scholarly journals Artefacts in statistical analyses of network motifs: general framework and application to metabolic networks

2012 ◽  
Vol 9 (77) ◽  
pp. 3426-3435 ◽  
Author(s):  
Moritz Emanuel Beber ◽  
Christoph Fretter ◽  
Shubham Jain ◽  
Nikolaus Sonnenschein ◽  
Matthias Müller-Hannemann ◽  
...  
Keyword(s):  
General Framework ◽  
Metabolic Networks ◽  
Dynamic Behaviour ◽  
Null Model ◽  
Building Blocks ◽  
Emergent Properties ◽  
Network Motifs ◽  
Metabolic Reactions ◽  
Motif Signature

Few-node subgraphs are the smallest collective units in a network that can be investigated. They are beyond the scale of individual nodes but more local than, for example, communities. When statistically over- or under-represented, they are called network motifs. Network motifs have been interpreted as building blocks that shape the dynamic behaviour of networks. It is this promise of potentially explaining emergent properties of complex systems with relatively simple structures that led to an interest in network motifs in an ever-growing number of studies and across disciplines. Here, we discuss artefacts in the analysis of network motifs arising from discrepancies between the network under investigation and the pool of random graphs serving as a null model. Our aim was to provide a clear and accessible catalogue of such incongruities and their effect on the motif signature. As a case study, we explore the metabolic network of Escherichia coli and show that only by excluding ever more artefacts from the motif signature a strong and plausible correlation with the essentiality profile of metabolic reactions emerges.

scholarly journals The stubborn roots of metabolic cycles

2013 ◽  
Vol 10 (83) ◽  
pp. 20130087 ◽  
Author(s):  
Ed Reznik ◽  
Alex Watson ◽  
Osman Chaudhary
Keyword(s):  
Topological Structure ◽  
Metabolic Networks ◽  
Dynamic Behaviour ◽  
Sufficient Conditions ◽  
Rate Laws ◽  
Metabolite Concentrations ◽  
Metabolic Reactions ◽  
Classical Fields ◽  
The Stability ◽  
Genome Scale

Efforts to catalogue the structure of metabolic networks have generated highly detailed, genome-scale atlases of biochemical reactions in the cell. Unfortunately, these atlases fall short of capturing the kinetic details of metabolic reactions, instead offering only topological information from which to make predictions. As a result, studies frequently consider the extent to which the topological structure of a metabolic network determines its dynamic behaviour, irrespective of kinetic details. Here, we study a class of metabolic networks known as non-autocatalytic metabolic cycles, and analytically prove an open conjecture regarding the stability of their steady states. Importantly, our results are invariant to the choice of kinetic parameters, rate laws, equilibrium fluxes and metabolite concentrations. Unexpectedly, our proof exposes an elementary but apparently open problem of locating the roots of a sum of two polynomials S = P + Q , when the roots of the summand polynomials P and Q are known. We derive two new results named the Stubborn Roots Theorems, which provide sufficient conditions under which the roots of S remain qualitatively identical to the roots of P . Our study illustrates how complementary feedback, from classical fields such as dynamical systems to biology and vice versa, can expose fundamental and potentially overlooked questions.

Language, procedures, and the non-perceptual origin of natural number concepts

2016 ◽  
Author(s):  
David Barner
Keyword(s):  
General Framework ◽  
Ad Hoc ◽  
Building Blocks ◽  
Number Words ◽  
Linguistic Markers ◽  
Logical Foundations ◽  
Large Numbers ◽  
Perceptual Representations ◽  
Positive Integers ◽  
Perceptual Systems

Perceptual representations – e.g., of objects or approximate magnitudes –are often invoked as building blocks that children combine with linguisticsymbols when they acquire the positive integers. Systems of numericalperception are either assumed to contain the logical foundations ofarithmetic innately, or to supply the basis for their induction. Here Ipropose an alternative to this general framework, and argue that theintegers are not learned from perceptual systems, but instead arise toexplain perception as part of language acquisition. Drawing oncross-linguistic data and developmental data, I show that small numbers(1-4) and large numbers (~5+) arise both historically and in individualchildren via entirely distinct mechanisms, constituting independentlearning problems, neither of which begins with perceptual building blocks.Specifically, I propose that children begin by learning small numbers(i.e., *one, two, three*) using the same logical resources that supportother linguistic markers of number (e.g., singular, plural). Several yearslater, children discover the logic of counting by inferring the logicalrelations between larger number words from their roles in blind countingprocedures, and only incidentally associate number words with perception ofapproximate magnitudes, in an *ad hoc* and highly malleable fashion.Counting provides a form of explanation for perception but is not causallyderived from perceptual systems.

scholarly journals Attrition as a bottom-up pathway to subnational democratization

