Protein-Protein Interactions (PPI) via Deep Neural Network (DNN)

2022 ◽  
pp. 154-176
Author(s):  
Zizhe Gao ◽  
Hao Lin
Keyword(s):  
Neural Network ◽  
Protein Interactions ◽  
Rapid Development ◽  
Biological Research ◽  
Data Sets ◽  
Biological Interactions ◽  
Protein Protein Interactions ◽  
H Pylori ◽  
The Impact ◽  
Significant Health

Entering the 21st century, computer science and biological research have entered a stage of rapid development. With the rapid inflow of capital into the field of significant health research, a large number of scholars and investors have begun to focus on the impact of neural network science on biometrics, especially the study of biological interactions. With the rapid development of computer technology, scientists improve or perfect traditional experimental methods. This chapter aims to prove the reliability of the methodology and computing algorithms developed by Satyajit Mahapatra and Ivek Raj Gupta's project team. In this chapter, three datasets take the responsibility to testify the computing algorithms, and they are S. cerevisiae, H. pylori, and Human-B. Anthracis. Among these three sets of data, the S. cerevisiae is the core subset. The result shows 87%, 87.5%, and 89% accuracy and 87%, 86%, and 87% precision for these three data sets, respectively.

scholarly journals The evolution of gene duplicates in angiosperms and the impact of protein-protein interactions and the mechanism of duplication

2019 ◽  
Author(s):  
Jonas Defoort ◽  
Yves Van de Peer ◽  
Lorenzo Carretero-Paulet
Keyword(s):  
Protein Interactions ◽  
Specific Property ◽  
Small Scale ◽  
Biological Interactions ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
Functional Dynamics ◽  
Dosage Balance ◽  
Gene Duplicates ◽  
The Impact

Abstract Gene duplicates, generated either through whole genome duplication (WGD) or small-scale duplication (SSD), are prominent in angiosperms and are believed to play an important role in adaptation and in generating evolutionary novelty. Previous studies reported contrasting evolutionary and functional dynamics of duplicate genes depending on the mechanism of origin, a behaviour that is hypothesized to stem from constraints to maintain the relative dosage balance between the genes concerned and their interaction context. However, the mechanisms ultimately influencing loss and retention of gene duplicates over evolutionary time are not yet fully elucidated. Here, by using a robust classification of gene duplicates in Arabidopsis thaliana, Solanum lycopersicum and Zea mays, large RNAseq expression compendia and an extensive protein-protein interaction (PPI) network from Arabidopsis, we investigated the impact of PPIs on the differential evolutionary and functional fate of WGD and SSD duplicates. In all three species, retained WGD duplicates show stronger constraints to diverge at the sequence and expression level than SSD ones, a pattern that is also observed for shared PPI partners between Arabidopsis duplicates. PPIs are preferentially distributed among WGD duplicates and specific functional categories. Furthermore, duplicates with PPIs tend to be under stronger constraints to evolve than their counterparts without PPIs regardless of their mechanism of origin. Our results support dosage balance constraint as a specific property of genes involved in biological interactions, including physical PPIs, and suggest that additional factors may be differently influencing the evolution of genes following duplication, depending on the species, time and mechanism of origin.

Research on behavior recognition based on feature fusion of automatic coder and recurrent neural network

2020 ◽  
Vol 39 (6) ◽  
pp. 8927-8935
Author(s):  
Bing Zheng ◽  
Dawei Yun ◽  
Yan Liang
Keyword(s):  
Neural Network ◽  
Recurrent Neural Network ◽  
Behavior Pattern ◽  
Rapid Development ◽  
Video Data ◽  
Support Vector ◽  
Behavior Recognition ◽  
Learning Methods ◽  
The Impact ◽  
Internet Of Things Technology

Under the impact of COVID-19, research on behavior recognition are highly needed. In this paper, we combine the algorithm of self-adaptive coder and recurrent neural network to realize the research of behavior pattern recognition. At present, most of the research of human behavior recognition is focused on the video data, which is based on the video number. At the same time, due to the complexity of video image data, it is easy to violate personal privacy. With the rapid development of Internet of things technology, it has attracted the attention of a large number of experts and scholars. Researchers have tried to use many machine learning methods, such as random forest, support vector machine and other shallow learning methods, which perform well in the laboratory environment, but there is still a long way to go from practical application. In this paper, a recursive neural network algorithm based on long and short term memory (LSTM) is proposed to realize the recognition of behavior patterns, so as to improve the accuracy of human activity behavior recognition.

scholarly journals The Protein Interactome of Glycolysis in Escherichia coli

Proteomes ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 16
Author(s):  
Shomeek Chowdhury ◽  
Stephen Hepper ◽  
Mudassir K. Lodi ◽  
Milton H. Saier ◽  
Peter Uetz
Keyword(s):  
Escherichia Coli ◽  
Protein Interactions ◽  
Allosteric Regulation ◽  
Glycolytic Enzymes ◽  
Protein Protein Interactions ◽  
Post Translational Modification ◽  
Interacting Protein ◽  
E Coli ◽  
Protein Interactome ◽  
The Impact

