scholarly journals Inference of Granger-Causal Relations in Molecular Systems — a Case Study of the Functional Hierarchy Among Actin Regulators in Lamellipodia

2021 ◽  
Author(s):  
Jungsik Noh ◽  
Tadamoto Isogai ◽  
Joseph Chi ◽  
Kushal Bhatt ◽  
Gaudenz Danuser
Keyword(s):  
Causal Relations ◽  
Molecular Systems ◽  
Functional Hierarchy

scholarly journals Inference of Granger-causal relations in molecular systems — a case study of the functional hierarchy among actin regulators in lamellipodia

2021 ◽  
Author(s):  
Jungsik Noh ◽  
Tadamoto Isogai ◽  
Joseph Chi ◽  
Kushal Bhatt ◽  
Gaudenz Danuser
Keyword(s):  
Active Regions ◽  
Unperturbed System ◽  
Limited Information ◽  
Causal Relations ◽  
Molecular Systems ◽  
Regulatory Systems ◽  
Specificity And Sensitivity ◽  
The Individual ◽  
Rich Data

Many cell regulatory systems implicate significant level of nonlinearity and redundancy among its components. The actin regulatory network driving the formation of a lamellipodium is prototypical of such system, containing tens of actin nucleating and modulating molecules with strong functional overlap. Due to instantaneous compensation, the standard paradigm of perturbing individual components followed by phenotyping provides limited information on the roles the targeted component plays in the unperturbed system. Accordingly, despite the very rich data on lamellipoidial actin assembly, we have an incomplete understanding of the actual contributions the individual modulators make towards the lamellipodial dynamics. Here, we present a case study of the implementation of Granger-causal inference of the functional cause-effect relations among actin regulators, using the constitutive image fluctuations reporting regulator recruitment/activation as the input. Our analytical pipeline defines specific active regions of actin regulators within the lamellipodia and lamella and establishes actin-dependent and actin-independent causal relations of actin regulators with F-actin and edge motion. We demonstrate the specificity and sensitivity of the pipeline and suggest the existence of two discrete yet independently operating F-actin networks that drive edge motion.

scholarly journals Causal Relations of Upscaled Urban Aquaponics and the Food-Water-Energy Nexus—A Berlin Case Study

Water ◽  
2021 ◽  
Vol 13 (15) ◽  
pp. 2029
Author(s):  
Gösta F.M. Baganz ◽  
Manfred Schrenk ◽  
Oliver Körner ◽  
Daniela Baganz ◽  
Karel J. Keesman ◽  
...  
Keyword(s):  
Urban Areas ◽  
Causal Link ◽  
Supply Side ◽  
Demand Side ◽  
Annual Fish ◽  
Causal Relations ◽  
Water Energy Nexus ◽  
Facility Level ◽  
Predominant Effect

Aquaponics, the water-reusing production of fish and crops, is taken as an example to investigate the consequences of upscaling a nature-based solution in a circular city. We developed an upscaled-aquaponic scenario for the German metropolis of Berlin, analysed the impacts, and studied the system dynamics. To meet the annual fish, tomato, and lettuce demand of Berlin’s 3.77 million residents would require approximately 370 aquaponic facilities covering a total area of 224 hectares and the use of different combinations of fish and crops: catfish/tomato (56%), catfish/lettuce (13%), and tilapia/tomato (31%). As a predominant effect, in terms of water, aquaponic production would save about 2.0 million m3 of water compared to the baseline. On the supply-side, we identified significant causal link chains concerning the Food-Water-Energy nexus at the aquaponic facility level as well as causal relations of a production relocation to Berlin. On the demand-side, a ‘freshwater pescatarian diet’ is discussed. The new and comprehensive findings at different system levels require further investigations on this topic. Upscaled aquaponics can produce a relevant contribution to Berlin’s sustainability and to implement it, research is needed to find suitable sites for local aquaponics in Berlin, possibly inside buildings, on urban roofscape, or in peri-urban areas.

scholarly journals Framework for the Analysis of Simplified Texts Taking Discourse into Account: the Basque Causal Relations as Case Study

2017 ◽  
Author(s):  
Itziar Gonzalez-Dios ◽  
Arantza Diaz de Ilarraza ◽  
Mikel Iruskieta
Keyword(s):  
Causal Relations

