scholarly journals Constraint-Based Modeling in Systems Biology

10.29007/8w4w ◽  
2018 ◽  
Author(s):  
Alexander Bockmayr

The idea of constraint-based modeling in systems biology is to describe a biological system by a set of constraints, i.e., by pieces of partial information about its structure and dynamics. Using constraint-based reasoning one may then draw conclusions about the possible system behaviors.In this talk, we will focus on constraint-based modeling techniques for regulatory networks starting from the discrete logical formalism of René Thomas. In this framework, logic and constraints arise at two different levels. On the one hand, Boolean or multi-valued logic formulae provide a natural way to represent the structure of a regulatory network, which is given by positive and negative interactions (i.e., activation and inhibition) between the network components. On the other hand, temporal logic formulae (e.g. CTL) may be used to reason about the dynamics of the system, represented by a state transition graph or Kripke model.

2020 ◽  
Vol 49 (1) ◽  
pp. 181-197 ◽  
Author(s):  
Philippe Nghe ◽  
Marjon G.J. de Vos ◽  
Enzo Kingma ◽  
Manjunatha Kogenaru ◽  
Frank J. Poelwijk ◽  
...  

The limits of evolution have long fascinated biologists. However, the causes of evolutionary constraint have remained elusive due to a poor mechanistic understanding of studied phenotypes. Recently, a range of innovative approaches have leveraged mechanistic information on regulatory networks and cellular biology. These methods combine systems biology models with population and single-cell quantification and with new genetic tools, and they have been applied to a range of complex cellular functions and engineered networks. In this article, we review these developments, which are revealing the mechanistic causes of epistasis at different levels of biological organization—in molecular recognition, within a single regulatory network, and between different networks—providing first indications of predictable features of evolutionary constraint.


2017 ◽  
Vol 28 (1-2) ◽  
pp. 28-35 ◽  
Author(s):  
B. A. Baranovski

Nowadays, bioecological characteristics of species are the basis for flora and vegetation studying on the different levels. Bioecological characteristics of species is required in process of flora studying on the different levels such as biotopes or phytocenoses, floras of particular areas (floras of ecologically homogeneous habitats), and floras of certain territories. Ramensky scale is the one of first detailed ecological scales on plant species ordination in relation to various environmental factors; it developed in 1938 (Ramensky, 1971). A little later (1941), Pogrebnyak’s scale of forest stands was proposed. Ellenberg’s system developed in 1950 (Ellenberg, 1979) and Tsyganov’s system (Tsyganov, 1975) are best known as the systems of ecological scales on vascular plant species; these systems represent of habitat detection by ecotopic ecomorphs of plant species (phytoindication). Basically, the system proposed by Alexander Lyutsianovich Belgard was the one of first system of plant species that identiified ectomorphs in relation to environmental factors. As early as 1950, Belgard developed the tabulated system of ecomorphs using the Latin ecomorphs abbreviation; he also used the terminology proposed in the late 19th century by Dekandol (1956) and Warming (1903), as well as terminology of other authors. The article analyzes the features of Belgard’s system of ecomorphs on vascular plants. It has certain significance and advantages over other systems of ecomorphs. The use of abbreviated Latin names of ecomorphs in tabular form enables the use shortened form of ones. In the working scheme of Belgard’s system of ecomorphs relation of species to environmental factors are represented in the abbreviated Latin alphabetic version (Belgard, 1950). Combined into table, the ecomorphic analysis of plant species within association (ecological certification of species), biotope or area site (water area) gives an explicit pattern on ecological structure of flora within surveyed community, biotope or landscape, and on environmental conditions. Development and application by Belgrard the cenomorphs as «species’ adaptation to phytocenosis as a whole» were completely new in the development of systems of ecomorphs and, in this connection, different coenomorphs were distinguished. Like any concept, the system of ecomorphs by Belgard has the possibility and necessity to be developed and added. Long-time researches and analysis of literature sources allow to propose a new coenomorph in the context of Belgard’s system of ecomorphs development: silvomargoant (species of forest margin, from the Latin words margo – edge, boundary (Dvoretsky, 1976), margo – margin, ad margins silvarum – along the deciduous forest margins). As an example of ecomorphic characterization of species according to the system of ecomorphs by Belgard (when the abbreviated Latin ecomorph names are used in tabular form and the proposed cenomorph is used), it was given the part of the table on vascular plants ecomorphs in the National Nature Park «Orelsky» (Baranovsky et al). The Belgard’s system of ecomorphs is particularly convenient and can be successfully applied to data processing in the ecological analysis of the flora on wide areas with significant species richness, and the proposed ecomorph will be another necessary element in the Belgard’s system of ecomorphs. 


