scholarly journals Research on the Computational Prediction of Essential Genes

2021 ◽  
Vol 9 ◽  
Author(s):  
Yuxin Guo ◽  
Ying Ju ◽  
Dong Chen ◽  
Lihong Wang
Keyword(s):  
Genetic Testing ◽  
Essential Gene ◽  
Prediction Method ◽  
Computational Prediction ◽  
Essential Genes ◽  
Blood Type ◽  
Practical Significance ◽  
Biological Traits ◽  
Genome Database ◽  
Wide Range

Genes, the nucleotide sequences that encode a polypeptide chain or functional RNA, are the basic genetic unit controlling biological traits. They are the guarantee of the basic structures and functions in organisms, and they store information related to biological factors and processes such as blood type, gestation, growth, and apoptosis. The environment and genetics jointly affect important physiological processes such as reproduction, cell division, and protein synthesis. Genes are related to a wide range of phenomena including growth, decline, illness, aging, and death. During the evolution of organisms, there is a class of genes that exist in a conserved form in multiple species. These genes are often located on the dominant strand of DNA and tend to have higher expression levels. The protein encoded by it usually either performs very important functions or is responsible for maintaining and repairing these essential functions. Such genes are called persistent genes. Among them, the irreplaceable part of the body’s life activities is the essential gene. For example, when starch is the only source of energy, the genes related to starch digestion are essential genes. Without them, the organism will die because it cannot obtain enough energy to maintain basic functions. The function of the proteins encoded by these genes is thought to be fundamental to life. Nowadays, DNA can be extracted from blood, saliva, or tissue cells for genetic testing, and detailed genetic information can be obtained using the most advanced scientific instruments and technologies. The information gained from genetic testing is useful to assess the potential risks of disease, and to help determine the prognosis and development of diseases. Such information is also useful for developing personalized medication and providing targeted health guidance to improve the quality of life. Therefore, it is of great theoretical and practical significance to identify important and essential genes. In this paper, the research status of essential genes and the essential genome database of bacteria are reviewed, the computational prediction method of essential genes based on communication coding theory is expounded, and the significance and practical application value of essential genes are discussed.

scholarly journals R1352Q CACNA1A Variant in a Patient with Sporadic Hemiplegic Migraine, Ataxia, Seizures and Cerebral Oedema: A Case Report

2021 ◽  
pp. 123-130
Author(s):  
Anker Stubberud ◽  
Emer O’Connor ◽  
Erling Tronvik ◽  
Henry Houlden ◽  
Manjit Matharu
Keyword(s):  
Mental Retardation ◽  
Case Report ◽  
Genetic Testing ◽  
Head Trauma ◽  
Cerebral Oedema ◽  
De Novo ◽  
Minor Head Trauma ◽  
Hemiplegic Migraine ◽  
Wide Range ◽  
History Of

Mutations in the <i>CACNA1A</i> gene show a wide range of neurological phenotypes including hemiplegic migraine, ataxia, mental retardation and epilepsy. In some cases, hemiplegic migraine attacks can be triggered by minor head trauma and culminate in encephalopathy and cerebral oedema. A 37-year-old male without a family history of complex migraine experienced hemiplegic migraine attacks from childhood. The attacks were usually triggered by minor head trauma, and on several occasions complicated with encephalopathy and cerebral oedema. Genetic testing of the proband and unaffected parents revealed a de novo heterozygous nucleotide missense mutation in exon 25 of the <i>CACNA1A</i> gene (c.4055G&#x3e;A, p.R1352Q). The R1352Q <i>CACNA1A</i> variant shares the phenotype with other described <i>CACNA1A</i> mutations and highlights the interesting association of trauma as a precipitant for hemiplegic migraine. Subjects with early-onset sporadic hemiplegic migraine triggered by minor head injury or associated with seizures, ataxia or episodes of encephalopathy should be screened for mutations. These patients should also be advised to avoid activities that may result in head trauma, and anticonvulsants should be considered as prophylactic migraine therapy.

