Robust normalization and transformation techniques for constructing gene coexpression networks from RNA-seq data

Background Constructing gene coexpression networks is a powerful approach for analyzing high-throughput gene expression data towards module identification, gene function prediction, and disease-gene prioritization. While optimal workflows for constructing coexpression networks, including good choices for data pre-processing, normalization, and network transformation, have been developed for microarray-based expression data, such well-tested choices do not exist for RNA-seq data. Almost all studies that compare data processing and normalization methods for RNA-seq focus on the end goal of determining differential gene expression. Results Here, we present a comprehensive benchmarking and analysis of 36 different workflows, each with a unique set of normalization and network transformation methods, for constructing coexpression networks from RNA-seq datasets. We test these workflows on both large, homogenous datasets and small, heterogeneous datasets from various labs. We analyze the workflows in terms of aggregate performance, individual method choices, and the impact of multiple dataset experimental factors. Our results demonstrate that between-sample normalization has the biggest impact, with counts adjusted by size factors producing networks that most accurately recapitulate known tissue-naive and tissue-aware gene functional relationships. Conclusions Based on this work, we provide concrete recommendations on robust procedures for building an accurate coexpression network from an RNA-seq dataset. In addition, researchers can examine all the results in great detail at https://krishnanlab.github.io/RNAseq_coexpression to make appropriate choices for coexpression analysis based on the experimental factors of their RNA-seq dataset.

Theoretical investigation of methane hydrate nucleation kinetic from “water + gas” and “sea water + gas” mixtures

In this work we studied transition mechanics of a dynamic hydrogen bond network of water into a stable hydrogen bond network during gas clathrate hydrate formation process. For this purpose, we used Molecular Dynamic simulation methods and a bunch of home-made programs for determining structural properties during transition process. We have found that at certain conditions the network transformation process involves the whole system from the very beginning and could be considered as a collective effect, that results in high speed of hydrate formation.

Highly specialized dental care in Ukraine in the conditions of transformation of the healthcare system of Ukraine

The gradual transformation of the health care system from April 1, 2020 impacted the reform of secondary (specialized) health care. Planning a model of hospital network transformation should take into account the needs of the population and ensure the creation of a multidisciplinary hospital with a focus on a patient. The article analyzes the human resources and infrastructure of medical institutions that provide dental care, including multidisciplinary hospitals. The main aspects that need to be taken into account when planning the transformation of the hospital network considering the interdisciplinary interaction of dentists, maxillofacial surgeons with general practitioners to improve the quality of care are also identified.

An orderly charge and discharge control method of considering electric vehicle V2G and photovoltaic complementation in residential area

In order to resolve the problems of distribution network overload and increased peak-valley difference caused by large-scale electric vehicles’ disordered charging, taking the residential community as the research object, an orderly charging method of electric vehicles (EVs) based on power line carrier communication was proposed, and a model of ordered charge and discharge control and load peak regulation considering the complementary of EVs V2G and photovoltaic (PV) was established. It makes full use of the ability of EVs to cut peaks and valleys and restrain the fluctuation of PV output, alleviates the load pressure of the distribution network and reduces the cost of network transformation, which not only brings great benefits to the owners of EVs and power supply operators, but also promotes the consumption of new energy.

Moral and Political Crisis of Intersubjectivity in Europe and Ukraine: Implementation of Deliberative Democracy Idea

The article explores formation of new ideals and values that has become a key task of the European community after overcoming totalitarianism. Many researchers of that time were looking for methods to prevent atomization and establish democracy, and one of the methods was communicative philosophy. This approach helped to shape the main narratives that still shape the politics of Western Europe. However, Brexit, the international economic crisis of 2008-2011, the COVID-19 pandemic are Black Swans that each time set the tone for the mood of society and determine the meanings of narratives on social networks (virtual and real). The communicative-network transformation of society is capable of materializing the discourse around new problems of the world in order to prevent a moral split. The virtual dimension of our everyday life acquires key roles in the dissemination of thoughts and shaping the mood of society. This transformation creates new threats to liberal values that were formed long before the “state in the smartphone”. Focusing attention on the modern conditions of human life will help to better understand its political behavior and ways to create better conditions for democracy in modern society.

