a normal law of fuzziness using two different laws of randomness. In this article, two fuzzy queues FM...
Fuzzy upper bounds and their applications
Soleimani-damaneh, M. [Department of Mathematics, Faculty of Mathematical Science and Computer Engineering, Teacher Training University, 599 Taleghani Avenue, Tehran 15618 (Iran, Islamic Republic of)], E-mail: soleimani_d@yahoo.com
2008-04-15
This paper considers the concept of fuzzy upper bounds and provides some relevant applications. Considering a fuzzy DEA model, the existence of a fuzzy upper bound for the objective function of the model is shown and an effective approach to solve that model is introduced. Some dual interpretations are provided, which are useful for practical purposes. Applications of the concept of fuzzy upper bounds in two physical problems are pointed out.
Neuro-fuzzy Control of Integrating Processes
Anna Vasičkaninová
2011-11-01
Full Text Available Fuzzy technology is adaptive and easily applicable in different areas.Fuzzy logic provides powerful tools to capture the perceptionof natural phenomena. The paper deals with tuning of neuro-fuzzy controllers for integrating plant and for integrating plantswith time delay. The designed approach is verified on three examples by simulations and compared plants with classical PID control.Designed fuzzy controllers lead to better closed-loop control responses then classical PID controllers.
FFLP problem with symmetric trapezoidal fuzzy numbers
Reza Daneshrad
2015-04-01
Full Text Available The most popular approach for solving fully fuzzy linear programming (FFLP problems is to convert them into the corresponding deterministic linear programs. Khan et al. (2013 [Khan, I. U., Ahmad, T., & Maan, N. (2013. A simplified novel technique for solving fully fuzzy linear programming problems. Journal of Optimization Theory and Applications, 159(2, 536-546.] claimed that there had been no method in the literature to find the fuzzy optimal solution of a FFLP problem without converting it into crisp linear programming problem, and proposed a technique for the same. Others showed that the fuzzy arithmetic operation used by Khan et al. (2013 had some problems in subtraction and division operations, which could lead to misleading results. Recently, Ezzati et al. (2014 [Ezzati, R., Khorram, E., & Enayati, R. (2014. A particular simplex algorithm to solve fuzzy lexicographic multi-objective linear programming problems and their sensitivity analysis on the priority of the fuzzy objective functions. Journal of Intelligent and Fuzzy Systems, 26(5, 2333-2358.] defined a new operation on symmetric trapezoidal fuzzy numbers and proposed a new algorithm to find directly a lexicographic/preemptive fuzzy optimal solution of a fuzzy lexicographic multi-objective linear programming problem by using new fuzzy arithmetic operations, but their model was not fully fuzzy optimization. In this paper, a new method, by using Ezzati et al. (2014’s fuzzy arithmetic operation and a fuzzy version of simplex algorithm, is proposed for solving FFLP problem whose parameters are represented by symmetric trapezoidal fuzzy number without converting the given problem into crisp equivalent problem. By using the proposed method, the fuzzy optimal solution of FFLP problem can be easily obtained. A numerical example is provided to illustrate the proposed method.
John A Capra
2010-07-01
Full Text Available G-quadruplex DNA is a four-stranded DNA structure formed by non-Watson-Crick base pairing between stacked sets of four guanines. Many possible functions have been proposed for this structure, but its in vivo role in the cell is still largely unresolved. We carried out a genome-wide survey of the evolutionary conservation of regions with the potential to form G-quadruplex DNA structures (G4 DNA motifs across seven yeast species. We found that G4 DNA motifs were significantly more conserved than expected by chance, and the nucleotide-level conservation patterns suggested that the motif conservation was the result of the formation of G4 DNA structures. We characterized the association of conserved and non-conserved G4 DNA motifs in Saccharomyces cerevisiae with more than 40 known genome features and gene classes. Our comprehensive, integrated evolutionary and functional analysis confirmed the previously observed associations of G4 DNA motifs with promoter regions and the rDNA, and it identified several previously unrecognized associations of G4 DNA motifs with genomic features, such as mitotic and meiotic double-strand break sites (DSBs. Conserved G4 DNA motifs maintained strong associations with promoters and the rDNA, but not with DSBs. We also performed the first analysis of G4 DNA motifs in the mitochondria, and surprisingly found a tenfold higher concentration of the motifs in the AT-rich yeast mitochondrial DNA than in nuclear DNA. The evolutionary conservation of the G4 DNA motif and its association with specific genome features supports the hypothesis that G4 DNA has in vivo functions that are under evolutionary constraint.
A SELF-ORGANISING FUZZY LOGIC CONTROLLER
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One major drawback of fuzzy logic controllers is the difficulty encountered in the construction of a rule- base ... The greatest limitation of fuzzy logic control is the lack ..... c(kT)= e(kT)-e((k-1)T). (16) .... with the aid of fuzzy models”, It in Industrial.
Forecasting Enrollments with Fuzzy Time Series.
Song, Qiang; Chissom, Brad S.
The concept of fuzzy time series is introduced and used to forecast the enrollment of a university. Fuzzy time series, an aspect of fuzzy set theory, forecasts enrollment using a first-order time-invariant model. To evaluate the model, the conventional linear regression technique is applied and the predicted values obtained are compared to the…
On the intuitionistic fuzzy inner product spaces
Goudarzi, M.; Vaezpour, S.M.; Saadati, R.
2009-01-01
In this paper, the definition of intuitionistic fuzzy inner product is given. By virtue of this definition, some convergence theorems, Schwarts inequality and the orthogonal concept for intuitionistic fuzzy inner product spaces are established and introduced. Moreover the relationship between this kind of spaces and intuitionistic fuzzy normed spaces is considered.
Fuzzy control of pressurizer dynamic process
Ming Zhedong; Zhao Fuyu
2006-01-01
Considering the characteristics of pressurizer dynamic process, the fuzzy control system that takes the advantages of both fuzzy controller and PID controller is designed for the dynamic process in pressurizer. The simulation results illustrate this type of composite control system is with better qualities than those of single fuzzy controller and single PID controller. (authors)
Possible use of fuzzy logic in database
Vaclav Bezdek
2011-04-01
Full Text Available The article deals with fuzzy logic and its possible use in database systems. At first fuzzy thinking style is shown on a simple example. Next the advantages of the fuzzy approach to database searching are considered on the database of used cars in the Czech Republic.
Effectiveness of Securities with Fuzzy Probabilistic Return
Krzysztof Piasecki
2011-01-01
Full Text Available The generalized fuzzy present value of a security is defined here as fuzzy valued utility of cash flow. The generalized fuzzy present value cannot depend on the value of future cash flow. There exists such a generalized fuzzy present value which is not a fuzzy present value in the sense given by some authors. If the present value is a fuzzy number and the future value is a random one, then the return rate is given as a probabilistic fuzzy subset on a real line. This kind of return rate is called a fuzzy probabilistic return. The main goal of this paper is to derive the family of effective securities with fuzzy probabilistic return. Achieving this goal requires the study of the basic parameters characterizing fuzzy probabilistic return. Therefore, fuzzy expected value and variance are determined for this case of return. These results are a starting point for constructing a three-dimensional image. The set of effective securities is introduced as the Pareto optimal set determined by the maximization of the expected return rate and minimization of the variance. Finally, the set of effective securities is distinguished as a fuzzy set. These results are obtained without the assumption that the distribution of future values is Gaussian. (original abstract
The majority rule in a fuzzy environment.
Montero, Javier
1986-01-01
In this paper, an axiomatic approach to rational decision making in a fuzzy environment is studied. In particular, the majority rule is proposed as a rational way for aggregating fuzzy opinions in a group, when such agroup is defined as a fuzzy set.
The fuzzy approach to statistical analysis
Coppi, Renato; Gil, Maria A.; Kiers, Henk A. L.
2006-01-01
For the last decades, research studies have been developed in which a coalition of Fuzzy Sets Theory and Statistics has been established with different purposes. These namely are: (i) to introduce new data analysis problems in which the objective involves either fuzzy relationships or fuzzy terms;
Fuzzy commutative algebra and its application in mechanical engineering
Han, J.; Song, H.
1996-01-01
Based on literature data, this paper discusses the whole mathematical structure about point-fuzzy number set F(R). By introducing some new operations about addition, subtraction, multiplication, division and scalar multiplication, we prove that F(R) can form fuzzy linear space, fuzzy commutative ring, fuzzy commutative algebra in order. Furthermore, we get that A is fuzzy commutative algebra for any fuzzy subset. At last, we give an application of point-fuzzy number to mechanical engineering
Fuzzy logic of Aristotelian forms
Perlovsky, L.I. [Nichols Research Corp., Lexington, MA (United States)
1996-12-31
Model-based approaches to pattern recognition and machine vision have been proposed to overcome the exorbitant training requirements of earlier computational paradigms. However, uncertainties in data were found to lead to a combinatorial explosion of the computational complexity. This issue is related here to the roles of a priori knowledge vs. adaptive learning. What is the a-priori knowledge representation that supports learning? I introduce Modeling Field Theory (MFT), a model-based neural network whose adaptive learning is based on a priori models. These models combine deterministic, fuzzy, and statistical aspects to account for a priori knowledge, its fuzzy nature, and data uncertainties. In the process of learning, a priori fuzzy concepts converge to crisp or probabilistic concepts. The MFT is a convergent dynamical system of only linear computational complexity. Fuzzy logic turns out to be essential for reducing the combinatorial complexity to linear one. I will discuss the relationship of the new computational paradigm to two theories due to Aristotle: theory of Forms and logic. While theory of Forms argued that the mind cannot be based on ready-made a priori concepts, Aristotelian logic operated with just such concepts. I discuss an interpretation of MFT suggesting that its fuzzy logic, combining a-priority and adaptivity, implements Aristotelian theory of Forms (theory of mind). Thus, 2300 years after Aristotle, a logic is developed suitable for his theory of mind.
Implementing fuzzy polynomial interpolation (FPI and fuzzy linear regression (LFR
Maria Cristina Floreno
1996-05-01
Full Text Available This paper presents some preliminary results arising within a general framework concerning the development of software tools for fuzzy arithmetic. The program is in a preliminary stage. What has been already implemented consists of a set of routines for elementary operations, optimized functions evaluation, interpolation and regression. Some of these have been applied to real problems.This paper describes a prototype of a library in C++ for polynomial interpolation of fuzzifying functions, a set of routines in FORTRAN for fuzzy linear regression and a program with graphical user interface allowing the use of such routines.
Annotating RNA motifs in sequences and alignments.
Gardner, Paul P; Eldai, Hisham
2015-01-01
RNA performs a diverse array of important functions across all cellular life. These functions include important roles in translation, building translational machinery and maturing messenger RNA. More recent discoveries include the miRNAs and bacterial sRNAs that regulate gene expression, the thermosensors, riboswitches and other cis-regulatory elements that help prokaryotes sense their environment and eukaryotic piRNAs that suppress transposition. However, there can be a long period between the initial discovery of a RNA and determining its function. We present a bioinformatic approach to characterize RNA motifs, which are critical components of many RNA structure-function relationships. These motifs can, in some instances, provide researchers with functional hypotheses for uncharacterized RNAs. Moreover, we introduce a new profile-based database of RNA motifs--RMfam--and illustrate some applications for investigating the evolution and functional characterization of RNA. All the data and scripts associated with this work are available from: https://github.com/ppgardne/RMfam. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
Dynamic motifs in socio-economic networks
Zhang, Xin; Shao, Shuai; Stanley, H. Eugene; Havlin, Shlomo
2014-12-01
Socio-economic networks are of central importance in economic life. We develop a method of identifying and studying motifs in socio-economic networks by focusing on “dynamic motifs,” i.e., evolutionary connection patterns that, because of “node acquaintances” in the network, occur much more frequently than random patterns. We examine two evolving bi-partite networks: i) the world-wide commercial ship chartering market and ii) the ship build-to-order market. We find similar dynamic motifs in both bipartite networks, even though they describe different economic activities. We also find that “influence” and “persistence” are strong factors in the interaction behavior of organizations. When two companies are doing business with the same customer, it is highly probable that another customer who currently only has business relationship with one of these two companies, will become customer of the second in the future. This is the effect of influence. Persistence means that companies with close business ties to customers tend to maintain their relationships over a long period of time.
Quick fuzzy backpropagation algorithm.
Nikov, A; Stoeva, S
2001-03-01
A modification of the fuzzy backpropagation (FBP) algorithm called QuickFBP algorithm is proposed, where the computation of the net function is significantly quicker. It is proved that the FBP algorithm is of exponential time complexity, while the QuickFBP algorithm is of polynomial time complexity. Convergence conditions of the QuickFBP, resp. the FBP algorithm are defined and proved for: (1) single output neural networks in case of training patterns with different targets; and (2) multiple output neural networks in case of training patterns with equivalued target vector. They support the automation of the weights training process (quasi-unsupervised learning) establishing the target value(s) depending on the network's input values. In these cases the simulation results confirm the convergence of both algorithms. An example with a large-sized neural network illustrates the significantly greater training speed of the QuickFBP rather than the FBP algorithm. The adaptation of an interactive web system to users on the basis of the QuickFBP algorithm is presented. Since the QuickFBP algorithm ensures quasi-unsupervised learning, this implies its broad applicability in areas of adaptive and adaptable interactive systems, data mining, etc. applications.
On Intuitionistic Fuzzy Context-Free Languages
Jianhua Jin
2013-01-01
automata theory. Additionally, we introduce the concepts of Chomsky normal form grammar (IFCNF and Greibach normal form grammar (IFGNF based on intuitionistic fuzzy sets. The results of our study indicate that intuitionistic fuzzy context-free languages generated by IFCFGs are equivalent to those generated by IFGNFs and IFCNFs, respectively, and they are also equivalent to intuitionistic fuzzy recognizable step functions. Then some operations on the family of intuitionistic fuzzy context-free languages are discussed. Finally, pumping lemma for intuitionistic fuzzy context-free languages is investigated.
Schildt, G.H.
1997-01-01
A fuzzy controller for safety related process control is presented for applications in the field of NPPs. The size of necessary rules is relatively small. Thus, there exists a real chance for verification and validation of software due to the fact that the whole software can be structured into standard fuzzy software (like fuzzyfication, inference algorithms, and defuzzyfication), real-time operating system software, and the contents of the rule base. Furthermore, there is an excellent advantage fuel to real-time behaviour, because program execution time is much more predictable than for conventional PID-controller software. Additionally, up to now special know-how does exist to prove stability of fuzzy controller. Hardware design has been done due to fundamental principles of safety technique like watch dog function, dynamization principles, and quiescent current principle. (author). 3 refs, 5 figs
Schildt, G.H.
1996-01-01
After an introduction into safety terms a fuzzy controller for safety related process control will be presented, especially for applications in the field of NPPs. One can show that the size of necessary rules is relatively small. Thus, there exists a real chance for verification and validation of software due to the fact that the whole software can be structured into standard fuzzy software (like fuzzyfication, inference algorithms, and defuzzyfication), real-time operating system software, and the contents of the rule base. Furthermore, there is an excellent advantage due to real-time behaviour, because program execution time can be much more planned than for conventional PID-controller software. Additionally, up to now special know-how does exist to prove stability of fuzzy controller. Hardware design has been done due to fundamental principles of safety technique like watch dog function, dynamization principle, and quiescent current principle
Schildt, G H [Technische Univ., Vienna (Austria)
1997-07-01
A fuzzy controller for safety related process control is presented for applications in the field of NPPs. The size of necessary rules is relatively small. Thus, there exists a real chance for verification and validation of software due to the fact that the whole software can be structured into standard fuzzy software (like fuzzyfication, inference algorithms, and defuzzyfication), real-time operating system software, and the contents of the rule base. Furthermore, there is an excellent advantage fuel to real-time behaviour, because program execution time is much more predictable than for conventional PID-controller software. Additionally, up to now special know-how does exist to prove stability of fuzzy controller. Hardware design has been done due to fundamental principles of safety technique like watch dog function, dynamization principles, and quiescent current principle. (author). 3 refs, 5 figs.
Combining fuzzy mathematics with fuzzy logic to solve business management problems
Vrba, Joseph A.
1993-12-01
Fuzzy logic technology has been applied to control problems with great success. Because of this, many observers fell that fuzzy logic is applicable only in the control arena. However, business management problems almost never deal with crisp values. Fuzzy systems technology--a combination of fuzzy logic, fuzzy mathematics and a graphical user interface--is a natural fit for developing software to assist in typical business activities such as planning, modeling and estimating. This presentation discusses how fuzzy logic systems can be extended through the application of fuzzy mathematics and the use of a graphical user interface to make the information contained in fuzzy numbers accessible to business managers. As demonstrated through examples from actual deployed systems, this fuzzy systems technology has been employed successfully to provide solutions to the complex real-world problems found in the business environment.
Global sensitivity analysis for fuzzy inputs based on the decomposition of fuzzy output entropy
Shi, Yan; Lu, Zhenzhou; Zhou, Yicheng
2018-06-01
To analyse the component of fuzzy output entropy, a decomposition method of fuzzy output entropy is first presented. After the decomposition of fuzzy output entropy, the total fuzzy output entropy can be expressed as the sum of the component fuzzy entropy contributed by fuzzy inputs. Based on the decomposition of fuzzy output entropy, a new global sensitivity analysis model is established for measuring the effects of uncertainties of fuzzy inputs on the output. The global sensitivity analysis model can not only tell the importance of fuzzy inputs but also simultaneously reflect the structural composition of the response function to a certain degree. Several examples illustrate the validity of the proposed global sensitivity analysis, which is a significant reference in engineering design and optimization of structural systems.
Frechet differentiation of nonlinear operators between fuzzy normed spaces
Yilmaz, Yilmaz
2009-01-01
By the rapid advances in linear theory of fuzzy normed spaces and fuzzy bounded linear operators it is natural idea to set and improve its nonlinear peer. We aimed in this work to realize this idea by introducing fuzzy Frechet derivative based on the fuzzy norm definition in Bag and Samanta [Bag T, Samanta SK. Finite dimensional fuzzy normed linear spaces. J Fuzzy Math 2003;11(3):687-705]. The definition is divided into two part as strong and weak fuzzy Frechet derivative so that it is compatible with strong and weak fuzzy continuity of operators. Also we restate fuzzy compact operator definition of Lael and Nouroizi [Lael F, Nouroizi K. Fuzzy compact linear operators. Chaos, Solitons and Fractals 2007;34(5):1584-89] as strongly and weakly fuzzy compact by taking into account the compatibility. We prove also that weak Frechet derivative of a nonlinear weakly fuzzy compact operator is also weakly fuzzy compact.
Fuzzy Entropy： Axiomatic Definition and Neural Networks Model
QINGMing; CAOYue; HUANGTian-min
2004-01-01
The measure of uncertainty is adopted as a measure of information. The measures of fuzziness are known as fuzzy information measures. The measure of a quantity of fuzzy information gained from a fuzzy set or fuzzy system is known as fuzzy entropy. Fuzzy entropy has been focused and studied by many researchers in various fields. In this paper, firstly, the axiomatic definition of fuzzy entropy is discussed. Then, neural networks model of fuzzy entropy is proposed, based on the computing capability of neural networks. In the end, two examples are discussed to show the efficiency of the model.
Application of fuzzy logic to social choice theory
Mordeson, John N; Clark, Terry D
2015-01-01
Fuzzy social choice theory is useful for modeling the uncertainty and imprecision prevalent in social life yet it has been scarcely applied and studied in the social sciences. Filling this gap, Application of Fuzzy Logic to Social Choice Theory provides a comprehensive study of fuzzy social choice theory.The book explains the concept of a fuzzy maximal subset of a set of alternatives, fuzzy choice functions, the factorization of a fuzzy preference relation into the ""union"" (conorm) of a strict fuzzy relation and an indifference operator, fuzzy non-Arrowian results, fuzzy versions of Arrow's
Ellipsoidal fuzzy learning for smart car platoons
Dickerson, Julie A.; Kosko, Bart
1993-12-01
A neural-fuzzy system combined supervised and unsupervised learning to find and tune the fuzzy-rules. An additive fuzzy system approximates a function by covering its graph with fuzzy rules. A fuzzy rule patch can take the form of an ellipsoid in the input-output space. Unsupervised competitive learning found the statistics of data clusters. The covariance matrix of each synaptic quantization vector defined on ellipsoid centered at the centroid of the data cluster. Tightly clustered data gave smaller ellipsoids or more certain rules. Sparse data gave larger ellipsoids or less certain rules. Supervised learning tuned the ellipsoids to improve the approximation. The supervised neural system used gradient descent to find the ellipsoidal fuzzy patches. It locally minimized the mean-squared error of the fuzzy approximation. Hybrid ellipsoidal learning estimated the control surface for a smart car controller.