scholarly journals Tribological Aspects, Optimization and Analysis of Cu-B-CrC Composites Fabricated by Powder Metallurgy

Materials ◽  
2021 ◽  
Vol 14 (15) ◽  
pp. 4217
Author(s):  
Üsame Ali Usca ◽  
Mahir Uzun ◽  
Mustafa Kuntoğlu ◽  
Serhat Şap ◽  
Khaled Giasin ◽  
...  
Keyword(s):  
Weight Loss ◽  
Wear Rate ◽  
Coefficient Of Friction ◽  
Applied Load ◽  
Practical Significance ◽  
Tribological Characteristics ◽  
M 10 ◽  
Wide Range ◽  
The Coefficient Of Friction ◽  
Four Levels

Tribological properties of engineering components are a key issue due to their effect on the operational performance factors such as wear, surface characteristics, service life and in situ behavior. Thus, for better component quality, process parameters have major importance, especially for metal matrix composites (MMCs), which are a special class of materials used in a wide range of engineering applications including but not limited to structural, automotive and aeronautics. This paper deals with the tribological behavior of Cu-B-CrC composites (Cu-main matrix, B-CrC-reinforcement by 0, 2.5, 5 and 7.5 wt.%). The tribological characteristics investigated in this study are the coefficient of friction, wear rate and weight loss. For this purpose, four levels of sliding distance (1000, 1500, 2000 and 2500 m) and four levels of applied load (10, 15, 20 and 25 N) were used. In addition, two levels of sliding velocity (1 and 1.5 m/s), two levels of sintering time (1 and 2 h) and two sintering temperatures (1000 and 1050 °C) were used. Taguchi’s L16 orthogonal array was used to statistically analyze the aforementioned input parameters and to determine their best levels which give the desired values for the analyzed tribological characteristics. The results were analyzed by statistical analysis, optimization and 3D surface plots. Accordingly, it was determined that the most effective factor for wear rate, weight loss and friction coefficients is the contribution rate. According to signal-to-noise ratios, optimum solutions can be sorted as: the highest levels of parameters except for applied load and reinforcement ratio (2500 m, 10 N, 1.5 m/s, 2 h, 1050 °C and 0 wt.%) for wear rate, certain levels of all parameters (1000 m, 10 N, 1.5 m/s, 2 h, 1050 °C and 2.5 wt.%) for weight loss and 1000 m, 15 N, 1 m/s, 1 h, 1000 °C and 0 wt.% for the coefficient of friction. The comprehensive analysis of findings has practical significance and provides valuable information for a composite material from the production phase to the actual working conditions.

scholarly journals An information theoretic approach to link prediction in multiplex networks

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Seyed Hossein Jafari ◽  
Amir Mahdi Abdolhosseini-Qomi ◽  
Masoud Asadpour ◽  
Maseud Rahgozar ◽  
Naser Yazdani
Keyword(s):  
Real World ◽  
Link Prediction ◽  
Large Scale ◽  
Similarity Measures ◽  
Prediction Method ◽  
General Purpose ◽  
Fast Method ◽  
Theoretic Approach ◽  
Multiplex Networks ◽  
Wide Range

AbstractThe entities of real-world networks are connected via different types of connections (i.e., layers). The task of link prediction in multiplex networks is about finding missing connections based on both intra-layer and inter-layer correlations. Our observations confirm that in a wide range of real-world multiplex networks, from social to biological and technological, a positive correlation exists between connection probability in one layer and similarity in other layers. Accordingly, a similarity-based automatic general-purpose multiplex link prediction method—SimBins—is devised that quantifies the amount of connection uncertainty based on observed inter-layer correlations in a multiplex network. Moreover, SimBins enhances the prediction quality in the target layer by incorporating the effect of link overlap across layers. Applying SimBins to various datasets from diverse domains, our findings indicate that SimBins outperforms the compared methods (both baseline and state-of-the-art methods) in most instances when predicting links. Furthermore, it is discussed that SimBins imposes minor computational overhead to the base similarity measures making it a potentially fast method, suitable for large-scale multiplex networks.