2021 ◽  
pp. 019251212110192
Author(s):  
Trix van Mierlo
Keyword(s):  
Civil Society ◽  
Field Research ◽  
Building Blocks ◽  
The Philippines ◽  
Causal Process ◽  
Bottom Up ◽  
System A ◽  
Extensive Field ◽  
Democratic System

Oftentimes, democracy is not spread out evenly over the territory of a country. Instead, pockets of authoritarianism can persist within a democratic system. A growing body of literature questions how such subnational authoritarian enclaves can be democratized. Despite fascinating insights, all existing pathways rely on the actions of elites and are therefore top-down. This article seeks to kick-start the discussion on a bottom-up pathway to subnational democratization, by proposing the attrition mechanism. This mechanism consists of four parts and is the product of abductive inference through theory-building causal process tracing. The building blocks consist of subnational democratization literature, social movement theory, and original empirical data gathered during extensive field research. This case study focuses on the ‘Dynasty Slayer’ in the province of Isabela, the Philippines, where civil society actors used the attrition mechanism to facilitate subnational democratization. This study implies that civil society actors in subnational authoritarian enclaves have agency.

Building a Personal Brand as a CEO: A Case Study of Vivy Yusof, the Cofounder of FashionValet and the dUCk Group

SAGE Open ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 215824402110302
Author(s):  
Nor Hasliza Md Saad ◽  
Zulnaidi Yaacob
Keyword(s):  
Social Media ◽  
Building Blocks ◽  
Media Content ◽  
Fashion Industry ◽  
Personal Brand ◽  
Branding Strategies ◽  
Social Media Presence ◽  
Personal Branding ◽  
The Masses

Social media is a new platform for CEOs to build their image and create a strong personal brand to represent themselves and their company. This research examines an outstanding Malaysian fashion icon and social media–savvy businesswoman with over a million followers on Instagram, Vivy Yusof, the youngest Malaysian e-commerce mogul and an example of a successful CEO who has used personal branding to build an empire in the fashion industry. The objectives of this research are to identify the type of messages Vivy Yusof communicates to her audience through her personal Instagram posts and to identify the ways Vivy Yusof’s audience engages with her posts on Instagram. Her Instagram post content is classified using the Honeycomb framework that comprises seven functional building blocks, namely, presence, relationships, reputation, groups, identity, conversations, and sharing. In this study, the content of Vivy Yusof’s Instagram posts is categorized by how she focuses on the various functional building blocks in her posts and the implications these blocks have on how her audience interacts with the posts. Her social media presence confirms the importance of CEO personal branding because of her role and influence on the masses evidenced by the willingness of her followers to interact (through likes and comments) and engage with her posts on any subject matter, relating either to her business or personal life. The study contributes to a growing body of literature on personal branding strategies by shedding light on the association between content strategies and engagement with social media content.

scholarly journals Study on Structural Characteristics of China’s Passenger Airline Network Based on Network Motifs Analysis

2019 ◽  
Vol 11 (9) ◽  
pp. 2484 ◽  
Author(s):  
Ying Jin ◽  
Ye Wei ◽  
Chunliang Xiu ◽  
Wei Song ◽  
Kaixian Yang
Keyword(s):  
Airline Industry ◽  
Structural Characteristics ◽  
Building Blocks ◽  
Development Stage ◽  
Network Motifs ◽  
Characteristic Analysis ◽  
Airline Networks ◽  
Airline Network ◽  
Industry Sustainability ◽  
Advanced Development

The air passenger transport network system is an important agent of social and economic connections between cities. Studying on the airline network structure and providing optimization strategies can improve the airline industry sustainability evolution. As basic building blocks of broad networks, the concept of network motifs is cited in this paper to apply to the structural characteristic analysis of the passenger airline network. The ENUMERATE SUBGRAPHS (G, k) algorithm is used to identify the motifs and anti-motifs of the passenger airline network in China. A total of 37 airline companies are subjected to motif identification and exploring the structural and functional characteristics of the airline networks corresponding to different motifs. These 37 airline companies are classified according to the motif concentration curves into three development stages, which include mono-centric divergence companies at the low-level development stage, transitional companies at the intermediate development stage, and multi-centric and hierarchical companies at the advanced development stage. Finally, we found that adjusting the number of proper network motifs is useful to optimize the overall structure of airline networks, which is profitable for air transport sustainable development.

scholarly journals Modeling intentional agency: a neo-Gricean framework

Synthese ◽  
2021 ◽  
Author(s):  
Matti Sarkia
Keyword(s):  
Philosophy Of Mind ◽  
General Framework ◽  
Building Blocks ◽  
Theoretical Modeling ◽  
Model Construction ◽  
Coarse Grained ◽  
Scientific Model ◽  
Types Of Knowledge ◽  
Different Types ◽  
Intentional Agency