Fuzzy Stochastic Optimization Theory, Models and Applications
Wang, Shuming
2012-01-01
Covering in detail both theoretical and practical perspectives, this book is a self-contained and systematic depiction of current fuzzy stochastic optimization that deploys the fuzzy random variable as a core mathematical tool to model the integrated fuzzy random uncertainty. It proceeds in an orderly fashion from the requisite theoretical aspects of the fuzzy random variable to fuzzy stochastic optimization models and their real-life case studies. The volume reflects the fact that randomness and fuzziness (or vagueness) are two major sources of uncertainty in the real world, with significant implications in a number of settings. In industrial engineering, management and economics, the chances are high that decision makers will be confronted with information that is simultaneously probabilistically uncertain and fuzzily imprecise, and optimization in the form of a decision must be made in an environment that is doubly uncertain, characterized by a co-occurrence of randomness and fuzziness. This book begins...
Fuzzy logic controller using different inference methods
Liu, Z.; De Keyser, R.
1994-01-01
In this paper the design of fuzzy controllers by using different inference methods is introduced. Configuration of the fuzzy controllers includes a general rule-base which is a collection of fuzzy PI or PD rules, the triangular fuzzy data model and a centre of gravity defuzzification algorithm. The generalized modus ponens (GMP) is used with the minimum operator of the triangular norm. Under the sup-min inference rule, six fuzzy implication operators are employed to calculate the fuzzy look-up tables for each rule base. The performance is tested in simulated systems with MATLAB/SIMULINK. Results show the effects of using the fuzzy controllers with different inference methods and applied to different test processes
Introduction to fuzzy logic using Matlab
Sivanandam, SN; Deepa, S N
2006-01-01
Fuzzy Logic, at present is a hot topic, among academicians as well various programmers. This book is provided to give a broad, in-depth overview of the field of Fuzzy Logic. The basic principles of Fuzzy Logic are discussed in detail with various solved examples. The different approaches and solutions to the problems given in the book are well balanced and pertinent to the Fuzzy Logic research projects. The applications of Fuzzy Logic are also dealt to make the readers understand the concept of Fuzzy Logic. The solutions to the problems are programmed using MATLAB 6.0 and the simulated results are given. The MATLAB Fuzzy Logic toolbox is provided for easy reference.
CONTEMPORARY USAGE OF TRADITIONAL TURKISH MOTIFS IN PRODUCT DESIGNS
Tulay Gumuser
2012-12-01
Full Text Available The aim of this study is to identify the traditional Turkish motifs and its relations among present industrial designs. Traditional Turkish motifs played a very important role in 16th century onwards. The arts of the Ottoman Empire were used because of their symbolic meanings and unique styles. When we examine these motifs we encounter; Tiger Stripe, Three Spot (Çintemani, Rumi, Hatayi, Penç, Cloud, Crescent, Star, Crown, Hyacinth, Tulip and Carnation motifs. Nowadays, Turkish designers have begun to use these traditional Turkish motifs in their designs so as to create differences and awareness in the world design. The examples of these industrial designs, using the Turkish motifs, have survived and have Ottoman heritage and historical value. In this study, the Turkish motifs will be examined along with their focus on contemporary Turkish industrial designs used today.
Outdoor altitude stabilization of QuadRotor based on type-2 fuzzy and fuzzy PID
Wicaksono, H.; Yusuf, Y. G.; Kristanto, C.; Haryanto, L.
2017-11-01
This paper presents a design of altitude stabilization of QuadRotor based on type-2 fuzzy and fuzzy PID. This practical design is implemented outdoor. Barometric and sonar sensor were used in this experiment as an input for the controller YoHe. The throttle signal as a control input was provided by the controller to leveling QuadRotor in particular altitude and known well as altitude stabilization. The parameter of type-2 fuzzy and fuzzy PID was tuned in several heights to get the best control parameter for any height. Type-2 fuzzy produced better result than fuzzy PID but had a slow response in the beginning.
Complex Fuzzy Set-Valued Complex Fuzzy Measures and Their Properties
Ma, Shengquan; Li, Shenggang
2014-01-01
Let F*(K) be the set of all fuzzy complex numbers. In this paper some classical and measure-theoretical notions are extended to the case of complex fuzzy sets. They are fuzzy complex number-valued distance on F*(K), fuzzy complex number-valued measure on F*(K), and some related notions, such as null-additivity, pseudo-null-additivity, null-subtraction, pseudo-null-subtraction, autocontionuous from above, autocontionuous from below, and autocontinuity of the defined fuzzy complex number-valued measures. Properties of fuzzy complex number-valued measures are studied in detail. PMID:25093202
Aplikasi Ornamen Khas Maluku untuk Pengembangan Desain Motif Batik
Masiswo Masiswo
2016-04-01
Full Text Available ABSTRAKMaluku memiliki banyak ragam hias budaya warisan nilai leluhur berupa ornamen etnis yang merupakan kesenian dan keterampilan kerajinan. Hasil warisan tersebut sampai saat ini masih lestari hidup serta dapat dinikmati sebagai konsumsi rohani yang memuaskan manusia. Berkaitan dengan keberlangsungan nilai-nilai tradisi etnis yang berwujud pada ornamen-ornamen daerah Maluku, maka dikembangkan untuk kebutuhan manusia berupa motif batik pada kain. Pengembangan ornamen ini lebih menekankan pada representasi akan bentuk-bentuk ornamen yang diterapkan pada kerajinan batik berupa motif khas Maluku. Pengembangan alternatif desain motif batik dibuat tiga variasi yang bersumber dari ornamen khas Maluku dibuat prototipe produknya dan diuji ketahanan luntur warnanya. Hasil uji ketahanan luntur warna terhadap gosokan basah dari tiga prototipe produk berpredikat baik sekali terdapat pada “Motif Siwa” dan predikat baik pada motif “Siwa Talang” dan motif “Matahari Siwa Talang”.Kata kunci: desain, Maluku, motif batik, ornamenABSTRACTMaluku has much decorative ancestral cultural heritage value in the form of ornament ethnic arts and crafts skills. The result of the legacy is still sustainable living can be enjoyed as well as satisfying spiritual human consumption.Related to the sustainability of traditional values in the form of ethnic ornaments Maluku, it was developed for human needs in the form of batik cloth . The development of these ornaments will be more emphasis on the representation forms of ornamentation that is applied to a batik motif Maluku. Development of alternative design motif made three variations. The development of three alternative design motifs derived from the Maluku ornaments made and tested a prototype product color fastness. The test results of color fastness to wet rubbing of the three prototypes are excellent products predicated on the "Motif Siwa" and a good rating on the motif "Siwa Talang" and motif "Matahari Siwa
Identity and functions of CxxC-derived motifs.
Fomenko, Dmitri E; Gladyshev, Vadim N
2003-09-30
Two cysteines separated by two other residues (the CxxC motif) are employed by many redox proteins for formation, isomerization, and reduction of disulfide bonds and for other redox functions. The place of the C-terminal cysteine in this motif may be occupied by serine (the CxxS motif), modifying the functional repertoire of redox proteins. Here we found that the CxxC motif may also give rise to a motif, in which the C-terminal cysteine is replaced with threonine (the CxxT motif). Moreover, in contrast to a view that the N-terminal cysteine in the CxxC motif always serves as a nucleophilic attacking group, this residue could also be replaced with threonine (the TxxC motif), serine (the SxxC motif), or other residues. In each of these CxxC-derived motifs, the presence of a downstream alpha-helix was strongly favored. A search for conserved CxxC-derived motif/helix patterns in four complete genomes representing bacteria, archaea, and eukaryotes identified known redox proteins and suggested possible redox functions for several additional proteins. Catalytic sites in peroxiredoxins were major representatives of the TxxC motif, whereas those in glutathione peroxidases represented the CxxT motif. Structural assessments indicated that threonines in these enzymes could stabilize catalytic thiolates, suggesting revisions to previously proposed catalytic triads. Each of the CxxC-derived motifs was also observed in natural selenium-containing proteins, in which selenocysteine was present in place of a catalytic cysteine.
Bajat Branislav
2007-01-01
Full Text Available A period of fifty years has been reached since the introduction of the first applications based upon geographical information systems (GIS. GIS has not only influenced the development of methods, collection techniques, processing, manipulation and visualization of spatial data. It influenced also the expansion of scientific research in geosciences, as well as the technical disciplines that are engaged in spatial analysis. Nowadays, GIS is becoming the tool for verification and practical implementation of models and algorithms that have been developed within the frame of basic scientific disciplines. The meaning of the GIS acronym is becoming more and more related to term of Geographical or Geo Information Sciences. Scientific concepts that are increasingly applied in GIS are more emphasized in that way. GIS computational techniques, required also the development of geographical data models that should effectively support GIS operations. These models represent formal equivalents of conceptual models used by people in observing geographic phenomena. Spatial phenomena used to be mapped as clearly defined points with known coordinates, or as lines which connect the very same points, or as polygons with exactly defined borders. They were mapped previously in analog form and nowadays in digital format. This approach of perceiving a space, data analyses and visualization of spatial quires is limited on the application of basic rules of Boolean algebra and binary logic, with final results presented as classical thematic maps. The need for a mathematical model that would describe uncertainty of spatial data, resulted in the introduction of the theory of fuzzy sets in spatial analysis. Moreover, this model will provide a solution for visualization and grouping up of spatial phenomena in classes which do not have clearly defined borders.
JuanM. Medina
2012-08-01
Full Text Available This paper proposes a parameterized definition for fuzzy comparators on complex fuzzy datatypes like fuzzy collections with conjunctive semantics and fuzzy objects. This definition and its implementation on a Fuzzy Object-Relational Database Management System (FORDBMS provides the designer with a powerful tool to adapt the behavior of these operators to the semantics of the considered application.
Perlíková, P.; Karlsen, K.K.; Pedersen, E.B.
2014-01-01
The synthesis of two new phosphoramidite building blocks for the incorporation of 5-(pyren-1-yl)uracilyl unlocked nucleic acid (UNA) monomers into oligonucleotides has been developed. Monomers containing a pyrene-modified nucleobase component were found to destabilize an i-motif structure at pH 5...... intensities upon hybridization to DNA or RNA. Efficient quenching of fluorescence of pyrene-modified UNA monomers was observed after formation of i-motif structures at pH 5.2. The stabilizing/destabilizing effect of pyrene-modified nucleic acids might be useful for designing antisense oligonucleotides...
Kroupa, Tomáš
2008-01-01
Roč. 159, č. 14 (2008), s. 1773-1787 ISSN 0165-0114 R&D Projects: GA MŠk 1M0572; GA AV ČR KJB100300502 Institutional research plan: CEZ:AV0Z10750506 Keywords : filter * prime filter * fuzzy class theory Subject RIV: BA - General Mathematics Impact factor: 1.833, year: 2008
Structural Completeness in Fuzzy Logics
Cintula, Petr; Metcalfe, G.
2009-01-01
Roč. 50, č. 2 (2009), s. 153-183 ISSN 0029-4527 R&D Projects: GA MŠk(CZ) 1M0545 Institutional research plan: CEZ:AV0Z10300504 Keywords : structral logics * fuzzy logics * structural completeness * admissible rules * primitive variety * residuated lattices Subject RIV: BA - General Mathematics
Fuzzy Querying: Issues and Perspectives..
Kacprzyk, J.; Pasi, G.; Vojtáš, Peter; Zadrozny, S.
2000-01-01
Roč. 36, č. 6 (2000), s. 605-616 ISSN 0023-5954 Institutional research plan: AV0Z1030915 Keywords : flexible querying * information retrieval * fuzzy databases Subject RIV: BA - General Mathematics http://dml.cz/handle/10338.dmlcz/135376
Pilotto, F.; Vasconcellos, C.A.Z.; Coelho, H.T.
2001-01-01
In this work we develop a new version of the fuzzy bag model. Th main ideas is to include the conservation of energy and momentum in the model. This feature is not included in the original formulation of the fuzzy bag model, but is of paramount importance to interpret the model as being a bag model - that, is a model in which the outward pressure of the quarks inside the bag is balanced by the inward pressure of the non-perturbative vacuum outside the bag - as opposed to a relativistic potential model, in which there is no energy-momentum conservation. In the MT bag model, as well as in the original version of the fuzzy bag model, the non-perturbative QCD vacuum is parametrized by a constant B in the Lagrangian density. One immediate consequence of including energy-momentum conservation in the fuzzy bag model is that the bag constant B will acquire a radial dependence, B = B(r). (author)
Pilotto, F.; Vasconcellos, C.A.Z. [Rio Grande do Sul Univ., Porto Alegre, RS (Brazil). Inst. de Fisica; Coelho, H.T. [Pernambuco Univ., Recife, PE (Brazil). Inst. de Fisica
2001-07-01
In this work we develop a new version of the fuzzy bag model. Th main ideas is to include the conservation of energy and momentum in the model. This feature is not included in the original formulation of the fuzzy bag model, but is of paramount importance to interpret the model as being a bag model - that, is a model in which the outward pressure of the quarks inside the bag is balanced by the inward pressure of the non-perturbative vacuum outside the bag - as opposed to a relativistic potential model, in which there is no energy-momentum conservation. In the MT bag model, as well as in the original version of the fuzzy bag model, the non-perturbative QCD vacuum is parametrized by a constant B in the Lagrangian density. One immediate consequence of including energy-momentum conservation in the fuzzy bag model is that the bag constant B will acquire a radial dependence, B = B(r). (author)
Fuzzy audit risk modeling algorithm
Zohreh Hajihaa
2011-07-01
Full Text Available Fuzzy logic has created suitable mathematics for making decisions in uncertain environments including professional judgments. One of the situations is to assess auditee risks. During recent years, risk based audit (RBA has been regarded as one of the main tools to fight against fraud. The main issue in RBA is to determine the overall audit risk an auditor accepts, which impact the efficiency of an audit. The primary objective of this research is to redesign the audit risk model (ARM proposed by auditing standards. The proposed model of this paper uses fuzzy inference systems (FIS based on the judgments of audit experts. The implementation of proposed fuzzy technique uses triangular fuzzy numbers to express the inputs and Mamdani method along with center of gravity are incorporated for defuzzification. The proposed model uses three FISs for audit, inherent and control risks, and there are five levels of linguistic variables for outputs. FISs include 25, 25 and 81 rules of if-then respectively and officials of Iranian audit experts confirm all the rules.
UKIRAN KERAWANG ACEH GAYO SEBAGAI INSPIRASI PENCIPTAAN MOTIF BATIK KHAS GAYO
Irfa ina Rohana Salma
2016-12-01
Full Text Available ABSTRAK Industri batik mulai berkembang di Gayo, tetapi belum memiliki motif batik khas daerah. Oleh karena itu perlu diciptakan motif batik khas Gayo, dengan mengambil inspirasi dari ukiran yang terdapat pada rumah tradisional yang biasa disebut ukiran kerawang Gayo. Tujuan penciptaan seni ini adalah untuk menciptakan motif batik yang memiliki ciri khas Gayo. Metode yang digunakan yaitu eksplorasi ide, perancangan, dan perwujudan menjadi motif batik. Dalam kegiatan ini telah diciptakan enam motif batik khas Gayo yaitu: (1 Motif Ceplok Gayo; (2 Motif Gayo Tegak; (3 Motif Gayo Lurus; (4 Motif Parang Gayo; (5 Motif Gayo Lembut; dan (6 Motif Geometris Gayo. Hasil uji kesukaan terhadap motif kepada lima puluh responden menunjukkan bahwa Motif Ceplok Gayo paling banyak dipilih oleh responden yaitu sebesar 19%, sedangkan Motif Parang Gayo 18%, Motif Gayo Lembut 17%, Motif Geometris Gayo 17%, Motif Gayo Lurus 15% dan Motif Gayo Tegak 14%. Rata-rata motif yang dihasilkan mendapatkan apresiasi yang baik dari responden, sehingga semua motif layak diproduksi sebagai batik khas Gayo.Kata kunci: batik Gayo, Motif Ceplok Gayo, Motif Parang Gayo.ABSTRACTBatik industry began to develop in Gayo, but have not had a typical batik motif itself. Therefore, it is necessary to create batik motifs of Gayo, by taking inspiration from the carvings found in traditional houses commonly called kerawang Gayo. The purpose of this art is to create motifs those have a Gayo characteristic. The method used are the idea exploration, design, and motifs embodiment. In this activity has created six Gayo batik motifs, namely: (1 Motif Ceplok Gayo; (2 Motif Gayo Tegak; (3 Motif GayoLurus; (4 Motif Parang Gayo; (5 Motif Gayo Lembut; dan (6 Motif Geometris Gayo. The test results fondness of the motives to fifty respondents indicated that the Motif Ceplok Gayo most preferred by respondents ie 19%, while Motif Parang Gayo 18%, Motif Gayo Lembut 17%, Motif Geometris Gayo 17%, Motif Gayo
Fuzzy Evidence in Identification, Forecasting and Diagnosis
Rotshtein, Alexander P
2012-01-01
The purpose of this book is to present a methodology for designing and tuning fuzzy expert systems in order to identify nonlinear objects; that is, to build input-output models using expert and experimental information. The results of these identifications are used for direct and inverse fuzzy evidence in forecasting and diagnosis problem solving. The book is organised as follows: Chapter 1 presents the basic knowledge about fuzzy sets, genetic algorithms and neural nets necessary for a clear understanding of the rest of this book. Chapter 2 analyzes direct fuzzy inference based on fuzzy if-then rules. Chapter 3 is devoted to the tuning of fuzzy rules for direct inference using genetic algorithms and neural nets. Chapter 4 presents models and algorithms for extracting fuzzy rules from experimental data. Chapter 5 describes a method for solving fuzzy logic equations necessary for the inverse fuzzy inference in diagnostic systems. Chapters 6 and 7 are devoted to inverse fuzzy inference based on fu...
Fuzzy tree automata and syntactic pattern recognition.
Lee, E T
1982-04-01
An approach of representing patterns by trees and processing these trees by fuzzy tree automata is described. Fuzzy tree automata are defined and investigated. The results include that the class of fuzzy root-to-frontier recognizable ¿-trees is closed under intersection, union, and complementation. Thus, the class of fuzzy root-to-frontier recognizable ¿-trees forms a Boolean algebra. Fuzzy tree automata are applied to processing fuzzy tree representation of patterns based on syntactic pattern recognition. The grade of acceptance is defined and investigated. Quantitative measures of ``approximate isosceles triangle,'' ``approximate elongated isosceles triangle,'' ``approximate rectangle,'' and ``approximate cross'' are defined and used in the illustrative examples of this approach. By using these quantitative measures, a house, a house with high roof, and a church are also presented as illustrative examples. In addition, three fuzzy tree automata are constructed which have the capability of processing the fuzzy tree representations of ``fuzzy houses,'' ``houses with high roofs,'' and ``fuzzy churches,'' respectively. The results may have useful applications in pattern recognition, image processing, artificial intelligence, pattern database design and processing, image science, and pictorial information systems.
Fuzzy C-means method for clustering microarray data.
Dembélé, Doulaye; Kastner, Philippe
2003-05-22
Clustering analysis of data from DNA microarray hybridization studies is essential for identifying biologically relevant groups of genes. Partitional clustering methods such as K-means or self-organizing maps assign each gene to a single cluster. However, these methods do not provide information about the influence of a given gene for the overall shape of clusters. Here we apply a fuzzy partitioning method, Fuzzy C-means (FCM), to attribute cluster membership values to genes. A major problem in applying the FCM method for clustering microarray data is the choice of the fuzziness parameter m. We show that the commonly used value m = 2 is not appropriate for some data sets, and that optimal values for m vary widely from one data set to another. We propose an empirical method, based on the distribution of distances between genes in a given data set, to determine an adequate value for m. By setting threshold levels for the membership values, genes which are tigthly associated to a given cluster can be selected. Using a yeast cell cycle data set as an example, we show that this selection increases the overall biological significance of the genes within the cluster. Supplementary text and Matlab functions are available at http://www-igbmc.u-strasbg.fr/fcm/
RMOD: a tool for regulatory motif detection in signaling network.