SEMANTIC NETWORK TRANSFORMATION METHOD FOR AUTOMATION OF PROGRAMMING PROBLEMS SOLUTIONS EVALUATION IN E-LEARNING

The article presents a semantic network transformation method for a programcode into an N-dimensional vector. The proposed method allows automating the quality assessment of solving programming problems in the process of e-learning. The method includes the authentic algorithms of building and converting the network. In order to determine the algorithm in the program code there is a template of this algorithm, presented in the form of a subgraph of abstract concepts of the language in the semantic network, built on the basis of this code. The search for the algorithm by comparing the subgraph of the network with the template network helped to identify the BFS algorithm with a given accuracy: the cutoff threshold for the perceptron outputs is 0.85, which is based on the calculation of accuracy of the single-layer perceptron in the classification of the MNIST base equal to 88%, which confirms the effectiveness of the developed method and requires further research using machine learning methods to find the optimal value of the coordinates of the nodes of the semantic network and templates of algorithms.

Robust normalization and transformation techniques for constructing gene coexpression networks from RNA-seq data

BackgroundConstructing gene coexpression networks is a powerful approach for analyzing high-throughput gene expression data towards module identification, gene function prediction, and disease-gene prioritization. While optimal workflows for constructing coexpression networks – including good choices for data pre-processing, normalization, and network transformation – have been developed for microarray-based expression data, such well-tested choices do not exist for RNA-seq data. Almost all studies that compare data processing/normalization methods for RNA-seq focus on the end goal of determining differential gene expression.ResultsHere, we present a comprehensive benchmarking and analysis of 30 different workflows, each with a unique set of normalization and network transformation methods, for constructing coexpression networks from RNA-seq datasets. We tested these workflows on both large, homogenous datasets (Genotype-Tissue Expression project) and small, heterogeneous datasets from various labs (submitted to the Sequence Read Archive). We analyzed the workflows in terms of aggregate performance, individual method choices, and the impact of multiple dataset experimental factors. Our results demonstrate that between-sample normalization has the biggest impact, with trimmed mean of M-values or upper quartile normalization producing networks that most accurately recapitulate known tissue-naive and tissue-specific gene functional relationships.ConclusionsBased on this work, we provide concrete recommendations on robust procedures for building an accurate coexpression network from an RNA-seq dataset. In addition, researchers can examine all the results in great detail at https://krishnanlab.github.io/norm_for_RNAseq_coexp to make appropriate choices for coexpression analysis based on the experimental factors of their RNA-seq dataset.

Niche evolution, external circumstances, and network transformation

This article analyses the impact of external factors on niche evolution and, in particular, the change from a technical niche into a socio-technical niche. When we review the literature on niche evolution, we find that discussions on the impact of external factors on niche evolution are not clear, particularly, on new financial sponsors’ expectations. Therefore, this paper attempts to answer the following research question: Do changes in public financial resources contribute to transforming a technical niche into a socio-technical niche? We analysed an agricultural innovation niche case based on Butiá Native Fruits (e.g. Butiá odorata and others species), developed mainly by Temperate Climate Brazilian Agricultural Research Corporation (EMBRAPA) to understand whether and how external factors might contribute to an evolution of a niche. We found that new financial sponsors’ expectations can cause an important change in the evolution of a niche. Before the existence of a new external finance sponsor, the technical network niche was composed of research organisations and researchers working on isolated projects. However, after a new external finance sponsor was found, the network or organisations moved into experimental activities, upscaling, and outscaling, and began to incorporate multilevel organisations and people. Consequently, a more complex, coordinated organisation was created that incorporated social co-production, democracy, and participation, and the niche progressed towards a socio-technical niche.