scholarly journals A node-based informed modularity strategy to identify organizational modules in anatomical networks

Biology Open ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. bio056176
Author(s):  
Borja Esteve-Altava
Keyword(s):  
Combinatorial Theory ◽  
Modular Organization ◽  
Minor Variation ◽  
Network Partition ◽  
Detection Algorithms ◽  
Common Strategy ◽  
Network Modules ◽  
Q Function ◽  
Anatomical Network Analysis ◽  
Individual Node

ABSTRACTThe study of morphological modularity using anatomical networks is growing in recent years. A common strategy to find the best network partition uses community detection algorithms that optimize the modularity Q function. Because anatomical networks and their modules tend to be small, this strategy often produces two problems. One is that some algorithms find inexplicable different modules when one inputs slightly different networks. The other is that algorithms find asymmetric modules in otherwise symmetric networks. These problems have discouraged researchers to use anatomical network analysis and boost criticisms to this methodology. Here, I propose a node-based informed modularity strategy (NIMS) to identify modules in anatomical networks that bypass resolution and sensitivity limitations by using a bottom-up approach. Starting with the local modularity around every individual node, NIMS returns the modular organization of the network by merging non-redundant modules and assessing their intersection statistically using combinatorial theory. Instead of acting as a black box, NIMS allows researchers to make informed decisions about whether to merge non-redundant modules. NIMS returns network modules that are robust to minor variation and does not require optimization of a global modularity function. NIMS may prove useful to identify modules also in small ecological and social networks.

scholarly journals A Node-based Informed Modularity Strategy to Identify Organizational Modules in Anatomical Networks

2020 ◽  
Author(s):  
Borja Esteve-Altava
Keyword(s):  
Detection Algorithm ◽  
Combinatorial Theory ◽  
Modular Organization ◽  
Resolution Limit ◽  
Minor Variation ◽  
Common Strategy ◽  
Network Modules ◽  
Community Detection Algorithm ◽  
Q Function ◽  
Anatomical Network Analysis

AbstractThe use of anatomical networks to study the modular organization of morphological systems and their evolution is growing in recent years. A common strategy to find the best partition of anatomical networks into modules is to use a community detection algorithm that tries to optimize the modularity Q function. However, this strategy overlooks the fact that Q has a resolution limit for small modules, which is often the case in anatomical networks. This produces two problems. One is that some algorithms find inexplicable different modules when we input slightly different networks. The other is that algorithms find asymmetric modules in otherwise symmetric networks. These problems have discouraged researchers to use anatomical network analysis and boost criticisms to this methodology. Here, I propose a Node-based Informed Modularity Strategy (NIMS) to identify modules in anatomical networks that bypass resolution and sensitivity limitations by using a bottom-up approach. Starting with the local modularity around every individual node, NIMS returns the modular organization of the network by merging non-redundant modules and assessing their intersection statistically using combinatorial theory. Instead of acting as a black box, NIMS allows researcher to make informed decisions about whether to merge non-redundant modules. NIMS returns network modules that are robust to minor variation and does not require to optimize a global modularity function. NIMS may prove useful to identify modules also in small ecological and social networks.

scholarly journals The Role of Core and Variable Gene Regulatory Network Modules in Tooth Development and Evolution

2020 ◽  
Author(s):  
Alexa Sadier ◽  
Sharlene E Santana ◽  
Karen E Sears
Keyword(s):  
Regulatory Networks ◽  
Tooth Development ◽  
Experimental System ◽  
Model Organisms ◽  
Modular Organization ◽  
Shape Variation ◽  
Experimental Systems ◽  
Network Modules ◽  
Gene Regulatory ◽  
Evo Devo

Synopsis Among the developmental processes that have been proposed to influence the direction of evolution, the modular organization of developmental gene regulatory networks (GRNs) has shown particular promise. In theory, GRNs have core modules comprised of essential, conserved circuits of genes, and sub-modules of downstream, secondary circuits of genes that are more susceptible to variation. While this idea has received considerable interest as of late, the field of evo-devo lacks the experimental systems needed to rigorously evaluate this hypothesis. Here, we introduce an experimental system, the vertebrate tooth, that has great potential as a model for testing this hypothesis. Tooth development and its associated GRN have been well studied and modeled in both model and non-model organisms. We propose that the existence of modules within the tooth GRN explains both the conservation of developmental mechanisms and the extraordinary diversity of teeth among vertebrates. Based on experimental data, we hypothesize that there is a conserved core module of genes that is absolutely necessary to ensure tooth or cusp initiation and development. In regard to tooth shape variation between species, we suggest that more relaxed sub-modules activated at later steps of tooth development, for example, during the morphogenesis of the tooth and its cusps, control the different axes of tooth morphological variation.