Jinki Kim
Full Text Available Regulatory motifs are patterns of activation and inhibition that appear repeatedly in various signaling networks and that show specific regulatory properties. However, the network structures of regulatory motifs are highly diverse and complex, rendering their identification difficult. Here, we present a RMOD, a web-based system for the identification of regulatory motifs and their properties in signaling networks. RMOD finds various network structures of regulatory motifs by compressing the signaling network and detecting the compressed forms of regulatory motifs. To apply it into a large-scale signaling network, it adopts a new subgraph search algorithm using a novel data structure called path-tree, which is a tree structure composed of isomorphic graphs of query regulatory motifs. This algorithm was evaluated using various sizes of signaling networks generated from the integration of various human signaling pathways and it showed that the speed and scalability of this algorithm outperforms those of other algorithms. RMOD includes interactive analysis and auxiliary tools that make it possible to manipulate the whole processes from building signaling network and query regulatory motifs to analyzing regulatory motifs with graphical illustration and summarized descriptions. As a result, RMOD provides an integrated view of the regulatory motifs and mechanism underlying their regulatory motif activities within the signaling network. RMOD is freely accessible online at the following URL: http://pks.kaist.ac.kr/rmod.
On fuzzy quasi continuity and an application of fuzzy set theory
Mahmoud, R A
2003-01-01
Where as classical topology has been developed closely connected with classical analysis describing topological phenomena in analysis, fuzzy topology with its important application in quantum gravity indicated by Witten and Elnaschie, has only been introduced as an analogue of the classical topology. The development of fuzzy topology without close relations to analytical problems did not give the possibility of testing successfully the applicability of the new notions and results. Till now this situation did not change, essentially. Although, many types of fuzzy sets and fuzzy functions having the quasi-property in both of weak and strong than openness and continuity, respectively, have been studied in detail. Many properties on fuzzy topological spaces such as compactness are discussed via fuzzy notion. While others are far from being completely devoted in its foundation. So, this paper is devoted to present a new class of fuzzy quasi-continuous functions via fuzzy compactness has been defined. Some characte...
Influence of fuzzy norms and other heuristics on "Mixed fuzzy rule formation" - [Corrigendum
Gabriel, Thomas R.; Berthold, Michael R.
2008-01-01
We hereby correct an error in Ref. [2], in which we studied the influence of various parameters that affect the generalization performance of fuzzy models constructed using the mixed fuzzy rule formation method [1].
Minimal solution for inconsistent singular fuzzy matrix equations
M. Nikuie
2013-10-01
Full Text Available The fuzzy matrix equations $Ailde{X}=ilde{Y}$ is called a singular fuzzy matrix equations while the coefficients matrix of its equivalent crisp matrix equations be a singular matrix. The singular fuzzy matrix equations are divided into two parts: consistent singular matrix equations and inconsistent fuzzy matrix equations. In this paper, the inconsistent singular fuzzy matrix equations is studied and the effect of generalized inverses in finding minimal solution of an inconsistent singular fuzzy matrix equations are investigated.
An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers.
Wang, Rang Jian; Gao, Xiang Feng; Kong, Xiang Rui; Yang, Jun
2016-01-01
Microsatellites, or simple sequence repeats (SSRs), especially those with long-core motifs (tri-, tetra-, penta-, and hexa-nucleotide) represent an excellent tool for DNA fingerprinting. SSRs with long-core motifs are preferred since neighbor alleles are more easily separated and identified from each other, which render the interpretation of electropherograms and the true alleles more reliable. In the present work, with the purpose of characterizing a set of core SSR markers with long-core motifs for well fingerprinting clonal cultivars of tea (Camellia sinensis), we analyzed 66 elite clonal tea cultivars in China with 33 initially-chosen long-core motif SSR markers covering all the 15 linkage groups of tea plant genome. A set of 6 SSR markers were conclusively selected as core SSR markers after further selection. The polymorphic information content (PIC) of the core SSR markers was >0.5, with ≤5 alleles in each marker containing 10 or fewer genotypes. Phylogenetic analysis revealed that the core SSR markers were not strongly correlated with the trait 'cultivar processing-property'. The combined probability of identity (PID) between two random cultivars for the whole set of 6 SSR markers was estimated to be 2.22 × 10(-5), which was quite low, confirmed the usefulness of the proposed SSR markers for fingerprinting analyses in Camellia sinensis. Moreover, for the sake of quickly discriminating the clonal tea cultivars, a cultivar identification diagram (CID) was subsequently established using these core markers, which fully reflected the identification process and provided the immediate information about which SSR markers were needed to identify a cultivar chosen among the tested ones. The results suggested that long-core motif SSR markers used in the investigation contributed to the accurate and efficient identification of the clonal tea cultivars and enabled the protection of intellectual property.
Structural motifs of pre-nucleation clusters.
Zhang, Y; Türkmen, I R; Wassermann, B; Erko, A; Rühl, E
2013-10-07
Structural motifs of pre-nucleation clusters prepared in single, optically levitated supersaturated aqueous aerosol microparticles containing CaBr2 as a model system are reported. Cluster formation is identified by means of X-ray absorption in the Br K-edge regime. The salt concentration beyond the saturation point is varied by controlling the humidity in the ambient atmosphere surrounding the 15-30 μm microdroplets. This leads to the formation of metastable supersaturated liquid particles. Distinct spectral shifts in near-edge spectra as a function of salt concentration are observed, in which the energy position of the Br K-edge is red-shifted by up to 7.1 ± 0.4 eV if the dilute solution is compared to the solid. The K-edge positions of supersaturated solutions are found between these limits. The changes in electronic structure are rationalized in terms of the formation of pre-nucleation clusters. This assumption is verified by spectral simulations using first-principle density functional theory and molecular dynamics calculations, in which structural motifs are considered, explaining the experimental results. These consist of solvated CaBr2 moieties, rather than building blocks forming calcium bromide hexahydrates, the crystal system that is formed by drying aqueous CaBr2 solutions.
Parole, Sintagmatik, dan Paradigmatik Motif Batik Mega Mendung
Rudi - Nababan
2012-04-01
Full Text Available ABSTRACT Discussing traditional batik is related a lot to the organization system of fine arts element ac- companying it, either the pattern of the motif or the technique of the making. In this case, the motif of Mega Mendung Cirebon certainly has patterns and rules which are traditionally different from the other motifs in other areas. Through semiotics analysis especially with Saussure and Pierce concept, it can be traced that batik with Cirebon motif, in this case Mega Mendung motif, has parole and langue system, as unique fine arts language in batik, and structure of visual syntagmatic and paradigmatic. In the context of batik motif as fine arts language, it is surely related to sign system as symbol and icon. Keywords: visual semiotic, Cirebon’s batik.
Fuzzy systems for process identification and control
Gorrini, V.; Bersini, H.
1994-01-01
Various issues related to the automatic construction and on-line adaptation of fuzzy controllers are addressed. A Direct Adaptive Fuzzy Control (this is an adaptive control methodology requiring a minimal knowledge of the processes to be coupled with) derived in a way reminiscent of neurocontrol methods, is presented. A classical fuzzy controller and a fuzzy realization of a PID controller is discussed. These systems implement a highly non-linear control law, and provide to be quite robust, even in the case of noisy inputs. In order to identify dynamic processes of order superior to one, we introduce a more complex architecture, called Recurrent Fuzzy System, that use some fuzzy internal variables to perform an inferential chaining.I
Walendziak, Andrzej
2015-01-01
The notions of an ideal and a fuzzy ideal in BN-algebras are introduced. The properties and characterizations of them are investigated. The concepts of normal ideals and normal congruences of a BN-algebra are also studied, the properties of them are displayed, and a one-to-one correspondence between them is presented. Conditions for a fuzzy set to be a fuzzy ideal are given. The relationships between ideals and fuzzy ideals of a BN-algebra are established. The homomorphic properties of fuzzy ideals of a BN-algebra are provided. Finally, characterizations of Noetherian BN-algebras and Artinian BN-algebras via fuzzy ideals are obtained. PMID:26125050
Analysis of inventory difference using fuzzy controllers
Zardecki, A.
1994-01-01
The principal objectives of an accounting system for safeguarding nuclear materials are as follows: (a) to provide assurance that all material quantities are present in the correct amount; (b) to provide timely detection of material loss; and (c) to estimate the amount of any loss and its location. In fuzzy control, expert knowledge is encoded in the form of fuzzy rules, which describe recommended actions for different classes of situations represented by fuzzy sets. The concept of a fuzzy controller is applied to the forecasting problem in a time series, specifically, to forecasting and detecting anomalies in inventory differences. This paper reviews the basic notion underlying the fuzzy control systems and provides examples of application. The well-known material-unaccounted-for diffusion plant data of Jaech are analyzed using both feedforward neural networks and fuzzy controllers. By forming a deference between the forecasted and observed signals, an efficient method to detect small signals in background noise is implemented
Fuzzy associative memories for instrument fault detection
Heger, A.S.
1996-01-01
A fuzzy logic instrument fault detection scheme is developed for systems having two or three redundant sensors. In the fuzzy logic approach the deviation between each signal pairing is computed and classified into three fuzzy sets. A rule base is created allowing the human perception of the situation to be represented mathematically. Fuzzy associative memories are then applied. Finally, a defuzzification scheme is used to find the centroid location, and hence the signal status. Real-time analyses are carried out to evaluate the instantaneous signal status as well as the long-term results for the sensor set. Instantaneous signal validation results are used to compute a best estimate for the measured state variable. The long-term sensor validation method uses a frequency fuzzy variable to determine the signal condition over a specific period. To corroborate the methodology synthetic data representing various anomalies are analyzed with both the fuzzy logic technique and the parity space approach. (Author)
Optical Generation of Fuzzy-Based Rules
Gur, Eran; Mendlovic, David; Zalevsky, Zeev
2002-08-01
In the last third of the 20th century, fuzzy logic has risen from a mathematical concept to an applicable approach in soft computing. Today, fuzzy logic is used in control systems for various applications, such as washing machines, train-brake systems, automobile automatic gear, and so forth. The approach of optical implementation of fuzzy inferencing was given by the authors in previous papers, giving an extra emphasis to applications with two dominant inputs. In this paper the authors introduce a real-time optical rule generator for the dual-input fuzzy-inference engine. The paper briefly goes over the dual-input optical implementation of fuzzy-logic inferencing. Then, the concept of constructing a set of rules from given data is discussed. Next, the authors show ways to implement this procedure optically. The discussion is accompanied by an example that illustrates the transformation from raw data into fuzzy set rules.
Logika Fuzzy untuk Audit Sistem Informasi
Hari Setiabudi Husni
2013-06-01
Full Text Available The aim of this research is to study and introduce fuzzy logic into audit information system. Fuzzy logic is already adopted in other field of study. It helps decision process that incorporates subjective information and transforms it to scientific objective information which is more accepted. This research implements simulation scenario to see how fuzzy logic concept should be used in audit information process. The result shows that there is a possible concept of fuzzy logic that can be used for helping auditor in making objective decision in audit information system process. More researches needed to further explore the fuzzy logic concept such as creating the system of fuzzy logic and build application that can be used for daily information system audit process.
On Algebraic Study of Type-2 Fuzzy Finite State Automata
Anupam K. Singh
2017-08-01
Full Text Available Theories of fuzzy sets and type-2 fuzzy sets are powerful mathematical tools for modeling various types of uncertainty. In this paper we introduce the concept of type-2 fuzzy finite state automata and discuss the algebraic study of type-2 fuzzy finite state automata, i.e., to introduce the concept of homomorphisms between two type-2 fuzzy finite state automata, to associate a type-2 fuzzy transformation semigroup with a type-2 fuzzy finite state automata. Finally, we discuss several product of type-2 fuzzy finite state automata and shown that these product is a categorical product.
Fuzzy weakly preopen (preclosed) function in Kubiak-Sostak fuzzy topological spaces
Zahran, A.M.; Abd-Allah, M. Azab.; Abd El-Rahman, Abd El-Nasser G.
2009-01-01
In this paper, we introduce and characterize fuzzy weakly preopen and fuzzy weakly preclosed functions between L-fuzzy topological spaces in Kubiak-Sostak sense and also study these functions in relation to some other types of already known functions.
Combinational Reasoning of Quantitative Fuzzy Topological Relations for Simple Fuzzy Regions
Liu, Bo; Li, Dajun; Xia, Yuanping; Ruan, Jian; Xu, Lili; Wu, Huanyi
2015-01-01
In recent years, formalization and reasoning of topological relations have become a hot topic as a means to generate knowledge about the relations between spatial objects at the conceptual and geometrical levels. These mechanisms have been widely used in spatial data query, spatial data mining, evaluation of equivalence and similarity in a spatial scene, as well as for consistency assessment of the topological relations of multi-resolution spatial databases. The concept of computational fuzzy topological space is applied to simple fuzzy regions to efficiently and more accurately solve fuzzy topological relations. Thus, extending the existing research and improving upon the previous work, this paper presents a new method to describe fuzzy topological relations between simple spatial regions in Geographic Information Sciences (GIS) and Artificial Intelligence (AI). Firstly, we propose a new definition for simple fuzzy line segments and simple fuzzy regions based on the computational fuzzy topology. And then, based on the new definitions, we also propose a new combinational reasoning method to compute the topological relations between simple fuzzy regions, moreover, this study has discovered that there are (1) 23 different topological relations between a simple crisp region and a simple fuzzy region; (2) 152 different topological relations between two simple fuzzy regions. In the end, we have discussed some examples to demonstrate the validity of the new method, through comparisons with existing fuzzy models, we showed that the proposed method can compute more than the existing models, as it is more expressive than the existing fuzzy models. PMID:25775452
Identification of group specific motifs in Beta-lactamase family of proteins
Saxena Akansha
2009-12-01
Full Text Available Abstract Background Beta-lactamases are one of the most serious threats to public health. In order to combat this threat we need to study the molecular and functional diversity of these enzymes and identify signatures specific to these enzymes. These signatures will enable us to develop inhibitors and diagnostic probes specific to lactamases. The existing classification of beta-lactamases was developed nearly 30 years ago when few lactamases were available. DLact database contain more than 2000 beta-lactamase, which can be used to study the molecular diversity and to identify signatures specific to this family. Methods A set of 2020 beta-lactamase proteins available in the DLact database http://59.160.102.202/DLact were classified using graph-based clustering of Best Bi-Directional Hits. Non-redundant (> 90 percent identical protein sequences from each group were aligned using T-Coffee and annotated using information available in literature. Motifs specific to each group were predicted using PRATT program. Results The graph-based classification of beta-lactamase proteins resulted in the formation of six groups (Four major groups containing 191, 726, 774 and 73 proteins while two minor groups containing 50 and 8 proteins. Based on the information available in literature, we found that each of the four major groups correspond to the four classes proposed by Ambler. The two minor groups were novel and do not contain molecular signatures of beta-lactamase proteins reported in literature. The group-specific motifs showed high sensitivity (> 70% and very high specificity (> 90%. The motifs from three groups (corresponding to class A, C and D had a high level of conservation at DNA as well as protein level whereas the motifs from the fourth group (corresponding to class B showed conservation at only protein level. Conclusion The graph-based classification of beta-lactamase proteins corresponds with the classification proposed by Ambler, thus there is
New Definition and Properties of Fuzzy Entropy
Qing Ming; Qin Yingbing
2006-01-01
Let X = (x1,x2 ,…,xn ) and F(X) be a fuzzy set on a universal set X. A new definition of fuzzy entropy about a fuzzy set A on F(X), e*, is defined based on the order relation "≤" on [0,1/2] n. It is proved that e* is a σ-entropy under an additional requirement. Besides, some entropy formulas are presented and related properties are discussed.
Simulasi Kecepatan Kendaraan dengan Menggunakan Logika Fuzzy
Lukas, Samuel; Aribowo, Arnold; Tjia, Yogih Suharta
2008-01-01
Artificial intelligence has been implemented widely. Many of household products are designed based on artificial intellegence concept. One of them is fuzzy logic system. This paper describes on how a fuzzy logic system can also be implemented in controling the speed of a car in the road. The fuzzy inference system was designed according to Tsukamoto inferencing method and for the defuzzyfication method is used weighted average method. There are three inputs for the system. The are distance b...
Simulasi Kecepatan Kendaraan Dengan Menggunakan Logika Fuzzy
Lukas, Samuel; Aribowo, Arnold; Tjia, Yogih Suharta
2009-01-01
Artificial intelligence has been implemented widely. Many of household products are designed based on artificial intellegence concept. One of them is fuzzy logic system. This paper describes on how a fuzzy logic system can also be implemented in controling the speed of a car in the road. The fuzzy inference system was designed according to Tsukamoto inferencing method and for the defuzzyfication method is used weighted average method. There are three inputs for the system. The are distance b...
Fuzzy multiple linear regression: A computational approach
Juang, C. H.; Huang, X. H.; Fleming, J. W.
1992-01-01
This paper presents a new computational approach for performing fuzzy regression. In contrast to Bardossy's approach, the new approach, while dealing with fuzzy variables, closely follows the conventional regression technique. In this approach, treatment of fuzzy input is more 'computational' than 'symbolic.' The following sections first outline the formulation of the new approach, then deal with the implementation and computational scheme, and this is followed by examples to illustrate the new procedure.
Statistical convergence on intuitionistic fuzzy normed spaces
Karakus, S.; Demirci, K.; Duman, O.
2008-01-01
Saadati and Park [Saadati R, Park JH, Chaos, Solitons and Fractals 2006;27:331-44] has recently introduced the notion of intuitionistic fuzzy normed space. In this paper, we study the concept of statistical convergence on intuitionistic fuzzy normed spaces. Then we give a useful characterization for statistically convergent sequences. Furthermore, we display an example such that our method of convergence is stronger than the usual convergence on intuitionistic fuzzy normed spaces
Recent advances in fuzzy preference modelling
Van de Walle, B.; De Baets, B.; Kerre, E.
1996-01-01
Preference structures are well-known mathematical concepts having numerous applications in a variety of disciplines, such as economics, sociology and psychology. The generalization of preference structures to the fuzzy case has received considerable attention over the past years. Fuzzy preference structures allow a decision maker to express degrees of preference instead of the rigid classical yes-or-no preference assignment. This paper reports on the recent insights gained into the existence, construction and characterization of these fuzzy preference structures
Fuzzy Law and the Boundaries of Secularism
W Menski
2010-12-01
Full Text Available The author delivered a speech at a Religare Conference. Showing his distaste for fuzzy law, he argues that "moderate secularism" is not merely another fuzzy concept, but it is "super-fuzzy", and that lawyers claiming to love certainty "have a tendency to sit in judgment over matters and even pre-judge things they know little about, including legal pluralism" leading to much irritation.
Rapid identification of DNA-binding proteins by mass spectrometry
Nordhoff, E.; Korgsdam, A.-M.; Jørgensen, H.F.
1999-01-01
We report a protocol for the rapid identification of DNA-binding proteins. Immobilized DNA probes harboring a specific sequence motif are incubated with cell or nuclear extract. Proteins are analyzed directly off the solid support by matrix-assisted laser desorption/ionization time-of-flight mass...... was validated by the identification of known prokaryotic and eukaryotic DNA-binding proteins, and its use provided evidence that poly(ADP-ribose) polymerase exhibits DNA sequence-specific binding to DNA....
Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage
Stella, Stefano; Alcón, Pablo; Montoya, Guillermo
2017-01-01
involved in DNA unwinding to form a CRISPR RNA (crRNA)-DNA hybrid and a displaced DNA strand. The protospacer adjacent motif (PAM) is recognized by the PAM-interacting domain. The loop-lysine helix-loop motif in this domain contains three conserved lysine residues that are inserted in a dentate manner...... and the crRNA-DNA hybrid, avoiding DNA re-annealing. Mutations in key residues reveal a mechanism linking the PAM and DNA nuclease sites. Analysis of the Cpf1 structures proposes a singular working model of RNA-guided DNA cleavage, suggesting new avenues for redesign of Cpf1....
Integrating Fuzzy AHP and Fuzzy ARAS for evaluating financial performance
Abdolhamid Safaei Ghadikolaei; Saber Khalili Esbouei
2014-01-01
Multi Criteria Decision Making (MCDM) is an advanced field of Operation Research; recently MCDM methods are efficient and common tools for performance evaluation in many areas such as finance and economy. The aim of this study is to show one of applications of mathematics in real word. This study with considering value based measures and accounting based measures simultaneously, provided a hybrid approach of MCDM methods in fuzzy environment for financial performance evaluation of automotive ...
Word Similarity From Dictionaries: Inferring Fuzzy Measures From Fuzzy Graphs
Torra
2008-01-01
Full Text Available The computation of similarities between words is a basic element of information retrieval systems, when retrieval is not solely based on word matching. In this work we consider a measure between words based on dictionaries. This is achieved assuming that a dictionary is formalized as a fuzzy graph. We show that the approach permits to compute measures not only for pairs of words but for sets of them.