A novel way to purify recombinant baculoviruses by using bacmid

2009 ◽  
Vol 29 (2) ◽  
pp. 71-75 ◽  
Author(s):  
Wu-Jie Su ◽  
Wei-De Shen ◽  
Bing Li ◽  
Yan Wu ◽  
Guang Gao ◽  
...  
Keyword(s):  
Insect Cells ◽  
Nuclear Polyhedrosis Virus ◽  
Essential Gene ◽  
Essential Genes ◽  
Reading Frame ◽  
Recombinant Viruses ◽  
Recombinant Bacmid ◽  
Bmnpv Bacmid ◽  
Nuclear Polyhedrosis ◽  
Recombinant Bacmids

In the present study, we studied the feasibility of deleting essential genes in insect cells by using bacmid and purifying recombinant bacmid in Escherichia coli DH10B cells. To disrupt the orf4 (open reading frame 4) gene of BmNPV [Bm (Bombyx mori) nuclear polyhedrosis virus], a transfer vector was constructed and co-transfected with BmNPV bacmid into Bm cells. Three passages of viruses were carried out in Bm cells, followed by one round of purification. Subsequently, bacmid DNA was extracted and transformed into competent DH10B cells. A colony harbouring only orf4-disrupted bacmid DNA was identified by PCR. A mixture of recombinant (white colonies) and non-recombinant (blue colonies) bacmids were also transformed into DH10B cells. PCR with M13 primers showed that the recombinant and non-recombinant bacmids were separated after transformation. The result confirmed that purification of recombinant viruses could be carried out simply by transformation and indicated that this method could be used to delete essential genes. Orf4-disrupted bacmid DNA was extracted and transfected into Bm cells. Viable viruses were produced, showing that orf4 was not an essential gene.

scholarly journals Research on prediction method of S-wave velocity based on deep learning

2021 ◽  
Vol 2083 (4) ◽  
pp. 042065
Author(s):  
Guojie Yang ◽  
Shuhua Wang
Keyword(s):  
Deep Learning ◽  
Wave Velocity ◽  
Prediction Method ◽  
P Wave ◽  
Learning Technology ◽  
S Wave ◽  
Advantages And Disadvantages ◽  
Wave Prediction ◽  
Wide Range ◽  
Velocity Prediction

Abstract Aiming at the s-wave velocity prediction problem, based on the analysis of the advantages and disadvantages of the empirical formula method and the rock physics modeling method, combined with the s-wave velocity prediction principle, the deep learning method is introduced, and a deep learning-based logging s-wave velocity prediction method is proposed. This method uses a deep neural network algorithm to establish a nonlinear mapping relationship between reservoir parameters (acoustic time difference, density, neutron porosity, shale content, porosity) and s-wave velocity, and then applies it to the s-wave velocity prediction at the well point. Starting from the relationship between p-wave and s-wave velocity, the study explained the feasibility of applying deep learning technology to s-wave prediction and the principle of sample selection, and finally established a reliable s-wave prediction model. The model was applied to s-wave velocity prediction in different research areas, and the results show that the s-wave velocity prediction technology based on deep learning can effectively improve the accuracy and efficiency of s-wave velocity prediction, and has the characteristics of a wide range of applications. It can provide reliable s-wave data for pre-stack AVO analysis and pre-stack inversion, so it has high practical application value and certain promotion significance.

scholarly journals NetGenes: A database of essential genes predicted using features from interaction networks

2020 ◽  
Author(s):  
Vimaladhasan Senthamizhan ◽  
Balaraman Ravindran ◽  
Karthik Raman
Keyword(s):  
Prediction Models ◽  
Essential Gene ◽  
Gene Prediction ◽  
High Accuracy ◽  
Essential Genes ◽  
Interaction Networks ◽  
Functional Association ◽  
String Database ◽  
Feature Vectors ◽  
Link Type

