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Extended evolution: A conceptual framework for integrating regulatory networks and niche construction.

ABSTRACT: This paper introduces a conceptual framework for the evolution of complex systems based on the integration of regulatory network and niche construction theories. It is designed to apply equally to cases of biological, social and cultural evolution. Within the conceptual framework we focus especially on the transformation of complex networks through the linked processes of externalization and internalization of causal factors between regulatory networks and their corresponding niches and argue that these are an important part of evolutionary explanations. This conceptual framework extends previous evolutionary models and focuses on several challenges, such as the path-dependent nature of evolutionary change, the dynamics of evolutionary innovation and the expansion of inheritance systems.

SUBMITTER: Laubichler MD

PROVIDER: S-EPMC4744698 | biostudies-other | 2015 Nov

REPOSITORIES: biostudies-other

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A four-quadrant conceptual framework for analyzing extended producer responsibility in offshore prefabrication construction.

Project description:Prefabrication has been widely advocated as a green production strategy to minimize the adverse environmental impacts of construction. Amid economic globalization, prefabricated construction materials are commonly sourced offsite and even offshore. As an issue emerging alongside offshore prefabrication, extended producer responsibility (EPR) is yet to be clearly identified, allocated, and implemented. This research develops a conceptual framework using a design thinking process, through which EPR associated with offshore prefabrication can be analyzed, agreed upon, and allocated. By considering the scope and scale of the responsibility and the procurement methods, the framework comprises four quadrants representing four typical scenarios for implementation of the EPR principle. It is applicable for both short-term and lifelong EPR analysis, in both traditional and integrated project delivery contexts. The framework will be particularly useful for devising public policies to achieve an onshore and offshore stakeholder win-win situation.

| S-EPMC7540246 | biostudies-literature

A phylogenetic framework to study the evolution of transcriptional regulatory networks

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-07-01 | GSE94628 | GEO

Integrating external biological knowledge in the construction of regulatory networks from time-series expression data.

Project description:BackgroundInference about regulatory networks from high-throughput genomics data is of great interest in systems biology. We present a Bayesian approach to infer gene regulatory networks from time series expression data by integrating various types of biological knowledge.ResultsWe formulate network construction as a series of variable selection problems and use linear regression to model the data. Our method summarizes additional data sources with an informative prior probability distribution over candidate regression models. We extend the Bayesian model averaging (BMA) variable selection method to select regulators in the regression framework. We summarize the external biological knowledge by an informative prior probability distribution over the candidate regression models.ConclusionsWe demonstrate our method on simulated data and a set of time-series microarray experiments measuring the effect of a drug perturbation on gene expression levels, and show that it outperforms leading regression-based methods in the literature.

| S-EPMC3465231 | biostudies-literature

A phylogenetic framework to study the evolution of transcriptional regulatory networks [RNA-Seq]

Project description:Comparative expression analysis of HOG1 KOs during osmotic stress in the ascomycete yeasts

2017-07-01 | GSE94627 | GEO

A phylogenetic framework to study the evolution of transcriptional regulatory networks [Agilent microarray]

Project description:A phylogenetic framework to study the evolution of transcriptional regulatory networks

2017-07-01 | GSE94625 | GEO

European Reference networks for rare diseases: what is the conceptual framework?

Project description:With the Cross-Border Healthcare Directive (2011/24/EU) a mandatory framework was established to foster cooperation on a voluntary basis, within European Reference Networks (ERNs). These networks are composed of centres and healthcare providers. The exchange of knowledge is a central issue in this context. A detailed literature survey was carried out to determine the most important factors affecting information and knowledge exchange, as well as learning, in networks and how this can be supported. New communication technologies are identified as key tools for the European Reference Networks (ERN). This study recommends the elaboration of a systematic knowledge use and knowledge generation plan. The data of this study suggests that the future ERNs will mediate the adoption of the digitised and networked information society in medical practice.

| S-EPMC5547471 | biostudies-other

Determinants of successful clinical networks: the conceptual framework and study protocol.