O'Shea, Charlotte; Staby, Lasse; Bendsen, Sidsel Krogh
2017-01-01
Intrinsically disordered protein regions (IDRs) lack a well-defined three-dimensional structure, but often facilitate key protein functions. Some interactions between IDRs and folded protein domains rely on short linear motifs (SLiMs). These motifs are challenging to identify, but once found can...... point to larger networks of interactions, such as with proteins that serve as hubs for essential cellular functions. The stress-associated plant protein Radical-Induced Cell Death1 (RCD1) is one such hub, interacting with many transcription factors via their flexible IDRs. To identify the SLiM bound......046 formed different structures or were fuzzy in the complexes. These findings allow us to present a model of the stress-associated RCD1-transcription factor interactome and to contribute to the emerging understanding of the interactions between folded hubs and their intrinsically disordered partners....
Fuzzy logic control for camera tracking system
Lea, Robert N.; Fritz, R. H.; Giarratano, J.; Jani, Yashvant
1992-01-01
A concept utilizing fuzzy theory has been developed for a camera tracking system to provide support for proximity operations and traffic management around the Space Station Freedom. Fuzzy sets and fuzzy logic based reasoning are used in a control system which utilizes images from a camera and generates required pan and tilt commands to track and maintain a moving target in the camera's field of view. This control system can be implemented on a fuzzy chip to provide an intelligent sensor for autonomous operations. Capabilities of the control system can be expanded to include approach, handover to other sensors, caution and warning messages.
Fuzzy sets, rough sets, multisets and clustering
Dahlbom, Anders; Narukawa, Yasuo
2017-01-01
This book is dedicated to Prof. Sadaaki Miyamoto and presents cutting-edge papers in some of the areas in which he contributed. Bringing together contributions by leading researchers in the field, it concretely addresses clustering, multisets, rough sets and fuzzy sets, as well as their applications in areas such as decision-making. The book is divided in four parts, the first of which focuses on clustering and classification. The second part puts the spotlight on multisets, bags, fuzzy bags and other fuzzy extensions, while the third deals with rough sets. Rounding out the coverage, the last part explores fuzzy sets and decision-making.
Equipment Selection by using Fuzzy TOPSIS Method
Yavuz, Mahmut
2016-10-01
In this study, Fuzzy TOPSIS method was performed for the selection of open pit truck and the optimal solution of the problem was investigated. Data from Turkish Coal Enterprises was used in the application of the method. This paper explains the Fuzzy TOPSIS approaches with group decision-making application in an open pit coal mine in Turkey. An algorithm of the multi-person multi-criteria decision making with fuzzy set approach was applied an equipment selection problem. It was found that Fuzzy TOPSIS with a group decision making is a method that may help decision-makers in solving different decision-making problems in mining.
A computationally efficient fuzzy control s
Abdel Badie Sharkawy
2013-12-01
Full Text Available This paper develops a decentralized fuzzy control scheme for MIMO nonlinear second order systems with application to robot manipulators via a combination of genetic algorithms (GAs and fuzzy systems. The controller for each degree of freedom (DOF consists of a feedforward fuzzy torque computing system and a feedback fuzzy PD system. The feedforward fuzzy system is trained and optimized off-line using GAs, whereas not only the parameters but also the structure of the fuzzy system is optimized. The feedback fuzzy PD system, on the other hand, is used to keep the closed-loop stable. The rule base consists of only four rules per each DOF. Furthermore, the fuzzy feedback system is decentralized and simplified leading to a computationally efficient control scheme. The proposed control scheme has the following advantages: (1 it needs no exact dynamics of the system and the computation is time-saving because of the simple structure of the fuzzy systems and (2 the controller is robust against various parameters and payload uncertainties. The computational complexity of the proposed control scheme has been analyzed and compared with previous works. Computer simulations show that this controller is effective in achieving the control goals.
Fuzzy logic control and optimization system
Lou, Xinsheng [West Hartford, CT
2012-04-17
A control system (300) for optimizing a power plant includes a chemical loop having an input for receiving an input signal (369) and an output for outputting an output signal (367), and a hierarchical fuzzy control system (400) operably connected to the chemical loop. The hierarchical fuzzy control system (400) includes a plurality of fuzzy controllers (330). The hierarchical fuzzy control system (400) receives the output signal (367), optimizes the input signal (369) based on the received output signal (367), and outputs an optimized input signal (369) to the input of the chemical loop to control a process of the chemical loop in an optimized manner.
Fuzzy logic control of nuclear power plant
Yao Liangzhong; Guo Renjun; Ma Changwen
1996-01-01
The main advantage of the fuzzy logic control is that the method does not require a detailed mathematical model of the object to be controlled. In this paper, the shortcomings and limitations of the model-based method in nuclear power plant control were presented, the theory of the fuzzy logic control was briefly introduced, and the applications of the fuzzy logic control technology in nuclear power plant controls were surveyed. Finally, the problems to be solved by using the fuzzy logic control in nuclear power plants were discussed
Fuzzy neural network theory and application
Liu, Puyin
2004-01-01
This book systematically synthesizes research achievements in the field of fuzzy neural networks in recent years. It also provides a comprehensive presentation of the developments in fuzzy neural networks, with regard to theory as well as their application to system modeling and image restoration. Special emphasis is placed on the fundamental concepts and architecture analysis of fuzzy neural networks. The book is unique in treating all kinds of fuzzy neural networks and their learning algorithms and universal approximations, and employing simulation examples which are carefully designed to he
Fuzzy set classifier for waste classification tracking
Gavel, D.T.
1992-01-01
We have developed an expert system based on fuzzy logic theory to fuse the data from multiple sensors and make classification decisions for objects in a waste reprocessing stream. Fuzzy set theory has been applied in decision and control applications with some success, particularly by the Japanese. We have found that the fuzzy logic system is rather easy to design and train, a feature that can cut development costs considerably. With proper training, the classification accuracy is quite high. We performed several tests sorting radioactive test samples using a gamma spectrometer to compare fuzzy logic to more conventional sorting schemes
Application of fuzzy logic control in industry
Van der Wal, A.J.
1994-01-01
An overview is given of the various ways fuzzy logic can be used to improve industrial control. The application of fuzzy logic in control is illustrated by two case studies. The first example shows how fuzzy logic, incorporated in the hardware of an industrial controller, helps to finetune a PID controller, without the operator having any a priori knowledge of the system to be controlled. The second example is from process industry. Here, fuzzy logic supervisory control is implemented in software and enhances the operation of a sintering oven through a subtle combination of priority management and deviation-controlled timing
Fuzzy control of small servo motors
Maor, Ron; Jani, Yashvant
1993-01-01
To explore the benefits of fuzzy logic and understand the differences between the classical control methods and fuzzy control methods, the Togai InfraLogic applications engineering staff developed and implemented a motor control system for small servo motors. The motor assembly for testing the fuzzy and conventional controllers consist of servo motor RA13M and an encoder with a range of 4096 counts. An interface card was designed and fabricated to interface the motor assembly and encoder to an IBM PC. The fuzzy logic based motor controller was developed using the TILShell and Fuzzy C Development System on an IBM PC. A Proportional-Derivative (PD) type conventional controller was also developed and implemented in the IBM PC to compare the performance with the fuzzy controller. Test cases were defined to include step inputs of 90 and 180 degrees rotation, sine and square wave profiles in 5 to 20 hertz frequency range, as well as ramp inputs. In this paper we describe our approach to develop a fuzzy as well as PH controller, provide details of hardware set-up and test cases, and discuss the performance results. In comparison, the fuzzy logic based controller handles the non-linearities of the motor assembly very well and provides excellent control over a broad range of parameters. Fuzzy technology, as indicated by our results, possesses inherent adaptive features.
GNG Motifs Can Replace a GGG Stretch during G-Quadruplex Formation in a Context Dependent Manner.
Kohal Das
Full Text Available G-quadruplexes are one of the most commonly studied non-B DNA structures. Generally, these structures are formed using a minimum of 4, three guanine tracts, with connecting loops ranging from one to seven. Recent studies have reported deviation from this general convention. One such deviation is the involvement of bulges in the guanine tracts. In this study, guanines along with bulges, also referred to as GNG motifs have been extensively studied using recently reported HOX11 breakpoint fragile region I as a model template. By strategic mutagenesis approach we show that the contribution from continuous G-tracts may be dispensible during G-quadruplex formation when such motifs are flanked by GNGs. Importantly, the positioning and number of GNG/GNGNG can also influence the formation of G-quadruplexes. Further, we assessed three genomic regions from HIF1 alpha, VEGF and SHOX gene for G-quadruplex formation using GNG motifs. We show that HIF1 alpha sequence harbouring GNG motifs can fold into intramolecular G-quadruplex. In contrast, GNG motifs in mutant VEGF sequence could not participate in structure formation, suggesting that the usage of GNG is context dependent. Importantly, we show that when two continuous stretches of guanines are flanked by two independent GNG motifs in a naturally occurring sequence (SHOX, it can fold into an intramolecular G-quadruplex. Finally, we show the specific binding of G-quadruplex binding protein, Nucleolin and G-quadruplex antibody, BG4 to SHOX G-quadruplex. Overall, our study provides novel insights into the role of GNG motifs in G-quadruplex structure formation which may have both physiological and pathological implications.
Sugimoto, Asuka; Sumi, Takuya; Kang, Jiyoung; Tateno, Masaru
2017-07-01
Recognition in biological macromolecular systems, such as DNA-protein recognition, is one of the most crucial problems to solve toward understanding the fundamental mechanisms of various biological processes. Since specific base sequences of genome DNA are discriminated by proteins, such as transcription factors (TFs), finding TF binding motifs (TFBMs) in whole genome DNA sequences is currently a central issue in interdisciplinary biophysical and information sciences. In the present study, a novel strategy to create a discriminant function for discrimination of TFBMs by constituting mathematical neural networks (NNs) is proposed, together with a method to determine the boundary of signals (TFBMs) and noise in the NN-score (output) space. This analysis also leads to the mathematical limitation of discrimination in the recognition of features representing TFBMs, in an information geometrical manifold. Thus, the present strategy enables the identification of the whole space of TFBMs, right up to the noise boundary.
Mark D McDonnell
Full Text Available Complex networks are frequently characterized by metrics for which particular subgraphs are counted. One statistic from this category, which we refer to as motif-role fingerprints, differs from global subgraph counts in that the number of subgraphs in which each node participates is counted. As with global subgraph counts, it can be important to distinguish between motif-role fingerprints that are 'structural' (induced subgraphs and 'functional' (partial subgraphs. Here we show mathematically that a vector of all functional motif-role fingerprints can readily be obtained from an arbitrary directed adjacency matrix, and then converted to structural motif-role fingerprints by multiplying that vector by a specific invertible conversion matrix. This result demonstrates that a unique structural motif-role fingerprint exists for any given functional motif-role fingerprint. We demonstrate a similar result for the cases of functional and structural motif-fingerprints without node roles, and global subgraph counts that form the basis of standard motif analysis. We also explicitly highlight that motif-role fingerprints are elemental to several popular metrics for quantifying the subgraph structure of directed complex networks, including motif distributions, directed clustering coefficient, and transitivity. The relationships between each of these metrics and motif-role fingerprints also suggest new subtypes of directed clustering coefficients and transitivities. Our results have potential utility in analyzing directed synaptic networks constructed from neuronal connectome data, such as in terms of centrality. Other potential applications include anomaly detection in networks, identification of similar networks and identification of similar nodes within networks. Matlab code for calculating all stated metrics following calculation of functional motif-role fingerprints is provided as S1 Matlab File.
Fuzzy fractals, chaos, and noise
Zardecki, A.
1997-05-01
To distinguish between chaotic and noisy processes, the authors analyze one- and two-dimensional chaotic mappings, supplemented by the additive noise terms. The predictive power of a fuzzy rule-based system allows one to distinguish ergodic and chaotic time series: in an ergodic series the likelihood of finding large numbers is small compared to the likelihood of finding them in a chaotic series. In the case of two dimensions, they consider the fractal fuzzy sets whose {alpha}-cuts are fractals, arising in the context of a quadratic mapping in the extended complex plane. In an example provided by the Julia set, the concept of Hausdorff dimension enables one to decide in favor of chaotic or noisy evolution.
Stability analysis of polynomial fuzzy models via polynomial fuzzy Lyapunov functions
Bernal Reza, Miguel Ángel; Sala, Antonio; JAADARI, ABDELHAFIDH; Guerra, Thierry-Marie
2011-01-01
In this paper, the stability of continuous-time polynomial fuzzy models by means of a polynomial generalization of fuzzy Lyapunov functions is studied. Fuzzy Lyapunov functions have been fruitfully used in the literature for local analysis of Takagi-Sugeno models, a particular class of the polynomial fuzzy ones. Based on a recent Taylor-series approach which allows a polynomial fuzzy model to exactly represent a nonlinear model in a compact set of the state space, it is shown that a refinemen...
Rekayasa Pengembangan Desain Motif Batik Khas Melayu
Eustasia Sri Murwati
2016-04-01
Full Text Available ABSTRAKPengembangan desain batik melalui rancang bangun perekayasaan desain menurut ragam hias Melayu meliputi pengembangan motif dan proses, termasuk pemilihan komposisi warna. Proses yang sering dilakukan yaitu proses celup, penghilangan lilin dan celup warna tumpangan atau proses colet, celup, penghilangan lilin atau celup kemudian penghilangan lilin yang disebut Batik Kelengan. Setiap pulau di Indonesia mempunyai ciri khas budaya dan kesenian yang dikenal dengan corak/ragam hias khas daerah, juga ornamen yang diminati oleh masyarakat dari daerah tersebut atau dari daerah lain. Kondisi demikian mendorong pertumbuhan industri kerajinan yang memanfaatkan unsur–unsur seni. Adapun motif yang diperoleh adalah: Ayam Berlaga, Bungo Matahari, Kuntum Bersanding, Lancang Kuning, Encong Kerinci, Durian Pecah, Bungo Bintang, Bungo Pauh Kecil, Riang-riang, Bungo Nagaro. Pengembangan desain tersebut dipilih 3 produk terbaik yang dinilai oleh 5 penilai yang ahli di bidang desain batik, yaitu motif Durian Pecah, Ayam Berlaga, dan Bungo Matahari. Rancang bangun diversifikasi desain dengan memanfaatkan unsur–unsur seni dan ketrampilan etnis Melayu yaitu pemilihan ragam hias dan motif batik Melayu untuk diterapkan ke bahan sandang dengan komposisi warna yang menarik, sehingga produk memenuhi selera konsumen. Memperbaiki keberagaman batik dengan meningkatkan desain produk antara lain menuangkan ragam hias Melayu ke dalam proses batik yang menggunakan berbagai macam warna sehingga komposisi warna memadai. Diperoleh hasil produk batik dengan ragam hias Melayu yang berkualitas dan komposisi warna yang sesuai dengan karakter ragam hias Melayu. Rancang bangun desain produk untuk mendapatkan formulasi desain serta kelayakan prosesnya dengan penekanan pada teknologi akrab lingkungan dilaksanakan dengan alternatif pendekatan yaitu penciptaan desain bentuk baru.Kata kunci: desain, batik, rancang bangun, ragam hias, MelayuABSTRACTDevelopment of batik design through
Transnationalism as a motif in family stories.
Stone, Elizabeth; Gomez, Erica; Hotzoglou, Despina; Lipnitsky, Jane Y
2005-12-01
Family stories have long been recognized as a vehicle for assessing components of a family's emotional and social life, including the degree to which an immigrant family has been willing to assimilate. Transnationalism, defined as living in one or more cultures and maintaining connections to both, is now increasingly common. A qualitative study of family stories in the family of those who appear completely "American" suggests that an affiliation with one's home country is nevertheless detectable in the stories via motifs such as (1) positively connotated home remedies, (2) continuing denigration of home country "enemies," (3) extensive knowledge of the home country history and politics, (4) praise of endogamy and negative assessment of exogamy, (5) superiority of home country to America, and (6) beauty of home country. Furthermore, an awareness of which model--assimilationist or transnational--governs a family's experience may help clarify a clinician's understanding of a family's strengths, vulnerabilities, and mode of framing their cultural experiences.
Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2
Miller, Martin Lee; Hanke, S.; Hinsby, A. M.
2008-01-01
set of 481 unique phosphotyrosine (Tyr(P)) peptides by sequence similarity to known ligands of the Src homology 2 (SH2) and the phosphotyrosine binding (PTB) domains. From 20 clusters we extracted 16 known and four new interaction motifs. Using quantitative mass spectrometry we pulled down Tyr......(P)-specific binding partners for peptides corresponding to the extracted motifs. We confirmed numerous previously known interaction motifs and found 15 new interactions mediated by phosphosites not previously known to bind SH2 or PTB. Remarkably, a novel hydrophobic N-terminal motif ((L/V/I)(L/V/I)pY) was identified...
Lin, Kyaw Kyaw; Soe, Aung Kyaw; Thu, Theint Theint
2008-10-01
This research work investigates a Self-Tuning Proportional Derivative (PD) type Fuzzy Logic Controller (STPDFLC) for a two link robot system. The proposed scheme adjusts on-line the output Scaling Factor (SF) by fuzzy rules according to the current trend of the robot. The rule base for tuning the output scaling factor is defined on the error (e) and change in error (de). The scheme is also based on the fact that the controller always tries to manipulate the process input. The rules are in the familiar if-then format. All membership functions for controller inputs (e and de) and controller output (UN) are defined on the common interval [-1,1]; whereas the membership functions for the gain updating factor (α) is defined on [0,1]. There are various methods to calculate the crisp output of the system. Center of Gravity (COG) method is used in this application due to better results it gives. Performances of the proposed STPDFLC are compared with those of their corresponding PD-type conventional Fuzzy Logic Controller (PDFLC). The proposed scheme shows a remarkably improved performance over its conventional counterpart especially under parameters variation (payload). The two-link results of analysis are simulated. These simulation results are illustrated by using MATLAB® programming.
Dhruba Das
2015-04-01
Full Text Available In this article, based on Zadeh’s extension principle we have apply the parametric programming approach to construct the membership functions of the performance measures when the interarrival time and the service time are fuzzy numbers based on the Baruah’s Randomness- Fuzziness Consistency Principle. The Randomness-Fuzziness Consistency Principle leads to defining a normal law of fuzziness using two different laws of randomness. In this article, two fuzzy queues FM/M/1 and M/FM/1 has been studied and constructed their membership functions of the system characteristics based on the aforesaid principle. The former represents a queue with fuzzy exponential arrivals and exponential service rate while the latter represents a queue with exponential arrival rate and fuzzy exponential service rate.
Liseron-Monfils, Christophe; Lewis, Tim; Ashlock, Daniel; McNicholas, Paul D; Fauteux, François; Strömvik, Martina; Raizada, Manish N
2013-03-15
The discovery of genetic networks and cis-acting DNA motifs underlying their regulation is a major objective of transcriptome studies. The recent release of the maize genome (Zea mays L.) has facilitated in silico searches for regulatory motifs. Several algorithms exist to predict cis-acting elements, but none have been adapted for maize. A benchmark data set was used to evaluate the accuracy of three motif discovery programs: BioProspector, Weeder and MEME. Analysis showed that each motif discovery tool had limited accuracy and appeared to retrieve a distinct set of motifs. Therefore, using the benchmark, statistical filters were optimized to reduce the false discovery ratio, and then remaining motifs from all programs were combined to improve motif prediction. These principles were integrated into a user-friendly pipeline for motif discovery in maize called Promzea, available at http://www.promzea.org and on the Discovery Environment of the iPlant Collaborative website. Promzea was subsequently expanded to include rice and Arabidopsis. Within Promzea, a user enters cDNA sequences or gene IDs; corresponding upstream sequences are retrieved from the maize genome. Predicted motifs are filtered, combined and ranked. Promzea searches the chosen plant genome for genes containing each candidate motif, providing the user with the gene list and corresponding gene annotations. Promzea was validated in silico using a benchmark data set: the Promzea pipeline showed a 22% increase in nucleotide sensitivity compared to the best standalone program tool, Weeder, with equivalent nucleotide specificity. Promzea was also validated by its ability to retrieve the experimentally defined binding sites of transcription factors that regulate the maize anthocyanin and phlobaphene biosynthetic pathways. Promzea predicted additional promoter motifs, and genome-wide motif searches by Promzea identified 127 non-anthocyanin/phlobaphene genes that each contained all five predicted promoter
Zimmermann, Nils E. R.; Horton, Matthew K.; Jain, Anubhav; Haranczyk, Maciej
2017-11-01
Structure-property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells) of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal closed packed-like environments. Here, we showcase the usefulness of local order parameters to identify these basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP) database (61,422 compounds) for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT) facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.
