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.

Research on Structural Flexibility and Acceptance Model (SFAM) Reconstruction Based on Disruption Innovation in the Social Humanities and Education Sector

The research objectives are as follows: (1) Developing a flexible structural model of the relationship between variables. (2) Develop a structural model that is robust with the assumptions of normality and homoscedasticity. (3) Obtain estimator properties from the flexible and robust SFAM structural model. (4) Obtaining hypothesis testing of each relationship constructed from a flexible and robust SFAM structural model. This research is integrated with a flexible and robust model approach based on nonparametric smoothing spline (RNSS) regression analysis which can capture the form of relationships that depend on empirical data, and the robustness of the model based on the distribution assumption and the assumption of homoscedasticity error variance. There are at least three transformation methods, namely SRS, MSI, and RASCH, which will be used in the development of the Structural Flexibility and Acceptance Model (SFAM). The results obtained from the research progress report are obtaining the development of a flexible structural model of the form of the relationship between variables, obtaining the development of a robust structural model of the assumptions of normality and homoscedasticity, obtaining the estimator properties of the flexible and robust SFAM structural model, and obtaining hypothesis testing. of each relationship constructed from a flexible and robust SFAM structural model. The originality of the theory in this study is very visible in the discovery of a new model, namely SFAM which can accommodate several things, which are the weaknesses of several existing analysis tools such as reciprocal and recursive models, more than one endogenous variable, flexible and robust models, overcoming inadmissible solutions, reflective indicators, formative , and reflective/formative (on the second-order), metric and non-metric data, and simultaneous processing of the input score data (through transformation to scale).

Heat Transfer in Biological Spherical Tissues during Hyperthermia of Magnetoma

Hyperthermia therapy is now being used to treat cancer. However, understanding the pattern of temperature increase in biological tissues during hyperthermia treatment is essential. In recent years, many physicians and engineers have studied the use of computational and mathematical models of heat transfer in biological systems. The rapid progress in computing technology has intrigued many researchers. Many medical procedures also use engineering techniques and mathematical modeling to ensure their safety and assess the risks involved. One such model is the modified Pennes bioheat conduction equation. This paper provides an analytical solution to the modified Pennes bioheat conduction equation with a single relaxation time by incorporating in it the (MGT) equation. The suggested model examines heat transport in biological tissues as forming an infinite concentric spherical region during magnetic fluid hyperthermia. To investigate thermal reactions caused by temperature shock, specifically the influence of heat generation through heat treatment on a skin tumor [AEGP9], the Laplace transformation, and numerical inverse transformation methods are used. This model was able to explain the effects of different therapeutic approaches such as cryotherapy sessions, laser therapy, and physical occurrences, transfer, metabolism support, and blood perfusion. Comparison of the numerical results of the suggested model with those in the literature confirmed the validity of the model’s numerical results.

Evaluation of Compilers’ Capability of Automatic Vectorization Based on Source Code Analysis

Automatic vectorization is an important technique for compilers to improve the parallelism of programs. With the widespread usage of SIMD (Single Instruction Multiple Data) extensions in modern processors, automatic vectorization has become a hot topic in the research of compiler techniques. Accurately evaluating the effectiveness of automatic vectorization in typical compilers is quite valuable for compiler optimization and design. This paper evaluates the effectiveness of automatic vectorization, analyzes the limitation of automatic vectorization and the main causes, and improves the automatic vectorization technology. This paper firstly classifies the programs by two main factors: program characteristics and transformation methods. Then, it evaluates the effectiveness of automatic vectorization in three well-known compilers (GCC, LLVM, and ICC, including their multiple versions in recent 5 years) through TSVC (Test Suite for Vectorizing Compilers) benchmark. Furthermore, this paper analyzes the limitation of automatic vectorization based on source code analysis, and introduces the differences between academic research and engineering practice in automatic vectorization and the main causes, Finally, it gives some suggestions as to how to improve automatic vectorization capability.

Research on Green Transformation of Campus Sponge and Energy Saving Facilities on Sloping Land

Based on the renovation of sponge and energy-saving facilities in a middle school in Nanning, this paper systematically studies the overall elevation of the campus, the composition of the drainage system and the layout of space functions, and formulates a characteristic scheme for the renovation of sponge and energy-saving facilities according to the characteristics of the sloping campus. In order to control the total amount of rainwater runoff, the sponge transformation mainly adopts the transformation methods of partition catchment, upper storage and lower use, multi-stage detection and classification treatment. For the purpose of solar energy and wind energy utilization, solar photovoltaic panels and small-scale wind power generation system are adopted. The application effects of sponge and energy-saving facilities are estimated and evaluated.