Project description:BackgroundClinical networks are increasingly being viewed as an important strategy for increasing evidence-based practice and improving models of care, but success is variable and characteristics of networks with high impact are uncertain. This study takes advantage of the variability in the functioning and outcomes of networks supported by the Australian New South Wales (NSW) Agency for Clinical Innovation's non-mandatory model of clinical networks to investigate the factors that contribute to the success of clinical networks.Methods/designThe objective of this retrospective study is to examine the association between external support, organisational and program factors, and indicators of success among 19 clinical networks over a three-year period (2006-2008). The outcomes (health impact, system impact, programs implemented, engagement, user perception, and financial leverage) and explanatory factors will be collected using a web-based survey, interviews, and record review. An independent expert panel will provide judgements about the impact or extent of each network's initiatives on health and system impacts. The ratings of the expert panel will be the outcome used in multivariable analyses. Following the rating of network success, a qualitative study will be conducted to provide a more in-depth examination of the most successful networks.DiscussionThis is the first study to combine quantitative and qualitative methods to examine the factors that contribute to the success of clinical networks and, more generally, is the largest study of clinical networks undertaken. The adaptation of expert panel methods to rate the impacts of networks is the methodological innovation of this study. The proposed project will identify the conditions that should be established or encouraged by agencies developing clinical networks and will be of immediate use in forming strategies and programs to maximise the effectiveness of such networks.

| S-EPMC3328243 | biostudies-literature

Construction of ceRNA regulatory networks for osteoporosis.

Project description:Osteoporosis increases the risk of fracture. Improving the diagnosis and treatment of osteoporosis has clinical applications. The differentially expressed genes (DEcircRs, DEmRs, DEmiRs) of osteoporotic patients and controls were analyzed using the GEO database, and enrichment analysis of DEmRs was performed. circRNAs and mRNAs, which were predicted to have a target relationship with DEmRs, were obtained to compare competing endogenous RNA (ceRNA) regulatory networks by comparison with differentially expressed genes. Molecular experiments were utilized to validate the expression of genes within the network. The interactions between genes within the ceRNA network were validated by luciferase reporter assays. Following overexpression of circ_0070304 in bone marrow mesenchymal stem cells (BMSCs), the osteogenic differentiation of the cells was assessed by Alizarin Red staining. A total of 110 intersectional DEmRs between patients with osteoporosis and controls from GSE35958 and GSE56815, which were mainly enriched in estrogen, the thyroid hormone signaling pathway, and adherens junctions were identified. A ceRNA network [circ_0070304/miR‑183‑5p/ring finger and CCCH‑type domains 2 (RC3H2)] was then constructed. Circ_0070304 acted as a sponge for miR‑183‑5p and regulated RC3H2 expression. Overexpression of circ_0070304 upregulated ROCK1 and induced osteogenic differentiation. The ceRNA regulatory network that was obtained is expected to be a new target for osteoporosis treatment and to provide new insights into the diagnosis and treatment of osteoporosis in greater depth.

| S-EPMC10308483 | biostudies-literature

Nutritional ecology beyond the individual: a conceptual framework for integrating nutrition and social interactions.

Project description:Over recent years, modelling approaches from nutritional ecology (known as Nutritional Geometry) have been increasingly used to describe how animals and some other organisms select foods and eat them in appropriate amounts in order to maintain a balanced nutritional state maximising fitness. These nutritional strategies profoundly affect the physiology, behaviour and performance of individuals, which in turn impact their social interactions within groups and societies. Here, we present a conceptual framework to study the role of nutrition as a major ecological factor influencing the development and maintenance of social life. We first illustrate some of the mechanisms by which nutritional differences among individuals mediate social interactions in a broad range of species and ecological contexts. We then explain how studying individual- and collective-level nutrition in a common conceptual framework derived from Nutritional Geometry can bring new fundamental insights into the mechanisms and evolution of social interactions, using a combination of simulation models and manipulative experiments.

| S-EPMC4342766 | biostudies-literature

Construction of gene regulatory networks using biclustering and Bayesian networks.

Project description:BackgroundUnderstanding gene interactions in complex living systems can be seen as the ultimate goal of the systems biology revolution. Hence, to elucidate disease ontology fully and to reduce the cost of drug development, gene regulatory networks (GRNs) have to be constructed. During the last decade, many GRN inference algorithms based on genome-wide data have been developed to unravel the complexity of gene regulation. Time series transcriptomic data measured by genome-wide DNA microarrays are traditionally used for GRN modelling. One of the major problems with microarrays is that a dataset consists of relatively few time points with respect to the large number of genes. Dimensionality is one of the interesting problems in GRN modelling.ResultsIn this paper, we develop a biclustering function enrichment analysis toolbox (BicAT-plus) to study the effect of biclustering in reducing data dimensions. The network generated from our system was validated via available interaction databases and was compared with previous methods. The results revealed the performance of our proposed method.ConclusionsBecause of the sparse nature of GRNs, the results of biclustering techniques differ significantly from those of previous methods.

| S-EPMC3231811 | biostudies-literature

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