Nils E. R. Zimmermann
2017-11-01
Full Text Available Structure–property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors, as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal close packed-like environments. Here, we showcase the usefulness of local order parameters to identify these basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP database (61,422 compounds for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.
Jiménez-Losada, Andrés
2017-01-01
This book offers a comprehensive introduction to cooperative game theory and a practice-oriented reference guide to new models and tools for studying bilateral fuzzy relations among several agents or players. It introduces the reader to several fuzzy models, each of which is first analyzed in the context of classical games (crisp games) and subsequently in the context of fuzzy games. Special emphasis is given to the value of Shapley, which is presented for the first time in the context of fuzzy games. Students and researchers will find here a self-contained reference guide to cooperative fuzzy games, characterized by a wealth of examples, descriptions of a wide range of possible situations, step-by-step explanations of the basic mathematical concepts involved, and easy-to-follow information on axioms and properties.
K. A. Halim
2011-01-01
Full Text Available In this article, we consider a single-unit unreliable production system which produces a single item. During a production run, the production process may shift from the in-control state to the out-of-control state at any random time when it produces some defective items. The defective item production rate is assumed to be imprecise and is characterized by a trapezoidal fuzzy number. The production rate is proportional to the demand rate where the proportionality constant is taken to be a fuzzy number. Two production planning models are developed on the basis of fuzzy and stochastic demand patterns. The expected cost per unit time in the fuzzy sense is derived in each model and defuzzified by using the graded mean integration representation method. Numerical examples are provided to illustrate the optimal results of the proposed fuzzy models.
The identification of functional motifs in temporal gene expression analysis
Michael G. Surette
2005-01-01
Full Text Available The identification of transcription factor binding sites is essential to the understanding of the regulation of gene expression and the reconstruction of genetic regulatory networks. The in silico identification of cis-regulatory motifs is challenging due to sequence variability and lack of sufficient data to generate consensus motifs that are of quantitative or even qualitative predictive value. To determine functional motifs in gene expression, we propose a strategy to adopt false discovery rate (FDR and estimate motif effects to evaluate combinatorial analysis of motif candidates and temporal gene expression data. The method decreases the number of predicted motifs, which can then be confirmed by genetic analysis. To assess the method we used simulated motif/expression data to evaluate parameters. We applied this approach to experimental data for a group of iron responsive genes in Salmonella typhimurium 14028S. The method identified known and potentially new ferric-uptake regulator (Fur binding sites. In addition, we identified uncharacterized functional motif candidates that correlated with specific patterns of expression. A SAS code for the simulation and analysis gene expression data is available from the first author upon request.
RNA recognition motif (RRM)-containing proteins in Bombyx mori
STORAGESEVER
2009-03-20
Mar 20, 2009 ... Recognition Motif (RRM), sometimes referred to as. RNP1, is one of the first identified domains for RNA interaction. RRM is very common ..... Apart from the RRM motif, eIF3-S9 has a Trp-Asp. (WD) repeat domain, Poly (A) ...
BlockLogo: Visualization of peptide and sequence motif conservation
Olsen, Lars Rønn; Kudahl, Ulrich Johan; Simon, Christian
2013-01-01
BlockLogo is a web-server application for the visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from multiple sequence alignments. The user input consists of a multiple sequence alignment, se...
Fingerprint motifs of phytases | Fan | African Journal of Biotechnology
Among the total of potential 173 phytases gained in 11 plant genomes through MAST, PAPhys are the major phytases, and HAPhys are the minor, and other phytase groups are not found in planta. Keywords: Phytase, fingerprint motif, multiple EM for motif elicitation (MEME), MAST African Journal of Biotechnology Vol.
Environmental influences on DNA curvature
Ussery, David; Higgins, C.F.; Bolshoy, A.
1999-01-01
DNA curvature plays an important role in many biological processes. To study environmentalinfluences on DNA curvature we compared the anomalous migration on polyacrylamide gels ofligation ladders of 11 specifically-designed oligonucleotides. At low temperatures (25 degreesC and below) most......, whilst spermine enhanced theanomalous migration of a different set of sequences. Sequences with a GGC motif exhibitedgreater curvature than predicted by the presently-used angles for the nearest-neighbour wedgemodel and are especially sensitive to Mg2+. The data have implications for models...... for DNAcurvature and for environmentally-sensitive DNA conformations in the regulation of geneexpression....
Identification of sequence motifs significantly associated with antisense activity
Peek Andrew S
2007-06-01
Full Text Available Abstract Background Predicting the suppression activity of antisense oligonucleotide sequences is the main goal of the rational design of nucleic acids. To create an effective predictive model, it is important to know what properties of an oligonucleotide sequence associate significantly with antisense activity. Also, for the model to be efficient we must know what properties do not associate significantly and can be omitted from the model. This paper will discuss the results of a randomization procedure to find motifs that associate significantly with either high or low antisense suppression activity, analysis of their properties, as well as the results of support vector machine modelling using these significant motifs as features. Results We discovered 155 motifs that associate significantly with high antisense suppression activity and 202 motifs that associate significantly with low suppression activity. The motifs range in length from 2 to 5 bases, contain several motifs that have been previously discovered as associating highly with antisense activity, and have thermodynamic properties consistent with previous work associating thermodynamic properties of sequences with their antisense activity. Statistical analysis revealed no correlation between a motif's position within an antisense sequence and that sequences antisense activity. Also, many significant motifs existed as subwords of other significant motifs. Support vector regression experiments indicated that the feature set of significant motifs increased correlation compared to all possible motifs as well as several subsets of the significant motifs. Conclusion The thermodynamic properties of the significantly associated motifs support existing data correlating the thermodynamic properties of the antisense oligonucleotide with antisense efficiency, reinforcing our hypothesis that antisense suppression is strongly associated with probe/target thermodynamics, as there are no enzymatic
Fuzzy Logic and Arithmetical Hierarchy III
Hájek, Petr
2001-01-01
Roč. 68, č. 1 (2001), s. 129-142 ISSN 0039-3215 R&D Projects: GA AV ČR IAA1030004 Institutional research plan: AV0Z1030915 Keywords : fuzzy logic * basic fuzzy logic * Lukasiewicz logic * Godel logic * product logic * arithmetical hierarchy Subject RIV: BA - General Mathematics
Fuzziness and randomness in an optimization framework
Luhandjula, M.K.
1994-03-01
This paper presents a semi-infinite approach for linear programming in the presence of fuzzy random variable coefficients. As a byproduct a way for dealing with optimization problems including both fuzzy and random data is obtained. Numerical examples are provided for the sake of illustration. (author). 13 refs
Contraction theorems in fuzzy metric space
Farnoosh, R.; Aghajani, A.; Azhdari, P.
2009-01-01
In this paper, the results on fuzzy contractive mapping proposed by Dorel Mihet will be proved for B-contraction and C-contraction in the case of George and Veeramani fuzzy metric space. The existence of fixed point with weaker conditions will be proved; that is, instead of the convergence of subsequence, p-convergence of subsequence is used.
FINDING STANDARD DEVIATION OF A FUZZY NUMBER
Fokrul Alom Mazarbhuiya
2017-01-01
Two probability laws can be root of a possibility law. Considering two probability densities over two disjoint ranges, we can define the fuzzy standard deviation of a fuzzy variable with the help of the standard deviation two random variables in two disjoint spaces.
Fuzzy Treatment of Candidate Outliers in Measurements
Giampaolo E. D'Errico
2012-01-01
Full Text Available Robustness against the possible occurrence of outlying observations is critical to the performance of a measurement process. Open questions relevant to statistical testing for candidate outliers are reviewed. A novel fuzzy logic approach is developed and exemplified in a metrology context. A simulation procedure is presented and discussed by comparing fuzzy versus probabilistic models.
A physical analogy to fuzzy clustering
Jantzen, Jan
2004-01-01
This tutorial paper provides an interpretation of the membership assignment in the fuzzy clustering algorithm fuzzy c-means. The membership of a data point to several clusters is shown to be analogous to the gravitational forces between bodies of mass. This provides an alternative way to explain...
Mathematical Fuzzy Logic - State of Art 2001
Hájek, Petr
2003-01-01
Roč. 24, - (2003), s. 71-89 ISSN 0103-9059. [WOLLIC'2001. Brasília, 31.07.2001-03.08.2001] R&D Projects: GA MŠk LN00A056 Keywords : fuzzy logic * many valued logic * basic fuzzy logic BL Subject RIV: BA - General Mathematics http://www.mat.unb.br/~matcont/24_4.pdf
On the Power of Fuzzy Markup Language
Loia, Vincenzo; Lee, Chang-Shing; Wang, Mei-Hui
2013-01-01
One of the most successful methodology that arose from the worldwide diffusion of Fuzzy Logic is Fuzzy Control. After the first attempts dated in the seventies, this methodology has been widely exploited for controlling many industrial components and systems. At the same time, and very independently from Fuzzy Logic or Fuzzy Control, the birth of the Web has impacted upon almost all aspects of computing discipline. Evolution of Web, Web 2.0 and Web 3.0 has been making scenarios of ubiquitous computing much more feasible; consequently information technology has been thoroughly integrated into everyday objects and activities. What happens when Fuzzy Logic meets Web technology? Interesting results might come out, as you will discover in this book. Fuzzy Mark-up Language is a son of this synergistic view, where some technological issues of Web are re-interpreted taking into account the transparent notion of Fuzzy Control, as discussed here. The concept of a Fuzzy Control that is conceived and modeled in terms...
Modeling Research Project Risks with Fuzzy Maps
Bodea, Constanta Nicoleta; Dascalu, Mariana Iuliana
2009-01-01
The authors propose a risks evaluation model for research projects. The model is based on fuzzy inference. The knowledge base for fuzzy process is built with a causal and cognitive map of risks. The map was especially developed for research projects, taken into account their typical lifecycle. The model was applied to an e-testing research…
Homeopathic drug selection using Intuitionistic fuzzy sets.
Kharal, Athar
2009-01-01
Using intuitionistic fuzzy set theory, Sanchez's approach to medical diagnosis has been applied to the problem of selection of single remedy from homeopathic repertorization. Two types of Intuitionistic Fuzzy Relations (IFRs) and three types of selection indices are discussed. I also propose a new repertory exploiting the benefits of soft-intelligence.
Parallel fuzzy connected image segmentation on GPU
Zhuge, Ying; Cao, Yong; Udupa, Jayaram K.; Miller, Robert W.
2011-01-01
Purpose: Image segmentation techniques using fuzzy connectedness (FC) principles have shown their effectiveness in segmenting a variety of objects in several large applications. However, one challenge in these algorithms has been their excessive computational requirements when processing large image datasets. Nowadays, commodity graphics hardware provides a highly parallel computing environment. In this paper, the authors present a parallel fuzzy connected image segmentation algorithm impleme...
Aizawa, N; Chakrabarti, R
2007-01-01
We note that the recently introduced fuzzy torus can be regarded as a q-deformed parafermion. Based on this picture, classification of the Hermitian representations of the fuzzy torus is carried out. The result involves Fock-type representations and new finite-dimensional representations for q being a root of unity as well as already known finite-dimensional ones
Bounded Rationality of Generalized Abstract Fuzzy Economies
Lei Wang
2014-01-01
Full Text Available By using a nonlinear scalarization technique, the bounded rationality model M for generalized abstract fuzzy economies in finite continuous spaces is established. Furthermore, by using the model M, some new theorems for structural stability and robustness to (λ,ϵ-equilibria of generalized abstract fuzzy economies are proved.
Uzawa method for fuzzy linear system
Ke Wang
2013-01-01
An Uzawa method is presented for solving fuzzy linear systems whose coefficient matrix is crisp and the right-hand side column is arbitrary fuzzy number vector. The explicit iterative scheme is given. The convergence is analyzed with convergence theorems and the optimal parameter is obtained. Numerical examples are given to illustrate the procedure and show the effectiveness and efficiency of the method.
Fuzzy GML Modeling Based on Vague Soft Sets
Bo Wei
2017-01-01
Full Text Available The Open Geospatial Consortium (OGC Geography Markup Language (GML explicitly represents geographical spatial knowledge in text mode. All kinds of fuzzy problems will inevitably be encountered in spatial knowledge expression. Especially for those expressions in text mode, this fuzziness will be broader. Describing and representing fuzziness in GML seems necessary. Three kinds of fuzziness in GML can be found: element fuzziness, chain fuzziness, and attribute fuzziness. Both element fuzziness and chain fuzziness belong to the reflection of the fuzziness between GML elements and, then, the representation of chain fuzziness can be replaced by the representation of element fuzziness in GML. On the basis of vague soft set theory, two kinds of modeling, vague soft set GML Document Type Definition (DTD modeling and vague soft set GML schema modeling, are proposed for fuzzy modeling in GML DTD and GML schema, respectively. Five elements or pairs, associated with vague soft sets, are introduced. Then, the DTDs and the schemas of the five elements are correspondingly designed and presented according to their different chains and different fuzzy data types. While the introduction of the five elements or pairs is the basis of vague soft set GML modeling, the corresponding DTD and schema modifications are key for implementation of modeling. The establishment of vague soft set GML enables GML to represent fuzziness and solves the problem of lack of fuzzy information expression in GML.
A NEW APPROACH ON SHORTEST PATH IN FUZZY ENVIRONMENT
A. Nagoorgani; A. Mumtaj Begam
2010-01-01
This paper introduces a new type of fuzzy shortest path network problem using triangular fuzzy number. To find the smallest edge by the fuzzy distance using graded mean integration representation of generalized fuzzy number for every node. Thus the optimum shortest path for the given problem is obtained.
Solution of a System of Linear Equations with Fuzzy Numbers
Horčík, Rostislav
2008-01-01
Roč. 159, č. 14 (2008), s. 1788-1810 ISSN 0165-0114 R&D Projects: GA AV ČR KJB100300502 Institutional research plan: CEZ:AV0Z10300504 Keywords : fuzzy number * fuzzy interval * interval analysis * fuzzy arithmetic * fuzzy class theory * united solution set Subject RIV: BA - General Mathematics Impact factor: 1.833, year: 2008
Consolidity analysis for fully fuzzy functions, matrices, probability and statistics
Walaa Ibrahim Gabr
2015-03-01
Full Text Available The paper presents a comprehensive review of the know-how for developing the systems consolidity theory for modeling, analysis, optimization and design in fully fuzzy environment. The solving of systems consolidity theory included its development for handling new functions of different dimensionalities, fuzzy analytic geometry, fuzzy vector analysis, functions of fuzzy complex variables, ordinary differentiation of fuzzy functions and partial fraction of fuzzy polynomials. On the other hand, the handling of fuzzy matrices covered determinants of fuzzy matrices, the eigenvalues of fuzzy matrices, and solving least-squares fuzzy linear equations. The approach demonstrated to be also applicable in a systematic way in handling new fuzzy probabilistic and statistical problems. This included extending the conventional probabilistic and statistical analysis for handling fuzzy random data. Application also covered the consolidity of fuzzy optimization problems. Various numerical examples solved have demonstrated that the new consolidity concept is highly effective in solving in a compact form the propagation of fuzziness in linear, nonlinear, multivariable and dynamic problems with different types of complexities. Finally, it is demonstrated that the implementation of the suggested fuzzy mathematics can be easily embedded within normal mathematics through building special fuzzy functions library inside the computational Matlab Toolbox or using other similar software languages.
New approach to solve symmetric fully fuzzy linear systems
concepts of fuzzy set theory and then define a fully fuzzy linear system of equations. .... To represent the above problem as fully fuzzy linear system, we represent x .... Fully fuzzy linear systems can be solved by Linear programming approach, ...
Computing the eigenvalues and eigenvectors of a fuzzy matrix
A. Kumar
2012-08-01
Full Text Available Computation of fuzzy eigenvalues and fuzzy eigenvectors of a fuzzy matrix is a challenging problem. Determining the maximal and minimal symmetric solution can help to find the eigenvalues. So, we try to compute these eigenvalues by determining the maximal and minimal symmetric solution of the fully fuzzy linear system $widetilde{A}widetilde{X}= widetilde{lambda} widetilde{X}.$
Matthews, Lindsay A.; Duong, Andrew; Prasad, Ajai A.; Duncker, Bernard P.; Guarné, Alba
2009-01-01
To understand the role of the Cdc7–Dbf4 complex in checkpoint responses, a fragment of Saccharomyces cerevisiae Dbf4 encompassing motif N was isolated, overproduced and crystallized. The Cdc7–Dbf4 complex plays an instrumental role in the initiation of DNA replication and is a target of replication-checkpoint responses in Saccharomyces cerevisiae. Cdc7 is a conserved serine/threonine kinase whose activity depends on association with its regulatory subunit, Dbf4. A conserved sequence near the N-terminus of Dbf4 (motif N) is necessary for the interaction of Cdc7–Dbf4 with the checkpoint kinase Rad53. To understand the role of the Cdc7–Dbf4 complex in checkpoint responses, a fragment of Saccharomyces cerevisiae Dbf4 encompassing motif N was isolated, overproduced and crystallized. A complete native data set was collected at 100 K from crystals that diffracted X-rays to 2.75 Å resolution and structure determination is currently under way
Automatic annotation of protein motif function with Gene Ontology terms
Gopalakrishnan Vanathi
2004-09-01
Full Text Available Abstract Background Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist foridentifying candidate protein motifs at the whole genome level. However, amuch needed and importanttask is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base. Results This paperpresents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifsis viewed as both a binary classification and information retrieval problem, where PROSITE motifs are used as samples for mode training and functional prediction. The mutual information of a motif and aGO term association isfound to be a very useful feature. We take advantageof the known motifs to train a logistic regression classifier, which allows us to combine mutual information with other frequency-based features and obtain a probability of correctassociation. The trained logistic regression model has intuitively meaningful and logically plausible parameter values, and performs very well empirically according to our evaluation criteria. Conclusions In this research, different methods for automatic annotation of protein motifs have been investigated. Empirical result demonstrated that the methods have a great potential for detecting and augmenting information about thefunctions of newly discovered candidate protein motifs.
Fuzzy modeling and control theory and applications
Matía, Fernando; Jiménez, Emilio
2014-01-01
Much work on fuzzy control, covering research, development and applications, has been developed in Europe since the 90's. Nevertheless, the existing books in the field are compilations of articles without interconnection or logical structure or they express the personal point of view of the author. This book compiles the developments of researchers with demonstrated experience in the field of fuzzy control following a logic structure and a unified the style. The first chapters of the book are dedicated to the introduction of the main fuzzy logic techniques, where the following chapters focus on concrete applications. This book is supported by the EUSFLAT and CEA-IFAC societies, which include a large number of researchers in the field of fuzzy logic and control. The central topic of the book, Fuzzy Control, is one of the main research and development lines covered by these associations.
Markowitz portfolio optimization model employing fuzzy measure
Ramli, Suhailywati; Jaaman, Saiful Hafizah
2017-04-01
Markowitz in 1952 introduced the mean-variance methodology for the portfolio selection problems. His pioneering research has shaped the portfolio risk-return model and become one of the most important research fields in modern finance. This paper extends the classical Markowitz's mean-variance portfolio selection model applying the fuzzy measure to determine the risk and return. In this paper, we apply the original mean-variance model as a benchmark, fuzzy mean-variance model with fuzzy return and the model with return are modeled by specific types of fuzzy number for comparison. The model with fuzzy approach gives better performance as compared to the mean-variance approach. The numerical examples are included to illustrate these models by employing Malaysian share market data.
Integrated development environment for fuzzy logic applications
Pagni, Andrea; Poluzzi, Rinaldo; Rizzotto, GianGuido; Lo Presti, Matteo
1993-12-01
During the last five years, Fuzzy Logic has gained enormous popularity, both in the academic and industrial worlds, breaking up the traditional resistance against changes thanks to its innovative approach to problems formalization. The success of this new methodology is pushing the creation of a brand new class of devices, called Fuzzy Machines, to overcome the limitations of traditional computing systems when acting as Fuzzy Systems and adequate Software Tools to efficiently develop new applications. This paper aims to present a complete development environment for the definition of fuzzy logic based applications. The environment is also coupled with a sophisticated software tool for semiautomatic synthesis and optimization of the rules with stability verifications. Later it is presented the architecture of WARP, a dedicate VLSI programmable chip allowing to compute in real time a fuzzy control process. The article is completed with two application examples, which have been carried out exploiting the aforementioned tools and devices.