Метод непрямого приховування інформації в процесі стиснення відеозображень

It is substantiated that steganographic systems should be used to ensure the protection of special information resources in conditions of its prompt delivery. Here, steganographic technologies are an integral part of complex information protection systems. Simultaneously, for steganographic systems, there is a contradiction between the density of embedded data and level of information compaction of video container (level of reduction of volume bit volume of compact presented video image concerning bit volume of an initial video image). It leads to the fact that under the conditions of the required quality (reliability) of digital video information, the bit rate level of the covert channel is insufficient. Consequently, the scientific-applied problem concerns the necessity to increase the integrity (the level of correspondence of the hidden information before its embedding in a video container and after its extraction) and bit rate of the hidden channel of special information transmission. It is relevant. The solution of the described problem in the field of application of steganographic transformations can be realized based on the application of two different approaches. The first approach is based on methods of direct message embedding. But this approach is characterized by introducing distortions in the video images used as a container. Therefore, changes in structural and statistical patterns in the syntactic description of the video container happen. It reduces the potential for video container compaction. The second approach to creating steganographic transformation methods is based on information hiding using indirect embedding technique. Here, the embedding process exploits the functional dependency between the elements of the video container and the elements of the embedded message. Setting a specific dependency between the elements in the video container corresponds to the embedded element with a value of "0" or "1". However, the existing indirect steganographic transformation methods have a disadvantage. It consists of an insufficient value of embedded data density. To eliminate these disadvantages, it is proposed to develop an approach that allows using not only psychovisual but also structural redundancy of video container for concealment. Therefore, the research objective of this paper is to develop a method for indirect information withholding in the video container compression process to increase the bit rate of the hidden message channel. In the process of research, a steganographic multiagent system is constructed, which allows embedding hidden message elements without loss of information based on the indirect approach by modifying the active bases of the multiagent basis considering their uncertainty. To select transformants (data sets) as containers for information embedding, the requirement of the existence of a base system with all active bases is taken into account. The number of embedded bits of the hidden message is equal to the number of active bases in the base system of the multiadic space. Because of the made experiments, the following results have been received: in the process of embedding messages based on the created method distortions in a video container is not brought; for the created method the additional increase in the hidden channel bit rate in average 5 … 7 times are reached.

Utilizing CRISPR-Cas in Tropical Crop Improvement: A Decision Process for Fitting Genome Engineering to Your Species

Adopting modern gene-editing technologies for trait improvement in agriculture requires important workflow developments, yet these developments are not often discussed. Using tropical crop systems as a case study, we describe a workflow broken down into discrete processes with specific steps and decision points that allow for the practical application of the CRISPR-Cas gene editing platform in a crop of interest. While we present the steps of developing genome-edited plants as sequential, in practice parts can be done in parallel, which are discussed in this perspective. The main processes include 1) understanding the genetic basis of the trait along with having the crop’s genome sequence, 2) testing and optimization of the editing reagents, development of efficient 3) tissue culture and 4) transformation methods, and 5) screening methods to identify edited events with commercial potential. Our goal in this perspective is to help any lab that wishes to implement this powerful, easy-to-use tool in their pipeline, thus aiming to democratize the technology.

Genetic Transformation of Apomictic Grasses: Progress and Constraints

The available methods for plant transformation and expansion beyond its limits remain especially critical for crop improvement. For grass species, this is even more critical, mainly due to drawbacks in in vitro regeneration. Despite the existence of many protocols in grasses to achieve genetic transformation through Agrobacterium or biolistic gene delivery, their efficiencies are genotype-dependent and still very low due to the recalcitrance of these species to in vitro regeneration. Many plant transformation facilities for cereals and other important crops may be found around the world in universities and enterprises, but this is not the case for apomictic species, many of which are C4 grasses. Moreover, apomixis (asexual reproduction by seeds) represents an additional constraint for breeding. However, the transformation of an apomictic clone is an attractive strategy, as the transgene is immediately fixed in a highly adapted genetic background, capable of large-scale clonal propagation. With the exception of some species like Brachiaria brizantha which is planted in approximately 100 M ha in Brazil, apomixis is almost non-present in economically important crops. However, as it is sometimes present in their wild relatives, the main goal is to transfer this trait to crops to fix heterosis. Until now this has been a difficult task, mainly because many aspects of apomixis are unknown. Over the last few years, many candidate genes have been identified and attempts have been made to characterize them functionally in Arabidopsis and rice. However, functional analysis in true apomictic species lags far behind, mainly due to the complexity of its genomes, of the trait itself, and the lack of efficient genetic transformation protocols. In this study, we review the current status of the in vitro culture and genetic transformation methods focusing on apomictic grasses, and the prospects for the application of new tools assayed in other related species, with two aims: to pave the way for discovering the molecular pathways involved in apomixis and to develop new capacities for breeding purposes because many of these grasses are important forage or biofuel resources.

The reengineering of built-up areas: structure and composition

Introduction. Engineering solutions of construction facilities are becoming obsolete due to the impact of scientific and technological progress, changes in consumer needs and production capabilities of the construction industry. A gap between consumer needs and characteristics of construction products is bridged by updating, modernizing, retrofitting and transforming design solutions. Materials and methods. The subject of the study is capital construction facilities that have various functional purposes: they structure built-up urban areas (space planning), whose urban planning solutions need reengineering in the course of operation. The article considers the list of capital construction entities that include industrial facilities (manufacturing, agricultural, and communication facilities), non-industrial facilities (public buildings, residential housing) and linear objects (overpasses, pipelines, power grids). Functional, planning, structural, organizational and technological features of capital construction facilities, features of vital processes, production and technological procedures, that are underway inside them, determine the characteristic differences in the composition and structure of construction reengineering. Structural and functional analysis is the research method of the study. Results. The composition of actions and methods used to reengineer residential and industrial buildings, areas occupied by the engineering and transport infrastructure is described. The article presents changes introduced by reengineering actions with regard for the features of facilities that structure urban development. The co-authors acknowledge that the structure and composition of construction reengineering are highly variable, and their variability is determined by the types of built-up areas and their transformation methods. This dependence impacts a combination of reengineering actions, including those that determine the nature of transformation and supplement the principal change. The research results allow to develop reengineering process organization charts and outline the resource provision process.