scholarly journals An iterative network partition algorithm for accurate identification of dense network modules

2011 ◽  
Vol 40 (3) ◽  
pp. e18-e18 ◽  
Author(s):  
Siqi Sun ◽  
Xinran Dong ◽  
Yao Fu ◽  
Weidong Tian
Keyword(s):  
Dense Network ◽  
Accurate Identification ◽  
Network Partition ◽  
Network Modules

scholarly journals Evolutionary and ontogenetic changes of the anatomical organization and modularity in the skull of archosaurs

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Hiu Wai Lee ◽  
Borja Esteve-Altava ◽  
Arhat Abzhanov
Keyword(s):  
Comparative Anatomy ◽  
Alligator Mississippiensis ◽  
Modular Organization ◽  
Ontogenetic Changes ◽  
Anatomical Changes ◽  
Morphological Complexity ◽  
Diverse Species ◽  
Juvenile Bird ◽  
Functionally Diverse ◽  
Anatomical Network Analysis

Abstract Comparative anatomy studies of the skull of archosaurs provide insights on the mechanisms of evolution for the morphologically and functionally diverse species of crocodiles and birds. One of the key attributes of skull evolution is the anatomical changes associated with the physical arrangement of cranial bones. Here, we compare the changes in anatomical organization and modularity of the skull of extinct and extant archosaurs using an Anatomical Network Analysis approach. We show that the number of bones, their topological arrangement, and modular organization can discriminate birds from non-avian dinosaurs, and crurotarsans. We could also discriminate extant taxa from extinct species when adult birds were included. By comparing within the same framework, juveniles and adults for crown birds and alligator (Alligator mississippiensis), we find that adult and juvenile alligator skulls are topologically similar, whereas juvenile bird skulls have a morphological complexity and anisomerism more similar to those of non-avian dinosaurs and crurotarsans than of their own adult forms. Clade-specific ontogenetic differences in skull organization, such as extensive postnatal fusion of cranial bones in crown birds, can explain this pattern. The fact that juvenile and adult skulls in birds do share a similar anatomical integration suggests the presence of a specific constraint to their ontogenetic growth.

scholarly journals Evolutionary and ontogenetic changes of the anatomical organization and modularity in the skull of archosaurs

2020 ◽  
Author(s):  
Hiu Wai Lee ◽  
Borja Esteve-Altava ◽  
Arkhat Abzhanov
Keyword(s):  
Comparative Anatomy ◽  
Alligator Mississippiensis ◽  
Modular Organization ◽  
Ontogenetic Changes ◽  
Anatomical Changes ◽  
Morphological Complexity ◽  
Diverse Species ◽  
Juvenile Bird ◽  
Functionally Diverse ◽  
Anatomical Network Analysis

AbstractComparative anatomy studies of the skull of archosaurs provide insights on the mechanisms of evolution for the morphologically and functionally diverse species of crocodiles and birds. One of the key attributes of skull evolution is the anatomical changes associated with the physical arrangement of cranial bones. Here, we compare the changes in anatomical organization and modularity of the skull of extinct and extant archosaurs using an Anatomical Network Analysis approach. We show that the number of bones, their topological arrangement, and modular organization can discriminate birds from non-avian dinosaurs, and crurotarsans. We could also discriminate extant taxa from extinct species when adult birds were included. By comparing within the same framework, juveniles and adults for crown birds and alligator (Alligator mississippiensis), we find that adult and juvenile alligator skulls are topologically similar, whereas juvenile bird skulls have a morphological complexity and anisomerism more similar to those of non-avian dinosaurs and crurotarsans than of their own adult forms. Clade-specific ontogenetic differences in skull organization, such as extensive postnatal fusion of cranial bones in crown birds, can explain this pattern. The fact that juvenile and adult skulls in birds do share a similar anatomical integration suggests the presence of a specific constraint to their ontogenetic growth.