Is wa a Polysemous Connective? A Case Study of the Qur'anic waw al-'atf

2020 ◽  
Vol 28 (2) ◽  
Author(s):  
Yehudit Dror ◽  
Kai Borrmann
Keyword(s):  
Target Language ◽  
Reading Process ◽  
Causal Relations ◽  
Cause And Effect

The ways in which parts of a compound statement are related to each other are often easy to understand but hard to explain. A case in point is the “waw of attachment” or al-waw al-'atifa, which associates nouns, verbs and clauses but provides no clues as to its exact interpretation. The particle wa is often interpreted in the target language as “but”, “even if” or “although”. Does this make wa polysemous, comprising related but different meanings? This article argues that wa is part of an incremental reading process that unfolds until the meaning of the text is fully recovered. It shows that the functions of the particle wa can be grouped under four headings: adversative relations where certain features of the items complement each other, additive relations where items are grouped together, consecutive relations indicating the passing of time, and causal relations indicating cause and effect.

scholarly journals A Look at the Spatial Confining Effect on the Molecular Electrostatic Potential (MEP)—A Case Study of the HF and BrCN Molecules

Molecules ◽  
2021 ◽  
Vol 26 (19) ◽  
pp. 5924
Author(s):  
Paweł Lipkowski ◽  
Justyna Kozłowska ◽  
Wojciech Bartkowiak
Keyword(s):  
Electrostatic Potential ◽  
Molecular Electrostatic Potential ◽  
Theoretical Study ◽  
Cylindrical Symmetry ◽  
Spatial Confinement ◽  
Molecular Systems ◽  
Confining Effect ◽  
Repulsive Potentials ◽  
Preliminary Study

In this theoretical study, we report on the molecular electrostatic potential (MEP) of titled molecules confined by repulsive potentials of cylindrical symmetry mimicking a topology. Our calculations show that the spatial restriction significantly changes the picture of the MEP of molecules in a quantitative and qualitative sense. In particular, the drastic changes in the MEP as a function of the strength of spatial confinement are observed for the BrCN molecule. This preliminary study is the first step in the investigation of the behavior of the MEP of molecular systems under orbital compression.

How can fluorine directly and indirectly affect the hydrogen bonding in molecular systems? – A case study for monofluoroanilines

2021 ◽  
Vol 252 ◽  
pp. 119536
Author(s):  
Wojciech Pietruś ◽  
Rafał Kurczab ◽  
Rafał Kafel ◽  
Ewa Machalska ◽  
Justyna Kalinowska-Tłuścik ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Molecular Systems

scholarly journals EXPLOITATION OF MCDA TO LEARN THE RADIAL BASE NEURAL NETWORK (RBFNN) AIM PHYSICAL AND SOCIAL VULNERABILITY ANALYSIS VERSUS THE EARTHQUAKE (CASE STUDY: SANANDAJ CITY, IRAN)

2019 ◽  
Vol XLII-4/W18 ◽  
pp. 1071-1078 ◽  
Author(s):  
P. Yariyan ◽  
M. R. Karami ◽  
R. Ali Abbaspour
Keyword(s):  
Neural Network ◽  
Social Factors ◽  
Social Vulnerability ◽  
Training Data ◽  
Validation Data ◽  
Structural Problems ◽  
Functional Neural Network ◽  
Functional Hierarchy ◽  
The City

Abstract. Despite years of research on natural hazards and efforts to reduce physical and psychological damage, earthquake as a natural disaster is catastrophic. Though, human is the main axis in dealing with crisis and vulnerability, and since the space of cities encompasses largest population spectrum, managing this space is considered as an essential issue. Accordingly, the vulnerability of the City of Sanandaj was defined by environmental, physical and social criteria. In this regard, with the aim of modeling, and assessing the risk and vulnerability, the MCDA-ANN hybrid model was introduced as a new method for teaching of learning models. In order to determine the final value of each of the criteria, AHP analysis was performed as one of the MCDA methods to solve complex and non-structural problems by creating a functional hierarchy, and after that, a training data base for learning ANN was created randomly based on the AHP classification map. Then, for modeling, the radial base functional neural network (RBFNN) was used as one of the techniques of artificial neural networks. After the modeling, 30% of the points were selected as validation data to determine the accuracy of the model. After the implementation of RBFNN model, the area of AUC curve resulted is 0.922, which indicates the high accuracy of the model in assessing the risk of an earthquake. The results show high vulnerability in urban areas1 and 2 and in downtown Sanandaj that in these zones the physical and social factors dramatically affect the vulnerability of these areas.

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