scholarly journals Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model

2015 ◽  
Vol 22 (2) ◽  
pp. 85-110 ◽  
Author(s):  
Wei Lu ◽  
Takeyuki Tamura ◽  
Jiangning Song ◽  
Tatsuya Akutsu
2012 ◽  
pp. 774-791
Author(s):  
Takeyuki Tamura ◽  
Kazuhiro Takemoto ◽  
Tatsuya Akutsu

In this paper, the authors consider the problem of, given a metabolic network, a set of source compounds and a set of target compounds, finding a minimum size reaction cut, where a Boolean model is used as a model of metabolic networks. The problem has potential applications to measurement of structural robustness of metabolic networks and detection of drug targets. They develop an integer programming-based method for this optimization problem. In order to cope with cycles and reversible reactions, they further develop a novel integer programming (IP) formalization method using a feedback vertex set (FVS). When applied to an E. coli metabolic network consisting of Glycolysis/Glyconeogenesis, Citrate cycle and Pentose phosphate pathway obtained from KEGG database, the FVS-based method can find an optimal set of reactions to be inactivated much faster than a naive IP-based method and several times faster than a flux balance-based method. The authors also confirm that our proposed method works even for large networks and discuss the biological meaning of our results.


PLoS ONE ◽  
2014 ◽  
Vol 9 (3) ◽  
pp. e92637 ◽  
Author(s):  
Wei Lu ◽  
Takeyuki Tamura ◽  
Jiangning Song ◽  
Tatsuya Akutsu

Author(s):  
Takeyuki Tamura ◽  
Kazuhiro Takemoto ◽  
Tatsuya Akutsu

In this paper, the authors consider the problem of, given a metabolic network, a set of source compounds and a set of target compounds, finding a minimum size reaction cut, where a Boolean model is used as a model of metabolic networks. The problem has potential applications to measurement of structural robustness of metabolic networks and detection of drug targets. They develop an integer programming-based method for this optimization problem. In order to cope with cycles and reversible reactions, they further develop a novel integer programming (IP) formalization method using a feedback vertex set (FVS). When applied to an E. coli metabolic network consisting of Glycolysis/Glyconeogenesis, Citrate cycle and Pentose phosphate pathway obtained from KEGG database, the FVS-based method can find an optimal set of reactions to be inactivated much faster than a naive IP-based method and several times faster than a flux balance-based method. The authors also confirm that our proposed method works even for large networks and discuss the biological meaning of our results.


Author(s):  
Takeyuki Tamura ◽  
Kazuhiro Takemoto ◽  
Tatsuya Akutsu

In this paper, the authors consider the problem of, given a metabolic network, a set of source compounds and a set of target compounds, finding a minimum size reaction cut, where a Boolean model is used as a model of metabolic networks. The problem has potential applications to measurement of structural robustness of metabolic networks and detection of drug targets. They develop an integer programming-based method for this optimization problem. In order to cope with cycles and reversible reactions, they further develop a novel integer programming (IP) formalization method using a feedback vertex set (FVS). When applied to an E. coli metabolic network consisting of Glycolysis/Glyconeogenesis, Citrate cycle and Pentose phosphate pathway obtained from KEGG database, the FVS-based method can find an optimal set of reactions to be inactivated much faster than a naive IP-based method and several times faster than a flux balance-based method. The authors also confirm that our proposed method works even for large networks and discuss the biological meaning of our results.


Author(s):  
José G. Centeno

Abstract The steady increase in linguistic and cultural diversity in the country, including the number of bilingual speakers, has been predicted to continue. Minorities are expected to be the majority by 2042. Strokes, the third leading cause of death and the leading cause of long-term disability in the U.S., are quite prevalent in racial and ethnic minorities, so population estimates underscore the imperative need to develop valid clinical procedures to serve the predicted increase in linguistically and culturally diverse bilingual adults with aphasia in post-stroke rehabilitation. Bilingualism is a complex phenomenon that interconnects culture, cognition, and language; thus, as aphasia is a social phenomenon, treatment of bilingual aphasic persons would benefit from conceptual frameworks that exploit the culture-cognition-language interaction in ways that maximize both linguistic and communicative improvement leading to social re-adaptation. This paper discusses a multidisciplinary evidence-based approach to develop ecologically-valid treatment strategies for bilingual aphasic individuals. Content aims to spark practitioners' interest to explore conceptually broad intervention strategies beyond strictly linguistic domains that would facilitate linguistic gains, communicative interactions, and social functioning. This paper largely emphasizes Spanish-English individuals in the United States. Practitioners, however, are advised to adapt the proposed principles to the unique backgrounds of other bilingual aphasic clients.


Author(s):  
Elena Dukhovny ◽  
E. Betsy Kelly

According to the 2010 U.S. Census, over 20% of Americans speak a language other than English in the home, with Spanish, Chinese, and French being the languages most commonly spoken, aside from English. However, few augmentative and alternative communication (AAC) systems offer multilingual support for individuals with limited functional speech. There has been much discussion in the AAC community about best practices in AAC system design and intervention strategies, but limited resources exist to help us provide robust, flexible systems for users who speak languages other than English. We must provide services that take into consideration the unique needs of culturally and linguistically diverse users of AAC and help them reach their full communication potential. This article outlines basic guidelines for best practices in AAC design and selection, and presents practical applications of these best practices to multilingual/multicultural clients.


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