Utilisation of Robotic Navigation Systems in the Treatment of Atrial Fibrillation

2010 ◽  
Vol 6 (3) ◽  
pp. 60
Author(s):  
Richard Schilling ◽  
Keyword(s):  
Atrial Fibrillation ◽  
Catheter Ablation ◽  
Navigation System ◽  
Antiarrhythmic Drugs ◽  
Rhythm Control ◽  
Navigation Systems ◽  
Robotic Navigation ◽  
Increased Risk ◽  
Common Strategy ◽  
Catheter Navigation

Atrial fibrillation (AF) is linked to an increased risk of adverse cardiovascular events. While rhythm control with antiarrhythmic drugs (AADs) is a common strategy for managing patients with AF, catheter ablation may be a more efficacious and safer alternative to AADs for sinus rhythm control. Conventional catheter ablation has been associated with challenges during the arrhythmia mapping and ablation stages; however, the introduction of two remote catheter navigation systems (a robotic and a magnetic navigation system) may potentially overcome these challenges. Initial clinical experience with the robotic navigation system suggests that it offers similar procedural times, efficacy and safety to conventional manual ablation. Furthermore, it has been associated with reduced fluoroscopy exposure to the patient and the operator as well as a shorter fluoroscopy time compared with conventional catheter ablation. In the future, the remote navigation systems may become routinely used for complex catheter ablation procedures.

Fuzzy ART Neural Network Model for Automated Detection of Freeway Incidents

1998 ◽  
Vol 1634 (1) ◽  
pp. 56-63 ◽  
Author(s):  
Sherif S. Ishak ◽  
Haitham M. Al-Deek
Keyword(s):  
Neural Networks ◽  
False Alarm ◽  
False Alarm Rate ◽  
Back Propagation ◽  
Incident Detection ◽  
Traffic Patterns ◽  
Traffic Pattern ◽  
Detection Algorithms ◽  
Fuzzy Art ◽  
Freeway Incidents

Pattern recognition techniques such as artificial neural networks continue to offer potential solutions to many of the existing problems associated with freeway incident-detection algorithms. This study focuses on the application of Fuzzy ART neural networks to incident detection on freeways. Unlike back-propagation models, Fuzzy ART is capable of fast, stable learning of recognition categories. It is an incremental approach that has the potential for on-line implementation. Fuzzy ART is trained with traffic patterns that are represented by 30-s loop-detector data of occupancy, speed, or a combination of both. Traffic patterns observed at the incident time and location are mapped to a group of categories. Each incident category maps incidents with similar traffic pattern characteristics, which are affected by the type and severity of the incident and the prevailing traffic conditions. Detection rate and false alarm rate are used to measure the performance of the Fuzzy ART algorithm. To reduce the false alarm rate that results from occasional misclassification of traffic patterns, a persistence time period of 3 min was arbitrarily selected. The algorithm performance improves when the temporal size of traffic patterns increases from one to two 30-s periods for all traffic parameters. An interesting finding is that the speed patterns produced better results than did the occupancy patterns. However, when combined, occupancy–speed patterns produced the best results. When compared with California algorithms 7 and 8, the Fuzzy ART model produced better performance.

A general practice provider federation in a mixed health economy in England: a case study investigation

2018 ◽  
Vol 68 (suppl 1) ◽  
pp. bjgp18X696929
Author(s):  
Jill Mitchell
Keyword(s):  
General Practice ◽  
Shared Vision ◽  
Health Economy ◽  
Structured Interviews ◽  
The North ◽  
Common Strategy ◽  
Common Purpose ◽  
Collaborative Working ◽  
The Impact

BackgroundThere is an emerging debate that general practice in its current format is out-dated and there is a requirement to move to a federated model of provision where groups of Practices come together. The emergence of federations has developed over the past 5 years but the factors that influence how federations develop and the impact of this new model is an under researched area.AimThe study explored the rationale around why a group of independent GP practices opted to pursue an alternative business venture and the benefits that this strategy offered.MethodA single organisational case study of a federation in the North of England was conducted between 2011–2016. Mixed methods data collection included individual and group semi-structured interviews and quantitative surveys.ResultsFederations promote collaborative working, relying on strategic coherence of multiple individual GP practices through a shared vision and common purpose. Findings revealed many complexities in implementing a common strategy across multiple independent businesses. The ability of the federation to gain legitimacy was two dimensional – externally and internally. The venture had mixed successes, but their approach to quality improvement proved innovative and demonstrated outcomes on a population basis. The study identified significant pressures that practices were experiencing and the need to seek alternative ways of working but there was no shared vision or inclination to relinquish individual practice autonomy.ConclusionOrganisational development support is critical to reform General Practice. Whether central funding through the GP Five Year Forward View will achieve the scale of change required is yet to be evidenced.

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