Glycolysis is regulated by numerous mechanisms including allosteric regulation, post-translational modification or protein-protein interactions (PPI). While glycolytic enzymes have been found to interact with hundreds of proteins, the impact of only some of these PPIs on glycolysis is well understood. Here we investigate which of these interactions may affect glycolysis in E. coli and possibly across numerous other bacteria, based on the stoichiometry of interacting protein pairs (from proteomic studies) and their conservation across bacteria. We present a list of 339 protein-protein interactions involving glycolytic enzymes but predict that ~70% of glycolytic interactors are not present in adequate amounts to have a significant impact on glycolysis. Finally, we identify a conserved but uncharacterized subset of interactions that are likely to affect glycolysis and deserve further study.

scholarly journals Statistical Modeling and Prediction for Tourism Economy Using Dendritic Neural Network

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Ying Yu ◽  
Yirui Wang ◽  
Shangce Gao ◽  
Zheng Tang
Keyword(s):  
Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
Rapid Development ◽  
Seasonal Trend ◽  
Moving Averages ◽  
Forecasting Methods ◽  
Tourism Economy ◽  
The Impact ◽  
D Model

With the impact of global internationalization, tourism economy has also been a rapid development. The increasing interest aroused by more advanced forecasting methods leads us to innovate forecasting methods. In this paper, the seasonal trend autoregressive integrated moving averages with dendritic neural network model (SA-D model) is proposed to perform the tourism demand forecasting. First, we use the seasonal trend autoregressive integrated moving averages model (SARIMA model) to exclude the long-term linear trend and then train the residual data by the dendritic neural network model and make a short-term prediction. As the result showed in this paper, the SA-D model can achieve considerably better predictive performances. In order to demonstrate the effectiveness of the SA-D model, we also use the data that other authors used in the other models and compare the results. It also proved that the SA-D model achieved good predictive performances in terms of the normalized mean square error, absolute percentage of error, and correlation coefficient.

Swim-exercised mice show a decreased level of protein O-GlcNAcylation and expression of O-GlcNAc transferase in heart

2011 ◽  
Vol 111 (1) ◽  
pp. 157-162 ◽  
Author(s):  
Darrell D. Belke
Keyword(s):  
Protein Interactions ◽  
Contractile Function ◽  
Cell Physiology ◽  
Protein Protein Interactions ◽  
Training Exercise ◽  
General Protein ◽  
Exercise Induced ◽  
Glcnac Transferase ◽  
The Impact ◽  
Physiological Hypertrophy

Swim-training exercise in mice leads to cardiac remodeling associated with an improvement in contractile function. Protein O-linked N-acetylglucosamine ( O-GlcNAcylation) is a posttranslational modification of serine and threonine residues capable of altering protein-protein interactions affecting gene transcription, cell signaling pathways, and general cell physiology. Increased levels of protein O-GlcNAcylation in the heart have been associated with pathological conditions such as diabetes, ischemia, and hypertrophic heart failure. In contrast, the impact of physiological exercise on protein O-GlcNAcylation in the heart is currently unknown. Swim-training exercise in mice was associated with the development of a physiological hypertrophy characterized by an improvement in contractile function relative to sedentary mice. General protein O-GlcNAcylation was significantly decreased in swim-exercised mice. This effect was mirrored in the level of O-GlcNAcylation of individual proteins such as SP1. The decrease in protein O-GlcNAcylation was associated with a decrease in the expression of O-GlcNAc transferase (OGT) and glutamine-fructose amidotransferase (GFAT) 2 mRNA. O-GlcNAcase (OGA) activity was actually lower in swim-trained than sedentary hearts, suggesting that it did not contribute to the decreased protein O-GlcNAcylation. Thus it appears that exercise-induced physiological hypertrophy is associated with a decrease in protein O-GlcNAcylation, which could potentially contribute to changes in gene expression and other physiological changes associated with exercise.

scholarly journals A feature fusion deep-projection convolution neural network for vehicle detection in aerial images

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0250782
Author(s):  
Bin Wang ◽  
Bin Xu
Keyword(s):  
Neural Network ◽  
Feature Fusion ◽  
Rapid Development ◽  
Vehicle Detection ◽  
Convolution Neural Network ◽  
Aerial Images ◽  
Semantic Features ◽  
General Object ◽  
High Level ◽  
The Impact

With the rapid development of Unmanned Aerial Vehicles, vehicle detection in aerial images plays an important role in different applications. Comparing with general object detection problems, vehicle detection in aerial images is still a challenging research topic since it is plagued by various unique factors, e.g. different camera angle, small vehicle size and complex background. In this paper, a Feature Fusion Deep-Projection Convolution Neural Network is proposed to enhance the ability to detect small vehicles in aerial images. The backbone of the proposed framework utilizes a novel residual block named stepwise res-block to explore high-level semantic features as well as conserve low-level detail features at the same time. A specially designed feature fusion module is adopted in the proposed framework to further balance the features obtained from different levels of the backbone. A deep-projection deconvolution module is used to minimize the impact of the information contamination introduced by down-sampling/up-sampling processes. The proposed framework has been evaluated by UCAS-AOD, VEDAI, and DOTA datasets. According to the evaluation results, the proposed framework outperforms other state-of-the-art vehicle detection algorithms for aerial images.

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