Multi-dimensional Fuzzy Euler Approximation
Yangyang Hao
2017-05-01
Full Text Available Multi-dimensional Fuzzy differential equations driven by multi-dimen-sional Liu process, have been intensively applied in many fields. However, we can not obtain the analytic solution of every multi-dimensional fuzzy differential equation. Then, it is necessary for us to discuss the numerical results in most situations. This paper focuses on the numerical method of multi-dimensional fuzzy differential equations. The multi-dimensional fuzzy Taylor expansion is given, based on this expansion, a numerical method which is designed for giving the solution of multi-dimensional fuzzy differential equation via multi-dimensional Euler method will be presented, and its local convergence also will be discussed.
Molecular processors: from qubits to fuzzy logic.
Gentili, Pier Luigi
2011-03-14
Single molecules or their assemblies are information processing devices. Herein it is demonstrated how it is possible to process different types of logic through molecules. As long as decoherent effects are maintained far away from a pure quantum mechanical system, quantum logic can be processed. If the collapse of superimposed or entangled wavefunctions is unavoidable, molecules can still be used to process either crisp (binary or multi-valued) or fuzzy logic. The way for implementing fuzzy inference engines is declared and it is supported by the examples of molecular fuzzy logic systems devised so far. Fuzzy logic is drawing attention in the field of artificial intelligence, because it models human reasoning quite well. This ability may be due to some structural analogies between a fuzzy logic system and the human nervous system. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Flows in networks under fuzzy conditions
Bozhenyuk, Alexander Vitalievich; Kacprzyk, Janusz; Rozenberg, Igor Naymovich
2017-01-01
This book offers a comprehensive introduction to fuzzy methods for solving flow tasks in both transportation and networks. It analyzes the problems of minimum cost and maximum flow finding with fuzzy nonzero lower flow bounds, and describes solutions to minimum cost flow finding in a network with fuzzy arc capacities and transmission costs. After a concise introduction to flow theory and tasks, the book analyzes two important problems. The first is related to determining the maximum volume for cargo transportation in the presence of uncertain network parameters, such as environmental changes, measurement errors and repair work on the roads. These parameters are represented here as fuzzy triangular, trapezoidal numbers and intervals. The second problem concerns static and dynamic flow finding in networks under fuzzy conditions, and an effective method that takes into account the network’s transit parameters is presented here. All in all, the book provides readers with a practical reference guide to state-of-...
Transportation optimization with fuzzy trapezoidal numbers based on possibility theory.
He, Dayi; Li, Ran; Huang, Qi; Lei, Ping
2014-01-01
In this paper, a parametric method is introduced to solve fuzzy transportation problem. Considering that parameters of transportation problem have uncertainties, this paper develops a generalized fuzzy transportation problem with fuzzy supply, demand and cost. For simplicity, these parameters are assumed to be fuzzy trapezoidal numbers. Based on possibility theory and consistent with decision-makers' subjectiveness and practical requirements, the fuzzy transportation problem is transformed to a crisp linear transportation problem by defuzzifying fuzzy constraints and objectives with application of fractile and modality approach. Finally, a numerical example is provided to exemplify the application of fuzzy transportation programming and to verify the validity of the proposed methods.
A study on generalized hesitant intuitionistic Fuzzy soft sets
Nazra, A.; Syafruddin; Wicaksono, G. C.; Syafwan, M.
2018-03-01
By combining the concept of hesitant intuitionistic fuzzy sets, fuzzy soft sets and fuzzy sets, we extend hesitant intuitionistic fuzzy soft sets to a generalized hesitant intuitionistic fuzzy soft sets. Some operations on generalized hesitant intuitionistic fuzzy soft sets, such as union, complement, operations “AND” and “OR”, and intersection are defined. From such operations the authors obtain related properties such as commutative, associative and De Morgan's laws. The authors also get an algebraic structure of the collection of all generalized hesitant intuitionistic fuzzy soft sets over a set.
Vincenti Matthew P
2005-11-01
Full Text Available Abstract Background The responses to interleukin 1 (IL-1 in human chondrocytes constitute a complex regulatory mechanism, where multiple transcription factors interact combinatorially to transcription-factor binding motifs (TFBMs. In order to select a critical set of TFBMs from genomic DNA information and an array-derived data, an efficient algorithm to solve a combinatorial optimization problem is required. Although computational approaches based on evolutionary algorithms are commonly employed, an analytical algorithm would be useful to predict TFBMs at nearly no computational cost and evaluate varying modelling conditions. Singular value decomposition (SVD is a powerful method to derive primary components of a given matrix. Applying SVD to a promoter matrix defined from regulatory DNA sequences, we derived a novel method to predict the critical set of TFBMs. Results The promoter matrix was defined to establish a quantitative relationship between the IL-1-driven mRNA alteration and genomic DNA sequences of the IL-1 responsive genes. The matrix was decomposed with SVD, and the effects of 8 potential TFBMs (5'-CAGGC-3', 5'-CGCCC-3', 5'-CCGCC-3', 5'-ATGGG-3', 5'-GGGAA-3', 5'-CGTCC-3', 5'-AAAGG-3', and 5'-ACCCA-3' were predicted from a pool of 512 random DNA sequences. The prediction included matches to the core binding motifs of biologically known TFBMs such as AP2, SP1, EGR1, KROX, GC-BOX, ABI4, ETF, E2F, SRF, STAT, IK-1, PPARγ, STAF, ROAZ, and NFκB, and their significance was evaluated numerically using Monte Carlo simulation and genetic algorithm. Conclusion The described SVD-based prediction is an analytical method to provide a set of potential TFBMs involved in transcriptional regulation. The results would be useful to evaluate analytically a contribution of individual DNA sequences.
Fuzzy statistical decision-making theory and applications
Kabak, Özgür
2016-01-01
This book offers a comprehensive reference guide to fuzzy statistics and fuzzy decision-making techniques. It provides readers with all the necessary tools for making statistical inference in the case of incomplete information or insufficient data, where classical statistics cannot be applied. The respective chapters, written by prominent researchers, explain a wealth of both basic and advanced concepts including: fuzzy probability distributions, fuzzy frequency distributions, fuzzy Bayesian inference, fuzzy mean, mode and median, fuzzy dispersion, fuzzy p-value, and many others. To foster a better understanding, all the chapters include relevant numerical examples or case studies. Taken together, they form an excellent reference guide for researchers, lecturers and postgraduate students pursuing research on fuzzy statistics. Moreover, by extending all the main aspects of classical statistical decision-making to its fuzzy counterpart, the book presents a dynamic snapshot of the field that is expected to stimu...
East West Fuzzy colloquium 2000. 8. Zittau Fuzzy colloquium. Proceedings
Wagenknecht, M; Chaker, N; Hampel, R [comps.
2000-07-01
The Zittau Colloquium is organized annually with the objective to stimulate contacts between scientists in academic research, industrial development and university teaching from Eastern and Western European countries and from other parts of the world. A further aim of the colloquium is the exchange of information about the state-of-the-art in the field of Fuzzy Logic basic investigation and application in connection with other theories, for example Neuronal Networks. Therefore, we want to stimulate the discussion about proposals for common national, bilateral and international supported projects to incite research, teaching, as well as mobility of students and teachers. (orig.)
Fuzzy stochastic damage mechanics (FSDM based on fuzzy auto-adaptive control theory
Ya-jun Wang
2012-06-01
Full Text Available In order to fully interpret and describe damage mechanics, the origin and development of fuzzy stochastic damage mechanics were introduced based on the analysis of the harmony of damage, probability, and fuzzy membership in the interval of [0,1]. In a complete normed linear space, it was proven that a generalized damage field can be simulated through β probability distribution. Three kinds of fuzzy behaviors of damage variables were formulated and explained through analysis of the generalized uncertainty of damage variables and the establishment of a fuzzy functional expression. Corresponding fuzzy mapping distributions, namely, the half-depressed distribution, swing distribution, and combined swing distribution, which can simulate varying fuzzy evolution in diverse stochastic damage situations, were set up. Furthermore, through demonstration of the generalized probabilistic characteristics of damage variables, the cumulative distribution function and probability density function of fuzzy stochastic damage variables, which show β probability distribution, were modified according to the expansion principle. The three-dimensional fuzzy stochastic damage mechanical behaviors of the Longtan rolled-concrete dam were examined with the self-developed fuzzy stochastic damage finite element program. The statistical correlation and non-normality of random field parameters were considered comprehensively in the fuzzy stochastic damage model described in this paper. The results show that an initial damage field based on the comprehensive statistical evaluation helps to avoid many difficulties in the establishment of experiments and numerical algorithms for damage mechanics analysis.
Designing PID-Fuzzy Controller for Pendubot System
Ho Trong Nguyen
2017-12-01
Full Text Available In the paper, authors analize dynamic equation of a pendubot system. Familiar kinds of controller – PID, fuzzy controllers – are concerned. Then, a structure of PID-FUZZY is presented. The comparison of three kinds of controllers – PID, fuzzy and PID-FUZZY shows the better response of system under PID-FUZZY controller. Then, the experiments on the real model also prove the better stabilization of the hybrid controller which is combined between linear and intelligent controller.
A study of fuzzy control in nuclear scale system
Wang Yu; Zhang Yongming; Wu Ruisheng; Du Xianbin; Liu Shixing
2001-01-01
The new development of the nuclear scale system which uses fuzzy control strategy is presented. Good results have been obtained in using fuzzy control to solve the problems, such as un-linearities, instabilities, time delays, which are difficultly described by formula, etc. The fuzzy variance, membership function and fuzzy rules are given, and the noise disturbances of fuzzy control and PID control are also given
Motif statistics and spike correlations in neuronal networks
Hu, Yu; Shea-Brown, Eric; Trousdale, James; Josić, Krešimir
2013-01-01
Motifs are patterns of subgraphs of complex networks. We studied the impact of such patterns of connectivity on the level of correlated, or synchronized, spiking activity among pairs of cells in a recurrent network of integrate and fire neurons. For a range of network architectures, we find that the pairwise correlation coefficients, averaged across the network, can be closely approximated using only three statistics of network connectivity. These are the overall network connection probability and the frequencies of two second order motifs: diverging motifs, in which one cell provides input to two others, and chain motifs, in which two cells are connected via a third intermediary cell. Specifically, the prevalence of diverging and chain motifs tends to increase correlation. Our method is based on linear response theory, which enables us to express spiking statistics using linear algebra, and a resumming technique, which extrapolates from second order motifs to predict the overall effect of coupling on network correlation. Our motif-based results seek to isolate the effect of network architecture perturbatively from a known network state. (paper)
Computational analyses of synergism in small molecular network motifs.
Yili Zhang
2014-03-01
Full Text Available Cellular functions and responses to stimuli are controlled by complex regulatory networks that comprise a large diversity of molecular components and their interactions. However, achieving an intuitive understanding of the dynamical properties and responses to stimuli of these networks is hampered by their large scale and complexity. To address this issue, analyses of regulatory networks often focus on reduced models that depict distinct, reoccurring connectivity patterns referred to as motifs. Previous modeling studies have begun to characterize the dynamics of small motifs, and to describe ways in which variations in parameters affect their responses to stimuli. The present study investigates how variations in pairs of parameters affect responses in a series of ten common network motifs, identifying concurrent variations that act synergistically (or antagonistically to alter the responses of the motifs to stimuli. Synergism (or antagonism was quantified using degrees of nonlinear blending and additive synergism. Simulations identified concurrent variations that maximized synergism, and examined the ways in which it was affected by stimulus protocols and the architecture of a motif. Only a subset of architectures exhibited synergism following paired changes in parameters. The approach was then applied to a model describing interlocked feedback loops governing the synthesis of the CREB1 and CREB2 transcription factors. The effects of motifs on synergism for this biologically realistic model were consistent with those for the abstract models of single motifs. These results have implications for the rational design of combination drug therapies with the potential for synergistic interactions.
Triadic motifs in the dependence networks of virtual societies
Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing
2014-06-01
In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.
Triadic motifs in the dependence networks of virtual societies.
Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing
2014-06-10
In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.
Willerslev, Eske; Cooper, Alan
2004-01-01
ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...
Yann Blanco
2001-01-01
Full Text Available This paper outlines a methodology to study the stability of Takagi-Sugeno's (TS fuzzy models. The stability analysis of the TS model is performed using a quadratic Liapunov candidate function. This paper proposes a relaxation of Tanaka's stability condition: unlike related works, the equations to be solved are not Liapunov equations for each rule matrix, but a convex combination of them. The coefficients of this sums depend on the membership functions. This method is applied to the design of continuous controllers for the TS model. Three different control structures are investigated, among which the Parallel Distributed Compensation (PDC. An application to the inverted pendulum is proposed here.
Fuzzy methods and design; Fuzzy shuho to sekkei
Furuta, H. [Kwansei Gakuin Univ., Hyogo (Japan)
1996-03-05
This paper explains the application of the fuzzy theory to a design. A rational decision in design with only an objective logic requires conditions such that a set of selectable alternative plans and the results of executing them are known, and that a rule or a sequential relation exists to decide the order of preference of the alternative plans. In a case where the optimum anti-earthquake design was applied, for example, the seismic motion, subsoil and properties of materials or the like used to be treated stochastically and statistically as being of random nature. However, elements of uncertainty are actually involved other than the randomness, in consideration of cost effectiveness, safety and such. In the problems of anti-earthquake design by the fuzzy theory, the restrictive conditions are stipulated with a membership function respectively, such that the design earthquake motion is in a range larger than the maximum motion, and that the stress or displacement is each in the range smaller than the allowable stress or displacement of members; in addition, the weight is expressed to be the minimum as the objective function. 9 refs., 1 fig.
Gao, J.; Berden, G.; Rodgers, M.T.; Oomens, J.
2016-01-01
The Watson-Crick structure of DNA is among the most well-known molecular structures of our time. However, alternative base-pairing motifs are also known to occur, often depending on base sequence, pH, or the presence of cations. Pairing of cytosine (C) bases induced by the sharing of a single proton
DNA mimic proteins: functions, structures, and bioinformatic analysis.
Wang, Hao-Ching; Ho, Chun-Han; Hsu, Kai-Cheng; Yang, Jinn-Moon; Wang, Andrew H-J
2014-05-13
DNA mimic proteins have DNA-like negative surface charge distributions, and they function by occupying the DNA binding sites of DNA binding proteins to prevent these sites from being accessed by DNA. DNA mimic proteins control the activities of a variety of DNA binding proteins and are involved in a wide range of cellular mechanisms such as chromatin assembly, DNA repair, transcription regulation, and gene recombination. However, the sequences and structures of DNA mimic proteins are diverse, making them difficult to predict by bioinformatic search. To date, only a few DNA mimic proteins have been reported. These DNA mimics were not found by searching for functional motifs in their sequences but were revealed only by structural analysis of their charge distribution. This review highlights the biological roles and structures of 16 reported DNA mimic proteins. We also discuss approaches that might be used to discover new DNA mimic proteins.
Intuitionistic Fuzzy Time Series Forecasting Model Based on Intuitionistic Fuzzy Reasoning
Ya’nan Wang
2016-01-01
Full Text Available Fuzzy sets theory cannot describe the data comprehensively, which has greatly limited the objectivity of fuzzy time series in uncertain data forecasting. In this regard, an intuitionistic fuzzy time series forecasting model is built. In the new model, a fuzzy clustering algorithm is used to divide the universe of discourse into unequal intervals, and a more objective technique for ascertaining the membership function and nonmembership function of the intuitionistic fuzzy set is proposed. On these bases, forecast rules based on intuitionistic fuzzy approximate reasoning are established. At last, contrast experiments on the enrollments of the University of Alabama and the Taiwan Stock Exchange Capitalization Weighted Stock Index are carried out. The results show that the new model has a clear advantage of improving the forecast accuracy.
Intelligent control-I: review of fuzzy logic and fuzzy set theory
Nagrial, M.H.
2004-01-01
In the past decade or so, fuzzy systems have supplanted conventional technologies in many engineering systems, in particular in control systems and pattern recognition. Fuzzy logic has found applications in a variety of consumer products e.g. washing machines, camcorders, digital cameras, air conditioners, subway trains, cement kilns and many others. The fuzzy technology is also being applied in information technology, where it provides decision-support and expert systems with powerful reasoning capabilities. Fuzzy sets, introduced by Zadeh in 1965 as a mathematical way to represent vagueness in linguistics, can be considered a generalisation of classical set theory. Fuzziness is often confused with probability. This lecture will introduce the principal concepts and mathematical notions of fuzzy set theory. (author)
Uncertainty analysis of flexible rotors considering fuzzy parameters and fuzzy-random parameters
Fabian Andres Lara-Molina
Full Text Available Abstract The components of flexible rotors are subjected to uncertainties. The main sources of uncertainties include the variation of mechanical properties. This contribution aims at analyzing the dynamics of flexible rotors under uncertain parameters modeled as fuzzy and fuzzy random variables. The uncertainty analysis encompasses the modeling of uncertain parameters and the numerical simulation of the corresponding flexible rotor model by using an approach based on fuzzy dynamic analysis. The numerical simulation is accomplished by mapping the fuzzy parameters of the deterministic flexible rotor model. Thereby, the flexible rotor is modeled by using both the Fuzzy Finite Element Method and the Fuzzy Stochastic Finite Element Method. Numerical simulations illustrate the methodology conveyed in terms of orbits and frequency response functions subject to uncertain parameters.
Fuzzy Constraint-Based Agent Negotiation
Menq-Wen Lin; K. Robert Lai; Ting-Jung Yu
2005-01-01
Conflicts between two or more parties arise for various reasons and perspectives. Thus, resolution of conflicts frequently relies on some form of negotiation. This paper presents a general problem-solving framework for modeling multi-issue multilateral negotiation using fuzzy constraints. Agent negotiation is formulated as a distributed fuzzy constraint satisfaction problem (DFCSP). Fuzzy constrains are thus used to naturally represent each agent's desires involving imprecision and human conceptualization, particularly when lexical imprecision and subjective matters are concerned. On the other hand, based on fuzzy constraint-based problem-solving, our approach enables an agent not only to systematically relax fuzzy constraints to generate a proposal, but also to employ fuzzy similarity to select the alternative that is subject to its acceptability by the opponents. This task of problem-solving is to reach an agreement that benefits all agents with a high satisfaction degree of fuzzy constraints, and move towards the deal more quickly since their search focuses only on the feasible solution space. An application to multilateral negotiation of a travel planning is provided to demonstrate the usefulness and effectiveness of our framework.
Development of a new fuzzy exposure model
Vasconcelos, Wagner Eustaquio de; Lira, Carlos Alberto Brayner de Oliveira; Texeira, Marcello Goulart
2007-01-01
The main topic of this study is the development of an exposure fuzzy model to evaluate the exposure of inhabitants in an area containing uranium, which present a high natural background. In this work, a fuzzy model was created, based on some of the following main factors: activity concentration of uranium, physiological factors and characteristic customs of the exposed individuals. An inference block was created to evaluate some factors of radiation exposure. For this, AHP-fuzzy technique (Analytic Hierarchic Process) was used and its application was demonstrated for a subjected population to the radiation of the natural uranium. The Mandami type fuzzy model was also created from the opinion of specialists. The Monte Carlo method was used to generate a statistics of input data and the daily average exposure served as comparison parameter between the three techniques. The output fuzzy sets were expressed in form of linguistic variables, such as high, medium and low. In the qualitative analysis, the obtained results were satisfactory when translating the opinion of the specialists. In the quantitative analysis, the obtained values are part of the same fuzzy set as the values found in literature. The global results suggest that this type of fuzzy model is highly promising for analysis of exposure to ionizing radiation. (author)
Development of a new fuzzy exposure model
Vasconcelos, Wagner Eustaquio de; Lira, Carlos Alberto Brayner de Oliveira [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Dept. de Energia Nuclear. Grupo de Engenharia de Reatores], E-mail: wagner@ufpe.br, E-mail: cabol@ufpe.br; Texeira, Marcello Goulart [Instituto Militar de Engenharia (IME), Rio de Janeiro, RJ (Brazil). Terrestrial Modelling Group], E-mail: marcellogt@ime.eb.br
2007-07-01
The main topic of this study is the development of an exposure fuzzy model to evaluate the exposure of inhabitants in an area containing uranium, which present a high natural background. In this work, a fuzzy model was created, based on some of the following main factors: activity concentration of uranium, physiological factors and characteristic customs of the exposed individuals. An inference block was created to evaluate some factors of radiation exposure. For this, AHP-fuzzy technique (Analytic Hierarchic Process) was used and its application was demonstrated for a subjected population to the radiation of the natural uranium. The Mandami type fuzzy model was also created from the opinion of specialists. The Monte Carlo method was used to generate a statistics of input data and the daily average exposure served as comparison parameter between the three techniques. The output fuzzy sets were expressed in form of linguistic variables, such as high, medium and low. In the qualitative analysis, the obtained results were satisfactory when translating the opinion of the specialists. In the quantitative analysis, the obtained values are part of the same fuzzy set as the values found in literature. The global results suggest that this type of fuzzy model is highly promising for analysis of exposure to ionizing radiation. (author)
Design of supply chain in fuzzy environment
Rao, Kandukuri Narayana; Subbaiah, Kambagowni Venkata; Singh, Ganja Veera Pratap
2013-05-01
Nowadays, customer expectations are increasing and organizations are prone to operate in an uncertain environment. Under this uncertain environment, the ultimate success of the firm depends on its ability to integrate business processes among supply chain partners. Supply chain management emphasizes cross-functional links to improve the competitive strategy of organizations. Now, companies are moving from decoupled decision processes towards more integrated design and control of their components to achieve the strategic fit. In this paper, a new approach is developed to design a multi-echelon, multi-facility, and multi-product supply chain in fuzzy environment. In fuzzy environment, mixed integer programming problem is formulated through fuzzy goal programming in strategic level with supply chain cost and volume flexibility as fuzzy goals. These fuzzy goals are aggregated using minimum operator. In tactical level, continuous review policy for controlling raw material inventories in supplier echelon and controlling finished product inventories in plant as well as distribution center echelon is considered as fuzzy goals. A non-linear programming model is formulated through fuzzy goal programming using minimum operator in the tactical level. The proposed approach is illustrated with a numerical example.