2021 ◽  
Vol 37 (01) ◽  
pp. 045-052
Author(s):  
Mario Bazanelli Junqueira Ferraz ◽  
Guilherme Constante Preis Sella

AbstractNasal dorsal preservation surgery was described more than 100 years ago, but recently has gained prominence. Our objective is to show the surgical technique, the main indications and counterindications, and the complications. It is a technique that does not cause the detachment of the upper lateral cartilage (ULC) from the nasal septum, and has the main following sequence: preparation of the septum and its resection can be at different levels (high or low, i.e., SPAR [septum pyramidal adjustment and repositioning] A or B); preparation of the pyramid; transversal osteotomy; lateral osteotomy(s); and septopyramidal adjustment. The result is a nose with a lower radix than the original, a deprojection of the nasal dorsum tending to maintain its original shape; an increase in the interalar distance (IAD) and enlargement of the nasal middle ⅓; and loss of projection of the nasal tip and roundness of the nostrils. Thus, the ideal candidate is the one who benefits from such side effects, that is: tension nose, that is, high radix with projected dorsum, projected anterior nasal septal angle (ANSA), narrow middle ⅓, narrow IAD, thin nostrils and straight perpendicular plate of the ethmoid (PPE), and, depending on the characteristics, the deviated nose. The counterindications are low radix, irregularities in the nasal dorsum, ANSA lower than rhinion, and a wide middle ⅓. And the main stigmas are: a nose with a very low radix, middle ⅓ enlarged, residual hump, and saddling of the supratip area. Other issues of this technique are: the shape of the radix; the need or not to remove PPE; wide dorsum; irregular dorsum; ANSA lower than rhinion; weak cartilages; long nasal bone; deviated PPE; and obsessive patient. We conclude that this is a great technique for noses with characteristics suitable to it; care must be taken with the stigmas it can cause.


2021 ◽  
Vol 13 (2) ◽  
pp. 485
Author(s):  
Blanca L. Díaz Mariño ◽  
Frida Carmina Caballero-Rico ◽  
Ramón Ventura Roque Hernández ◽  
José Alberto Ramírez de León ◽  
Daniel Alejandro González-Bandala

Understanding the value of research for society has become a priority, and several methodologies have been developed to assess the social impact of research. This study aimed to determine how productive interactions are developed during the execution of research projects. A retrospective study was conducted on 33 projects from 1999 to 2020. Semi-structured interviews with the technical managers were conducted to analyze how different actors of the project—researchers, government officials, and civil society and private sector stakeholders—were involved, illustrating how productive interactions occur in specific biodiversity contexts. The results revealed different levels and intensities of productive interactions; on the one hand, three projects involved all actors; eight involved researchers outside the institution; and 25 involved community members. The number of participants ranged from 2 to 37. All research evaluated had a disciplinary orientation. The type and time of interactions with other interested parties depended on the amount of funding, project type, project duration, and, significantly, on the profile of the technical manager. The importance of assessing and valuing productive interactions was identified as a fundamental element in promoting the social impact of research, as well as integrating inter- or multidisciplinary projects that impact the conservation of socio-ecological systems.


RSC Advances ◽  
2017 ◽  
Vol 7 (37) ◽  
pp. 23222-23233 ◽  
Author(s):  
Wei Liu ◽  
Wen Zhu ◽  
Bo Liao ◽  
Haowen Chen ◽  
Siqi Ren ◽  
...  

Inferring gene regulatory networks from expression data is a central problem in systems biology.


2018 ◽  
Vol 120 (6) ◽  
pp. 2761-2774 ◽  
Author(s):  
Michaela Bruton ◽  
Nicholas O’Dwyer

At face value, the term “synergy” provides a unifying concept within a fractured field that encompasses complementary neural, computational, and behavioral approaches. However, the term is not used synonymously by different researchers but has substantially different meanings depending on the research approach. With so many operational definitions for the one term, it becomes difficult to use as either a descriptive or explanatory concept, yet it remains pervasive and apparently indispensable. Here we provide a summary of different approaches that invoke synergies in a descriptive or explanatory context, summarizing progress, not within the one approach, but across the theoretical landscape. Bernstein’s framework of flexible hierarchical control may provide a unifying framework here, since it can incorporate divergent ideas about synergies. In the current motor control literature, synergy may refer to conceptually different processes that could potentially operate in parallel, across different levels within the same hierarchical control scheme. There is evidence for the concurrent existence of synergies with different features, both “hard-wired” and “soft-wired,” and task independent and task dependent. By providing a comprehensive overview of the multifaceted ideas about synergies, our goal is to move away from the compartmentalization and narrow the focus on one level and promote a broader perspective on the control and coordination of movement.


Author(s):  
Vlad Glăveanu

This chapter addresses why people engage in creativity. This question can be answered at different levels. On the one hand, one can refer to what motivates creative people to do what they do. On the other hand, the question addresses a deeper level, that of how societies today are built and how they, in turn, construct the meaning and value of creativity. Nowadays, people consider creativity intrinsically valuable largely because of its direct and indirect economic benefits. However, creative expression also has a role for health and well-being. Creativity also relates to meaning in life. The chapter then considers how creativity can be used for good or for evil.


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