AbstractThis paper analyzes three contrasting strategies for modeling intentional agency in contemporary analytic philosophy of mind and action, and draws parallels between them and similar strategies of scientific model-construction. Gricean modeling involves identifying primitive building blocks of intentional agency, and building up from such building blocks to prototypically agential behaviors. Analogical modeling is based on picking out an exemplary type of intentional agency, which is used as a model for other agential types. Theoretical modeling involves reasoning about intentional agency in terms of some domain-general framework of lawlike regularities, which involves no detailed reference to particular building blocks or exemplars of intentional agency (although it may involve coarse-grained or heuristic reference to some of them). Given the contrasting procedural approaches that they employ and the different types of knowledge that they embody, the three strategies are argued to provide mutually complementary perspectives on intentional agency.

scholarly journals E-learning-Oriented Software Architecture Design and Case Study

2015 ◽  
Vol 10 (4) ◽  
pp. 59
Author(s):  
Peng Lu ◽  
Xiao Cong ◽  
Dongdai Zhou
Keyword(s):  
Software Architecture ◽  
Building Blocks ◽  
Domain Model ◽  
Learning System ◽  
Application Framework ◽  
Component Library ◽  
E Learning ◽  
The Difference ◽  
High Level

Nowadays, E-learning system has been widely applied to practical teaching. It was favored by people for its characterized course arrangement and flexible learning schedule. However, the system does have some problems in the process of application such as the functions of single software are not diversified enough to satisfy the requirements in teaching completely. In order to cater more applications in the teaching process, it is necessary to integrate functions from different systems. But the difference in developing techniques and the inflexibility in design makes it difficult to implement. The major reason of these problems is the lack of fine software architecture. In this article, we build domain model and component model of E-learning system and components integration method on the basis of WebService. And we proposed an abstract framework of E-learning which could express the semantic relationship among components and realize high level reusable on the basis of informationized teaching mode. On this foundation, we form an E-learning oriented layering software architecture contain component library layer, application framework layer and application layer. Moreover, the system contains layer division multiplexing and was not built upon developing language and tools. Under the help of the software architecture, we could build characterized E-learning system flexibly like building blocks through framework selection, component assembling and replacement. In addition, we exemplify how to build concrete E-learning system on the basis of this software architecture.

scholarly journals Simultaneous Parameters Identifiability and Estimation of anE. coliMetabolic Network Model

2015 ◽  
Vol 2015 ◽  
pp. 1-21 ◽  
Author(s):  
Kese Pontes Freitas Alberton ◽  
André Luís Alberton ◽  
Jimena Andrea Di Maggio ◽  
Vanina Gisela Estrada ◽  
María Soledad Díaz ◽  
...  
Keyword(s):  
Experimental Data ◽  
Escherichia Coli ◽  
Metabolic Networks ◽  
Initial Conditions ◽  
Model Fit ◽  
Real Problem ◽  
Kinetic Rates ◽  
K 12 ◽  
Procedure Model

This work proposes a procedure for simultaneous parameters identifiability and estimation in metabolic networks in order to overcome difficulties associated with lack of experimental data and large number of parameters, a common scenario in the modeling of such systems. As case study, the complex real problem of parameters identifiability of theEscherichia coliK-12 W3110 dynamic model was investigated, composed by 18 differential ordinary equations and 35 kinetic rates, containing 125 parameters. With the procedure, model fit was improved for most of the measured metabolites, achieving 58 parameters estimated, including 5 unknown initial conditions. The results indicate that simultaneous parameters identifiability and estimation approach in metabolic networks is appealing, since model fit to the most of measured metabolites was possible even when important measures of intracellular metabolites and good initial estimates of parameters are not available.

scholarly journals Towards reafirmation of the case study research method: From „building blocks“ and „process tracing“ to typological theories

Sociologija ◽  
2015 ◽  
Vol 57 (1) ◽  
pp. 152-167
Author(s):  
Ivana Milovanovic
Keyword(s):  
Social Sciences ◽  
Research Method ◽  
Case Study Research ◽  
Field Research ◽  
Building Blocks ◽  
Process Tracing ◽  
Case Study Method ◽  
Study Research

This paper represents a contribution to the consideration of the characteristics of the case study research method in sociological researches. In the first part of paper, some specifics of case study method are described, in the second part we represented ways of use of this method in field research. finally, third part of this paper indicates certain ?sub methods? within case study method, such as ?building blocks? and ?process tracing?, which are, at the same time, conditions for developing typological theories. Those ?sub methods? indicate evolution of case study method in social sciences during last few decades, as well as importance of existence and use of such ?elastic? method in all, especially field researches where researcher is facing with a series of cognitive concerns.

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