Towards the future of fuzzy logic
Trillas, Enric; Kacprzyk, Janusz
2015-01-01
This book provides readers with a snapshot of the state-of-the art in fuzzy logic. Throughout the chapters, key theories developed in the last fifty years as well as important applications to practical problems are presented and discussed from different perspectives, as the authors hail from different disciplines and therefore use fuzzy logic for different purposes. The book aims at showing how fuzzy logic has evolved since the first theory formulation by Lotfi A. Zadeh in his seminal paper on Fuzzy Sets in 1965. Fuzzy theories and implementation grew at an impressive speed and achieved significant results, especially on the applicative side. The study of fuzzy logic and its practice spread all over the world, from Europe to Asia, America and Oceania. The editors believe that, thanks to the drive of young researchers, fuzzy logic will be able to face the challenging goals posed by computing with words. New frontiers of knowledge are waiting to be explored. In order to motivate young people to engage in the ...
Design of fuzzy systems using neurofuzzy networks.
Figueiredo, M; Gomide, F
1999-01-01
This paper introduces a systematic approach for fuzzy system design based on a class of neural fuzzy networks built upon a general neuron model. The network structure is such that it encodes the knowledge learned in the form of if-then fuzzy rules and processes data following fuzzy reasoning principles. The technique provides a mechanism to obtain rules covering the whole input/output space as well as the membership functions (including their shapes) for each input variable. Such characteristics are of utmost importance in fuzzy systems design and application. In addition, after learning, it is very simple to extract fuzzy rules in the linguistic form. The network has universal approximation capability, a property very useful in, e.g., modeling and control applications. Here we focus on function approximation problems as a vehicle to illustrate its usefulness and to evaluate its performance. Comparisons with alternative approaches are also included. Both, nonnoisy and noisy data have been studied and considered in the computational experiments. The neural fuzzy network developed here and, consequently, the underlying approach, has shown to provide good results from the accuracy, complexity, and system design points of view.
Automatic approach to deriving fuzzy slope positions
Zhu, Liang-Jun; Zhu, A.-Xing; Qin, Cheng-Zhi; Liu, Jun-Zhi
2018-03-01
Fuzzy characterization of slope positions is important for geographic modeling. Most of the existing fuzzy classification-based methods for fuzzy characterization require extensive user intervention in data preparation and parameter setting, which is tedious and time-consuming. This paper presents an automatic approach to overcoming these limitations in the prototype-based inference method for deriving fuzzy membership value (or similarity) to slope positions. The key contribution is a procedure for finding the typical locations and setting the fuzzy inference parameters for each slope position type. Instead of being determined totally by users in the prototype-based inference method, in the proposed approach the typical locations and fuzzy inference parameters for each slope position type are automatically determined by a rule set based on prior domain knowledge and the frequency distributions of topographic attributes. Furthermore, the preparation of topographic attributes (e.g., slope gradient, curvature, and relative position index) is automated, so the proposed automatic approach has only one necessary input, i.e., the gridded digital elevation model of the study area. All compute-intensive algorithms in the proposed approach were speeded up by parallel computing. Two study cases were provided to demonstrate that this approach can properly, conveniently and quickly derive the fuzzy slope positions.
Sputtering properties of tungsten 'fuzzy' surfaces
Nishijima, D.; Baldwin, M.J.; Doerner, R.P.; Yu, J.H.
2011-01-01
Sputtering yields of He-induced W 'fuzzy' surfaces bombarded by Ar have been measured in the linear divertor plasma simulator PISCES-B. It is found that the sputtering yield of a fuzzy surface, Y fuzzy , decreases with increasing fuzzy layer thickness, L, and saturates at ∼10% of that of a smooth surface, Y smooth , at L > 1 μm. The reduction in the sputtering yield is suspected to be due mainly to the porous structure of fuzz, since the ratio, Y fuzzy /Y smooth follows (1 - p fuzz ), where p fuzz is the fuzz porosity. Further, Y fuzzy /Y smooth is observed to increase with incident ion energy, E i . This may be explained by an energy dependent change in the angular distribution of sputtered W atoms, since at lower E i , the angular distribution is observed to become more butterfly-shaped. That is, a larger fraction of sputtered W atoms can line-of-sight deposit/stick onto neighboring fuzz nanostructures for lower E i butterfly distributions, resulting in lower ratio of Y fuzzy /Y smooth .
Fuzziness and fuzzy modelling in Bulgaria's energy policy decision-making dilemma
Wang Xingquan
2006-01-01
The decision complexity resulting from imprecision in decision variables and parameters, a major difficulty for conventional decision analysis methods, can be relevantly analysed and modelled by fuzzy logic. Bulgaria's nuclear policy decision-making process implicates such complexity of imprecise nature: stakeholders, criteria, measurement, etc. Given the suitable applicability of fuzzy logic in this case, this article tries to offer a concrete fuzzy paradigm including delimitation of decision space, quantification of imprecise variables, and, of course, parameterisation. (author)
A new fuzzy Monte Carlo method for solving SLAE with ergodic fuzzy Markov chains
Maryam Gharehdaghi
2015-05-01
Full Text Available In this paper we introduce a new fuzzy Monte Carlo method for solving system of linear algebraic equations (SLAE over the possibility theory and max-min algebra. To solve the SLAE, we first define a fuzzy estimator and prove that this is an unbiased estimator of the solution. To prove unbiasedness, we apply the ergodic fuzzy Markov chains. This new approach works even for cases with coefficients matrix with a norm greater than one.
Targeting functional motifs of a protein family
Bhadola, Pradeep; Deo, Nivedita
2016-10-01
The structural organization of a protein family is investigated by devising a method based on the random matrix theory (RMT), which uses the physiochemical properties of the amino acid with multiple sequence alignment. A graphical method to represent protein sequences using physiochemical properties is devised that gives a fast, easy, and informative way of comparing the evolutionary distances between protein sequences. A correlation matrix associated with each property is calculated, where the noise reduction and information filtering is done using RMT involving an ensemble of Wishart matrices. The analysis of the eigenvalue statistics of the correlation matrix for the β -lactamase family shows the universal features as observed in the Gaussian orthogonal ensemble (GOE). The property-based approach captures the short- as well as the long-range correlation (approximately following GOE) between the eigenvalues, whereas the previous approach (treating amino acids as characters) gives the usual short-range correlations, while the long-range correlations are the same as that of an uncorrelated series. The distribution of the eigenvector components for the eigenvalues outside the bulk (RMT bound) deviates significantly from RMT observations and contains important information about the system. The information content of each eigenvector of the correlation matrix is quantified by introducing an entropic estimate, which shows that for the β -lactamase family the smallest eigenvectors (low eigenmodes) are highly localized as well as informative. These small eigenvectors when processed gives clusters involving positions that have well-defined biological and structural importance matching with experiments. The approach is crucial for the recognition of structural motifs as shown in β -lactamase (and other families) and selectively identifies the important positions for targets to deactivate (activate) the enzymatic actions.
ROMANIAN FOLKLORE MOTIFS IN FASHION DESIGN
MOCENCO Alexandra
2014-05-01
Full Text Available The traditional Romanian costume such as the entire popular art (architecture, woodcarvins, pottery etc. was born and lasted in our country since ancient times. Closely related to human existence, the traditional costume reflected over the years as reflected nowadays, the mentality and artistic conception of the people. Today the traditional Romanian costume became an inspiration source to the wholesale fashion production industry designers, both Romanian and international. Although the contemporary designers are working in accordance with a vision, using a wide area of styles, methods and current technology, they usually return to traditional techniques and ethnic folklore motifs, which converts and resize them, integrating them in their contemporary space. Adrian Oianu is a very appreciated Romanian designer who launched two collections inspired by his native’s country traditional costumes: “Suflecata pan’ la brau” (“Turned up ‘til the belt” and “Bucurie” (“Joy”. Dorin Negrau had as inspiration for his “Lost” collection the traditional costume from the Bihor region. Yves Saint Laurent had a collection inspired by the Romanian traditional flax blouses called “La blouse roumaine”. The paper presents the traditional Romanian values throw fashion collections. The research activity will create innovative concepts to support the garment industry in order to develop their own brand and to bring the design activities in Romania at an international level. The research was conducted during the initial stage of a project, financed through national founds, consisting in a documentary study on ethnographic characteristics of the popular costume from different regions of the country.
Steinhagen, Folkert; Zillinger, Thomas; Peukert, Konrad; Fox, Mario; Thudium, Marcus; Barchet, Winfried; Putensen, Christian; Klinman, Dennis; Latz, Eicke; Bode, Christian
2018-04-01
Type I interferon (IFN) is a critical mediator of autoimmune diseases such as systemic lupus erythematosus (SLE) and Aicardi-Goutières Syndrome (AGS). The recently discovered cyclic-GMP-AMP (cGAMP) synthase (cGAS) induces the production of type I IFN in response to cytosolic DNA and is potentially linked to SLE and AGS. Suppressive oligodeoxynucleotides (ODN) containing repetitive TTAGGG motifs present in mammalian telomeres have proven useful in the treatment of autoimmune diseases including SLE. In this study, we demonstrate that the suppressive ODN A151 effectively inhibits activation of cGAS in response to cytosolic DNA, thereby inhibiting type I IFN production by human monocytes. In addition, A151 abrogated cGAS activation in response to endogenous accumulation of DNA using TREX1-deficient monocytes. We demonstrate that A151 prevents cGAS activation in a manner that is competitive with DNA. This suppressive activity of A151 was dependent on both telomeric sequence and phosphorothioate backbone. To our knowledge this report presents the first cGAS inhibitor capable of blocking self-DNA. Collectively, these findings might lead to the development of new therapeutics against IFN-driven pathologies due to cGAS activation. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Managing Controversies in the Fuzzy Front End
Christiansen, John K.; Gasparin, Marta
2016-01-01
This research investigates the controversies that emerge in the fuzzy front end (FFE) and how they are closed so the innovation process can move on. The fuzzy front has been characterized in the literature as a very critical phase, but controversies in the FFE have not been studied before....... The analysis investigates the microprocesses around the controversies that emerge during the fuzzy front end of four products. Five different types of controversies are identified: profit, production, design, brand and customers/market. Each controversy represents a threat, but also an opportunity to search...
Fuzzy stability and synchronization of hyperchaos systems
Wang Junwei; Xiong Xiaohua; Zhao Meichun; Zhang Yanbin
2008-01-01
This paper studies stability and synchronization of hyperchaos systems via a fuzzy-model-based control design methodology. First, we utilize a Takagi-Sugeno fuzzy model to represent a hyperchaos system. Second, we design fuzzy-model-based controllers for stability and synchronization of the system, based on so-called 'parallel distributed compensation (PDC)'. Third, we reduce a question of stabilizing and synchronizing hyperchaos systems to linear matrix inequalities (LMI) so that convex programming techniques can solve these LMIs efficiently. Finally, the generalized Lorenz hyperchaos system is employed to illustrate the effectiveness of our designing controller
Using fuzzy arithmetic in containment event trees
Rivera, S.S.; Baron, Jorge H.
2000-01-01
The use of fuzzy arithmetic is proposed for the evaluation of containment event trees. Concepts such as improbable, very improbable, and so on, which are subjective by nature, are represented by fuzzy numbers. The quantitative evaluation of containment event trees is based on the extension principle, by which operations on real numbers are extended to operations on fuzzy numbers. Expert knowledge is considered as state of the base variable with a normal distribution, which is considered to represent the membership function. Finally, this paper presents results of an example calculation of a containment event tree for the CAREM-25 nuclear power plant, presently under detailed design stage at Argentina. (author)
Relative aggregation operator in database fuzzy querying
Luminita DUMITRIU
2005-12-01
Full Text Available Fuzzy selection criteria querying relational databases include vague terms; they usually refer linguistic values form the attribute linguistic domains, defined as fuzzy sets. Generally, when a vague query is processed, the definitions of vague terms must already exist in a knowledge base. But there are also cases when vague terms must be dynamically defined, when a particular operation is used to aggregate simple criteria in a complex selection. The paper presents a new aggregation operator and the corresponding algorithm to evaluate the fuzzy query.
Fuzzy image processing and applications with Matlab
Chaira, Tamalika
2009-01-01
In contrast to classical image analysis methods that employ ""crisp"" mathematics, fuzzy set techniques provide an elegant foundation and a set of rich methodologies for diverse image-processing tasks. However, a solid understanding of fuzzy processing requires a firm grasp of essential principles and background knowledge.Fuzzy Image Processing and Applications with MATLAB® presents the integral science and essential mathematics behind this exciting and dynamic branch of image processing, which is becoming increasingly important to applications in areas such as remote sensing, medical imaging,
Nomme, Julian; Renodon-Corniè re, Axelle; Asanomi, Yuya; Sakaguchi, Kazuyasu; Stasiak, Alicja Z; Stasiak, Andrzej; Norden, Bengt; Tran, Vinh; Takahashi, Masayuki
2010-01-01
We have previously shown that a 28-amino acid peptide derived from the BRC4 motif of BRCA2 tumor suppressor inhibits selectively human RAD51 recombinase (HsRad51). With the aim of designing better inhibitors for cancer treatment, we combined an in silico docking approach with in vitro biochemical testing to construct a highly efficient chimera peptide from eight existing human BRC motifs. We built a molecular model of all BRC motifs complexed with HsRad51 based on the crystal structure of the BRC4 motif-HsRad51 complex, computed the interaction energy of each residue in each BRC motif, and selected the best amino acid residue at each binding position. This analysis enabled us to propose four amino acid substitutions in the BRC4 motif. Three of these increased the inhibitory effect in vitro, and this effect was found to be additive. We thus obtained a peptide that is about 10 times more efficient in inhibiting HsRad51-ssDNA complex formation than the original peptide.
Nomme, Julian
2010-08-01
We have previously shown that a 28-amino acid peptide derived from the BRC4 motif of BRCA2 tumor suppressor inhibits selectively human RAD51 recombinase (HsRad51). With the aim of designing better inhibitors for cancer treatment, we combined an in silico docking approach with in vitro biochemical testing to construct a highly efficient chimera peptide from eight existing human BRC motifs. We built a molecular model of all BRC motifs complexed with HsRad51 based on the crystal structure of the BRC4 motif-HsRad51 complex, computed the interaction energy of each residue in each BRC motif, and selected the best amino acid residue at each binding position. This analysis enabled us to propose four amino acid substitutions in the BRC4 motif. Three of these increased the inhibitory effect in vitro, and this effect was found to be additive. We thus obtained a peptide that is about 10 times more efficient in inhibiting HsRad51-ssDNA complex formation than the original peptide.
ps-ro Fuzzy Open(Closed Functions and ps-ro Fuzzy Semi-Homeomorphism
Pankaj Chettri
2015-11-01
Full Text Available The aim of this paper is to introduce and characterize some new class of functions in a fuzzy topological space termed as ps-ro fuzzy open(closed functions, ps-ro fuzzy pre semiopen functions and ps-ro fuzzy semi-homeomorphism. The interrelation among these concepts and also their relations with the parallel existing concepts are established. It is also shown with the help of examples that these newly introduced concepts are independent of the well known existing allied concepts.
Fajar Ibnu Tufeil
2009-06-01
Full Text Available Model fuzzy memiliki kemampuan untuk menjelaskan secara linguistik suatu sistem yang terlalu kompleks. Aturan-aturan dalam model fuzzy pada umumnya dibangun berdasarkan keahlian manusia dan pengetahuan heuristik dari sistem yang dimodelkan. Teknik ini selanjutnya dikembangkan menjadi teknik yang dapat mengidentifikasi aturan-aturan dari suatu basis data yang telah dikelompokkan berdasarkan persamaan strukturnya. Dalam hal ini metode pengelompokan fuzzy berfungsi untuk mencari kelompok-kelompok data. Informasi yang dihasilkan dari metode pengelompokan ini, yaitu informasi tentang pusat kelompok, digunakan untuk membentuk aturan-aturan dalam sistem penalaran fuzzy. Dalam skripsi ini dibahas mengenai penerapan fuzzy infereance system dengan metode pengelompokan fuzzy subtractive clustering, yaitu untuk membentuk sistem penalaran fuzzy dengan menggunakan model fuzzy Takagi-Sugeno orde satu. Selanjutnya, metode pengelompokan fuzzy subtractive clustering diterapkan dalam memodelkan masalah dibidang pemasaran, yaitu untuk memprediksi permintaan pasar terhadap suatu produk susu. Aplikasi ini dibangun menggunakan Borland Delphi 6.0. Dari hasil pengujian diperoleh tingkat error prediksi terkecil yaitu dengan Error Average 0.08%.
Enric Trillas a passion for fuzzy sets : a collection of recent works on fuzzy logic
Verdegay, Jose; Esteva, Francesc
2015-01-01
This book presents a comprehensive collection of the latest and most significant research advances and applications in the field of fuzzy logic. It covers fuzzy structures, rules, operations and mathematical formalisms, as well as important applications of fuzzy logic in a number of fields, like decision-making, environmental prediction and prevention, communication, controls and many others. Dedicated to Enric Trillas in recognition of his pioneering research in the field, the book also includes a foreword by Lotfi A. Zadeh and an outlook on the future of fuzzy logic.
Shah, Mazlina Muzafar; Wahab, Abdul Fatah
2017-08-01
Epilepsy disease occurs because of there is a temporary electrical disturbance in a group of brain cells (nurons). The recording of electrical signals come from the human brain which can be collected from the scalp of the head is called Electroencephalography (EEG). EEG then considered in digital format and in fuzzy form makes it a fuzzy digital space data form. The purpose of research is to identify the area (curve and surface) in fuzzy digital space affected by inside epilepsy seizure in epileptic patient's brain. The main focus for this research is to generalize fuzzy topological digital space, definition and basic operation also the properties by using digital fuzzy set and the operations. By using fuzzy digital space, the theory of digital fuzzy spline can be introduced to replace grid data that has been use previously to get better result. As a result, the flat of EEG can be fuzzy topological digital space and this type of data can be use to interpolate the digital fuzzy spline.
Construction of Fuzzy Sets and Applying Aggregation Operators for Fuzzy Queries
Hudec, Miroslav; Sudzina, Frantisek
Flexible query conditions could use linguistic terms described by fuzzy sets. The question is how to properly construct fuzzy sets for each linguistic term and apply an adequate aggregation function. For construction of fuzzy sets, the lowest value, the highest value of attribute...... and the distribution of data inside its domain are used. The logarithmic transformation of domains appears to be suitable. This way leads to a balanced distribution of tuples over fuzzy sets. In addition, users’ opinions about linguistic terms as well as current content in database are merged. The second investigated...
Some fixed point theorems in fuzzy reflexive Banach spaces
Sadeqi, I.; Solaty kia, F.
2009-01-01
In this paper, we first show that there are some gaps in the fixed point theorems for fuzzy non-expansive mappings which are proved by Bag and Samanta, in [Bag T, Samanta SK. Fixed point theorems on fuzzy normed linear spaces. Inf Sci 2006;176:2910-31; Bag T, Samanta SK. Some fixed point theorems in fuzzy normed linear spaces. Inform Sci 2007;177(3):3271-89]. By introducing the notion of fuzzy and α- fuzzy reflexive Banach spaces, we obtain some results which help us to establish the correct version of fuzzy fixed point theorems. Second, by applying Theorem 3.3 of Sadeqi and Solati kia [Sadeqi I, Solati kia F. Fuzzy normed linear space and it's topological structure. Chaos, Solitons and Fractals, in press] which says that any fuzzy normed linear space is also a topological vector space, we show that all topological version of fixed point theorems do hold in fuzzy normed linear spaces.
Approximate Solution of LR Fuzzy Sylvester Matrix Equations
Xiaobin Guo
2013-01-01
Full Text Available The fuzzy Sylvester matrix equation AX~+X~B=C~ in which A,B are m×m and n×n crisp matrices, respectively, and C~ is an m×n LR fuzzy numbers matrix is investigated. Based on the Kronecker product of matrices, we convert the fuzzy Sylvester matrix equation into an LR fuzzy linear system. Then we extend the fuzzy linear system into two systems of linear equations according to the arithmetic operations of LR fuzzy numbers. The fuzzy approximate solution of the original fuzzy matrix equation is obtained by solving the crisp linear systems. The existence condition of the LR fuzzy solution is also discussed. Some examples are given to illustrate the proposed method.
Review article: The mountain motif in the plot of Matthew
Gert J. Volschenk
2010-09-01
Full Text Available This article reviewed T.L. Donaldson’s book, Jesus on the mountain: A study in Matthean theology, published in 1985 by JSOT Press, Sheffield, and focused on the mountain motif in the structure and plot of the Gospel of Matthew, in addition to the work of Donaldson on the mountain motif as a literary motif and as theological symbol. The mountain is a primary theological setting for Jesus’ ministry and thus is an important setting, serving as one of the literary devices by which Matthew structured and progressed his narrative. The Zion theological and eschatological significance and Second Temple Judaism serve as the historical and theological background for the mountain motif. The last mountain setting (Mt 28:16–20 is the culmination of the three theological themes in the plot of Matthew, namely Christology, ecclesiology and salvation history.
Methods and statistics for combining motif match scores.
Bailey, T L; Gribskov, M
1998-01-01
Position-specific scoring matrices are useful for representing and searching for protein sequence motifs. A sequence family can often be described by a group of one or more motifs, and an effective search must combine the scores for matching a sequence to each of the motifs in the group. We describe three methods for combining match scores and estimating the statistical significance of the combined scores and evaluate the search quality (classification accuracy) and the accuracy of the estimate of statistical significance of each. The three methods are: 1) sum of scores, 2) sum of reduced variates, 3) product of score p-values. We show that method 3) is superior to the other two methods in both regards, and that combining motif scores indeed gives better search accuracy. The MAST sequence homology search algorithm utilizing the product of p-values scoring method is available for interactive use and downloading at URL http:/(/)www.sdsc.edu/MEME.
DNA polymerase preference determines PCR priming efficiency.
Pan, Wenjing; Byrne-Steele, Miranda; Wang, Chunlin; Lu, Stanley; Clemmons, Scott; Zahorchak, Robert J; Han, Jian
2014-01-30
Polymerase chain reaction (PCR) is one of the most important developments in modern biotechnology. However, PCR is known to introduce biases, especially during multiplex reactions. Recent studies have implicated the DNA polymerase as the primary source of bias, particularly initiation of polymerization on the template strand. In our study, amplification from a synthetic library containing a 12 nucleotide random portion was used to provide an in-depth characterization of DNA polymerase priming bias. The synthetic library was amplified with three commercially available DNA polymerases using an anchored primer with a random 3' hexamer end. After normalization, the next generation sequencing (NGS) results of the amplified libraries were directly compared to the unamplified synthetic library. Here, high throughput sequencing was used to systematically demonstrate and characterize DNA polymerase priming bias. We demonstrate that certain sequence motifs are preferred over others as primers where the six nucleotide sequences at the 3' end of the primer, as well as the sequences four base pairs downstream of the priming site, may influence priming efficiencies. DNA polymerases in the same family from two different commercial vendors prefer similar motifs, while another commercially available enzyme from a different DNA polymerase family prefers different motifs. Furthermore, the preferred priming motifs are GC-rich. The DNA polymerase preference for certain sequence motifs was verified by amplification from single-primer templates. We incorporated the observed DNA polymerase preference into a primer-design program that guides the placement of the primer to an optimal location on the template. DNA polymerase priming bias was characterized using a synthetic library amplification system and NGS. The characterization of DNA polymerase priming bias was then utilized to guide the primer-design process and demonstrate varying amplification efficiencies among three commercially
Biophysical properties of regions flanking the bHLH-Zip motif in the p22 Max protein
Pursglove, Sharon E.; Fladvad, Malin; Bellanda, Massimo; Moshref, Ahmad; Henriksson, Marie; Carey, Jannette; Sunnerhagen, Maria
2004-01-01
The Max protein is the central dimerization partner in the Myc-Max-Mad network of transcriptional regulators, and a founding structural member of the family of basic-helix-loop-helix (bHLH)-leucine zipper (Zip) proteins. Biologically important regions flanking its bHLH-Zip motif have been disordered or absent in crystal structures. The present study shows that these regions are resistant to proteolysis in both the presence and absence of DNA, and that Max dimers containing both flanking regions have significantly higher helix content as measured by circular dichroism than that predicted from the crystal structures. Nuclear magnetic resonance measurements in the absence of DNA also support the inferred structural order. Deletion of both flanking regions is required to achieve maximal DNA affinity as measured by EMSA. Thus, the previously observed functionalities of these Max regions in DNA binding, phosphorylation, and apoptosis are suggested to be linked to structural properties
The primary structure of L37--a rat ribosomal protein with a zinc finger-like motif.
Chan, Y L; Paz, V; Olvera, J; Wool, I G
1993-04-30
The amino acid sequence of the rat 60S ribosomal subunit protein L37 was deduced from the sequence of nucleotides in a recombinant cDNA. Ribosomal protein L37 has 96 amino acids, the NH2-terminal methionine is removed after translation of the mRNA, and has a molecular weight of 10,939. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 13 or 14 copies of the L37 gene. The mRNA for the protein is about 500 nucleotides in length. Rat L37 is related to Saccharomyces cerevisiae ribosomal protein YL35 and to Caenorhabditis elegans L37. We have identified in the data base a DNA sequence that encodes the chicken homolog of rat L37.
YMDD motif mutations in chronic hepatitis B antiviral treatment naïve patients: a multi-center study
You-Wen Tan
Full Text Available OBJECTIVE: This study aimed to determine the natural prevalence of variants of tyrosine-methionine-aspartic acid-aspartic acid (YMDD motif in patients with chronic hepatitis B (CHB, and to explore its relation with demographic and clinical features, hepatitis B virus (HBV genotypes, and HBV DNA levels. METHODS: A total of 1,042 antiviral treatment naïve CHB patients (including with lamivudine [LAM] in the past year were recruited from outpatient and inpatient departments of six centers from December 2008 to June 2010. YMDD variants were analyzed using the HBV drug resistance line probe assay (Inno-Lipa HBV-DR. HBV genotypes were detected with polymerase chain reaction (PCR microcosmic nucleic acid cross-ELISA, and HBV deoxyribonucleic acid (DNA was quantitated with real-time PCR. All serum samples underwent tests for HBV, HCV, and HDV with ELISA. RESULTS: YMDD variants were detected in 23.3% (243/1042 of CHB patients. YMDD mutation was accompanied by L180M mutation in 154 (76.9% patients. Both wild-type HBV and YMDD variant HBV were present in 231 of 243 patients. Interestingly, 12 patients had only YIDD and/or YVDD variants without wild YMDD motif. In addition, 27.2% (98/359 of HbeAg-positive patients had YMDD mutations, which was higher than that in HbeAg-negative patients (21.2%, 145/683. The incidence of YMDD varied among patients with different HBV genotypes, but the difference was not significant. Moreover, the incidence of YMDD in patients with high HBV DNA level was significantly higher than that in those with low HBV DNA level. CONCLUSION: Mutation of YMDD motif was detectable at a high rate in CHB patients in this study. The incidence of YMDD may be correlated with HBeAg and HBV DNA level.
BEAM web server: a tool for structural RNA motif discovery.
Pietrosanto, Marco; Adinolfi, Marta; Casula, Riccardo; Ausiello, Gabriele; Ferrè, Fabrizio; Helmer-Citterich, Manuela
2018-03-15
RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies. The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance. BEAM is extremely fast thanks to the BEAR encoding that transforms each RNA secondary structure in a string of characters. BEAM also exploits the evolutionary knowledge contained in a substitution matrix of secondary structure elements, extracted from the RFAM database of families of homologous RNAs. The BEAM web server has been designed to streamline data pre-processing by automatically handling folding and encoding of RNA sequences, giving users a choice for the preferred folding program. The server provides an intuitive and informative results page with the list of secondary structure motifs identified, the logo of each motif, its significance, graphic representation and information about its position in the RNA molecules sharing it. The web server is freely available at http://beam.uniroma2.it/ and it is implemented in NodeJS and Python with all major browsers supported. marco.pietrosanto@uniroma2.it. Supplementary data are available at Bioinformatics online.
Characterizing Motif Dynamics of Electric Brain Activity Using Symbolic Analysis
Massimiliano Zanin
2014-10-01
Full Text Available Motifs are small recurring circuits of interactions which constitute the backbone of networked systems. Characterizing motif dynamics is therefore key to understanding the functioning of such systems. Here we propose a method to define and quantify the temporal variability and time scales of electroencephalogram (EEG motifs of resting brain activity. Given a triplet of EEG sensors, links between them are calculated by means of linear correlation; each pattern of links (i.e., each motif is then associated to a symbol, and its appearance frequency is analyzed by means of Shannon entropy. Our results show that each motif becomes observable with different coupling thresholds and evolves at its own time scale, with fronto-temporal sensors emerging at high thresholds and changing at fast time scales, and parietal ones at low thresholds and changing at slower rates. Finally, while motif dynamics differed across individuals, for each subject, it showed robustness across experimental conditions, indicating that it could represent an individual dynamical signature.
An experimental test of a fundamental food web motif.
Rip, Jason M K; McCann, Kevin S; Lynn, Denis H; Fawcett, Sonia
2010-06-07
Large-scale changes to the world's ecosystem are resulting in the deterioration of biostructure-the complex web of species interactions that make up ecological communities. A difficult, yet crucial task is to identify food web structures, or food web motifs, that are the building blocks of this baroque network of interactions. Once identified, these food web motifs can then be examined through experiments and theory to provide mechanistic explanations for how structure governs ecosystem stability. Here, we synthesize recent ecological research to show that generalist consumers coupling resources with different interaction strengths, is one such motif. This motif amazingly occurs across an enormous range of spatial scales, and so acts to distribute coupled weak and strong interactions throughout food webs. We then perform an experiment that illustrates the importance of this motif to ecological stability. We find that weak interactions coupled to strong interactions by generalist consumers dampen strong interaction strengths and increase community stability. This study takes a critical step by isolating a common food web motif and through clear, experimental manipulation, identifies the fundamental stabilizing consequences of this structure for ecological communities.
Luo, Yi; Zhang, Tao; Li, Xiao-song
2016-05-01
To explore the application of fuzzy time series model based on fuzzy c-means clustering in forecasting monthly incidence of Hepatitis E in mainland China. Apredictive model (fuzzy time series method based on fuzzy c-means clustering) was developed using Hepatitis E incidence data in mainland China between January 2004 and July 2014. The incidence datafrom August 2014 to November 2014 were used to test the fitness of the predictive model. The forecasting results were compared with those resulted from traditional fuzzy time series models. The fuzzy time series model based on fuzzy c-means clustering had 0.001 1 mean squared error (MSE) of fitting and 6.977 5 x 10⁻⁴ MSE of forecasting, compared with 0.0017 and 0.0014 from the traditional forecasting model. The results indicate that the fuzzy time series model based on fuzzy c-means clustering has a better performance in forecasting incidence of Hepatitis E.
IMPLEMENTATION OF FUZZY LOGIC BASED TEMPERATURE ...
transfer function is derived based on process reaction curve obtained from a heat exchanger pilot plant ... The results show that the control performance for a Fuzzy controller is quite similar to ..... Process. Control Instrumentation Technology.
Fuzzy logic for structural system control
Herbert Martins Gomes
Full Text Available This paper provides some information and numerical tests that aims to investigate the use of a Fuzzy Controller applied to control systems. Some advantages are reported regarding the use of this controller, such as the characteristic ease of implementation due to its semantic feature in the statement of the control rules. On the other hand, it is also hypothesized that these systems have a lower performance loss when the system to be controlled is nonlinear or has time varying parameters. Numerical tests are performed using modal LQR optimal control and Fuzzy control of non-collocated systems with full state feedback in a two-dimensional structure. The paper proposes a way of designing a controller that may be a supervisory Fuzzy controller for a traditional controller or even a fuzzy controller independent from the traditional control, consisting on individual mode controllers. Some comments are drawn regarding the performance of these proposals in a number of arrangements.
Fuzzy logic applications to control engineering
Langari, Reza
1993-12-01
This paper presents the results of a project presently under way at Texas A&M which focuses on the use of fuzzy logic in integrated control of manufacturing systems. The specific problems investigated here include diagnosis of critical tool wear in machining of metals via a neuro-fuzzy algorithm, as well as compensation of friction in mechanical positioning systems via an adaptive fuzzy logic algorithm. The results indicate that fuzzy logic in conjunction with conventional algorithmic based approaches or neural nets can prove useful in dealing with the intricacies of control/monitoring of manufacturing systems and can potentially play an active role in multi-modal integrated control systems of the future.
Reliability and safety analyses under fuzziness
Onisawa, T.; Kacprzyk, J.
1995-01-01
Fuzzy theory, for example possibility theory, is compatible with probability theory. What is shown so far is that probability theory needs not be replaced by fuzzy theory, but rather that the former works much better in applications if it is combined with the latter. In fact, it is said that there are two essential uncertainties in the field of reliability and safety analyses: One is a probabilistic uncertainty which is more relevant for mechanical systems and the natural environment, and the other is fuzziness (imprecision) caused by the existence of human beings in systems. The classical probability theory alone is therefore not sufficient to deal with uncertainties in humanistic system. In such a context this collection of works will put a milestone in the arguments of probability theory and fuzzy theory. This volume covers fault analysis, life time analysis, reliability, quality control, safety analysis and risk analysis. (orig./DG). 106 figs
A COMPARISON OF TWO FUZZY CLUSTERING TECHNIQUES
Samarjit Das
2013-10-01
Full Text Available - In fuzzy clustering, unlike hard clustering, depending on the membership value, a single object may belong exactly to one cluster or partially to more than one cluster. Out of a number of fuzzy clustering techniques Bezdek’s Fuzzy C-Means and GustafsonKessel clustering techniques are well known where Euclidian distance and Mahalanobis distance are used respectively as a measure of similarity. We have applied these two fuzzy clustering techniques on a dataset of individual differences consisting of fifty feature vectors of dimension (feature three. Based on some validity measures we have tried to see the performances of these two clustering techniques from three different aspects- first, by initializing the membership values of the feature vectors considering the values of the three features separately one at a time, secondly, by changing the number of the predefined clusters and thirdly, by changing the size of the dataset.
Fuzzy controllers in nuclear material accounting
Zardecki, A.
1994-01-01
Fuzzy controllers are applied to predicting and modeling a time series, with particular emphasis on anomaly detection in nuclear material inventory differences. As compared to neural networks, the fuzzy controllers can operate in real time; their learning process does not require many iterations to converge. For this reason fuzzy controllers are potentially useful in time series forecasting, where the authors want to detect and identify trends in real time. They describe an object-oriented implementation of the algorithm advanced by Wang and Mendel. Numerical results are presented both for inventory data and time series corresponding to chaotic situations, such as encountered in the context of strange attractors. In the latter case, the effects of noise on the predictive power of the fuzzy controller are explored
reactor power control using fuzzy logic
Ahmed, A.E.E.
2001-01-01
power stabilization is a critical issue in nuclear reactors. convention pd- controller is currently used in egypt second testing research reactor (ETRR-2). two fuzzy controllers are proposed to control the reactor power of ETRR-2 reactor. the design of the first one is based on a set of linguistic rules that were adopted from the human operators experience. after off-line fuzzy computations, the controller is a lookup table, and thus, real time controller is achieved. comparing this f lc response with the pd-controller response, which already exists in the system, through studying the expected transients during the normal operation of ETRR-2 reactor, the simulation results show that, fl s has the better response, the second controller is adaptive fuzzy controller, which is proposed to deal with system non-linearity . The simulation results show that the proposed adaptive fuzzy controller gives a better integral square error (i se) index than the existing conventional od controller
Supplier selection problem: A fuzzy multicriteria approach
kirstam
simultaneously: maximising the total value of purchases, minimising ... Keywords: Supplier selection, multi-criteria decision-making, fuzzy logic, satisfaction ... includes both qualitative and quantitative factors, and it is necessary to make a.
Fuzzy logic guided inverse treatment planning
Yan Hui; Yin Fangfang; Guan Huaiqun; Kim, Jae Ho
2003-01-01
A fuzzy logic technique was applied to optimize the weighting factors in the objective function of an inverse treatment planning system for intensity-modulated radiation therapy (IMRT). Based on this technique, the optimization of weighting factors is guided by the fuzzy rules while the intensity spectrum is optimized by a fast-monotonic-descent method. The resultant fuzzy logic guided inverse planning system is capable of finding the optimal combination of weighting factors for different anatomical structures involved in treatment planning. This system was tested using one simulated (but clinically relevant) case and one clinical case. The results indicate that the optimal balance between the target dose and the critical organ dose is achieved by a refined combination of weighting factors. With the help of fuzzy inference, the efficiency and effectiveness of inverse planning for IMRT are substantially improved
Fuzzy linear programming approach for solving transportation ...
ALI EBRAHIMNEJAD
Department of Mathematics, Qaemshahr Branch, Islamic Azad University, Qaemshahr, Iran e-mail: ..... est grade of membership at x are μ ˜AL (x) and μ ˜AU (x), respectively. ..... trapezoidal fuzzy numbers transportation problem (12) are.
Fuzzy logic applications in engineering science
Harris, J
2006-01-01
Fuzzy logic is a relatively new concept in science applications. Hitherto, fuzzy logic has been a conceptual process applied in the field of risk management. Its potential applicability is much wider than that, however, and its particular suitability for expanding our understanding of processes and information in science and engineering in our post-modern world is only just beginning to be appreciated. Written as a companion text to the author's earlier volume "An Introduction to Fuzzy Logic Applications", the book is aimed at professional engineers and students and those with an interest in exploring the potential of fuzzy logic as an information processing kit with a wide variety of practical applications in the field of engineering science and develops themes and topics introduced in the author's earlier text.
On a Fuzzy Algebra for Querying Graph Databases
Pivert , Olivier; Thion , Virginie; Jaudoin , Hélène; Smits , Grégory
2014-01-01
International audience; This paper proposes a notion of fuzzy graph database and describes a fuzzy query algebra that makes it possible to handle such database, which may be fuzzy or not, in a flexible way. The algebra, based on fuzzy set theory and the concept of a fuzzy graph, is composed of a set of operators that can be used to express preference queries on fuzzy graph databases. The preferences concern i) the content of the vertices of the graph and ii) the structure of the graph. In a s...
Fuzzy set theory for cumulative trauma prediction
Fonseca, Daniel J.; Merritt, Thomas W.; Moynihan, Gary P.
2001-01-01
A widely used fuzzy reasoning algorithm was modified and implemented via an expert system to assess the potential risk of employee repetitive strain injury in the workplace. This fuzzy relational model, known as the Priority First Cover Algorithm (PFC), was adapted to describe the relationship between 12 cumulative trauma disorders (CTDs) of the upper extremity, and 29 identified risk factors. The algorithm, which finds a suboptimal subset from a group of variables based on the criterion of...
Smart Spectrometer for Distributed Fuzzy Control
Benoit, Eric; Foulloy, Laurent
2009-01-01
Document rédigé sous FrameMaker (pas sous Latex); International audience; If the main use of colour measurement is the metrology, it is now possible to find industrial control applications which uses this information. Using colour in process control leads to specific problems where human perception has to be replaced by colour sensors. This paper relies on the fuzzy representation of colours that can be taken into account by fuzzy controllers. If smart sensors already include intelligent func...
On new solutions of fuzzy differential equations
Chalco-Cano, Y.; Roman-Flores, H.
2008-01-01
We study fuzzy differential equations (FDE) using the concept of generalized H-differentiability. This concept is based in the enlargement of the class of differentiable fuzzy mappings and, for this, we consider the lateral Hukuhara derivatives. We will see that both derivatives are different and they lead us to different solutions from a FDE. Also, some illustrative examples are given and some comparisons with other methods for solving FDE are made