AbstractEssential gene prediction models built so far are heavily reliant on sequence-based features and the scope of network-based features has been narrow. Previous work from our group demonstrated the importance of using network-based features for predicting essential genes with high accuracy. Here, we applied our approach for the prediction of essential genes to organisms from the STRING database and hosted the results in a standalone website. Our database, NetGenes, contains essential gene predictions for 2700+ bacteria predicted using features derived from STRING protein-protein functional association networks. Housing a total of 3.5M+ genes, NetGenes offers various features like essentiality scores, annotations and feature vectors for each gene. NetGenes is available at https://rbc-dsai.iitm.github.io/NetGenes/

Occurrence and Significance of Toxic Cyanobacteria in Southern Africa

1991 ◽  
Vol 23 (1-3) ◽  
pp. 175-180 ◽  
Author(s):  
W. E. Scott
Keyword(s):  
South Africa ◽  
Southern Africa ◽  
Single Species ◽  
Practical Significance ◽  
Toxic Species ◽  
Toxic Cyanobacteria ◽  
Cyanobacterial Species ◽  
Wide Range ◽  
Toxic Blooms ◽  
Different Parts

A comprehensive list is provided of more than forty cyanobacterial species and genera reported to have toxic properties. In South Africa the majority of animal poisonings since 1927 have been caused by a single species Microcystis aeruginosa. Although other toxic species also occur in southern Africa, to date they have been of little practical significance. The widespread distribution of M. aeruginosa throughout southern Africa indicates a tremendous potential for toxic blooms to develop with increasing eutrophication. Using HPLC techniques up to six different toxin variants have been quantified in natural blooms of M. aeruginosa collected in different parts of South Africa. The amounts and proportions of the different toxins in the different samples varied over a wide range. Several additional unidentified toxins were detected.

Implementation of the principles, standards and rules of international customs law: individual and overall levels

2021 ◽  
pp. 102-111
Author(s):  
Serhii Perepolkin
Keyword(s):  
International Law ◽  
Practical Significance ◽  
Clear Understanding ◽  
The European Union ◽  
Public Authorities ◽  
Customs Unions ◽  
Wide Range ◽  
And Control ◽  
Further Development

Purpose. The purpose of the study is to submit to the discussion of domestic international lawyers a proposal to introduce the use in scientific and educational works of the classification of the implementation of the principles, norms and standards of international customs law into two types: individual and overall. Methodology. In order to achieve the goal of the study, have been analyzed scientific approaches to understand the implementation of international law and the classification of its types. In article have been studied an Implementation articles developed under the auspices of the Customs Agreements Cooperation Council; recommendations and resolutions, conventions of the Member States of the European Union, current international agreements and other acts of Ukrainian legislation on customs matters. Results. In the article it was substantiated that individual implementation along with the states can be carried out also by separate customs territories which have full autonomy in the realization of foreign trade; customs unions; economic unions; international organizations and other participants in international customs relations. The joint implementation of the principles, norms, and standards of international customs law is carried out by two or more of its subjects simultaneously. To achieve this goal, the subjects of international customs law can use a wide range of law-making, organizational, coordination, information and control tools. Scientific novelty. It was proved that the classification of the implementation of principles, norms, and standards of international customs law into individual and overral, in contrast to its differentiation into domestic and international, most accurately reflects all types of subjects of international customs law capable of participating in such activities. Practical significance. The introduction of the classification of the implementation of principles, norms, and standards into individual and joint, will contribute to the further development of research in this area, as well as the development of a clear understanding of the implementation of officials of public authorities of Ukraine.

scholarly journals A Universal, Genomewide GuideFinder for CRISPR/Cas9 Targeting in Microbial Genomes

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Michelle Spoto ◽  
Changhui Guan ◽  
Elizabeth Fleming ◽  
Julia Oh
Keyword(s):  
Gene Function ◽  
Large Scale ◽  
Essential Gene ◽  
Bacterial Species ◽  
Bacterial Genome ◽  
Model Organisms ◽  
Design Parameters ◽  
Bacterial Genomes ◽  
Wide Range ◽  
User Friendly

ABSTRACT The CRISPR/Cas system has significant potential to facilitate gene editing in a variety of bacterial species. CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) represent modifications of the CRISPR/Cas9 system utilizing a catalytically inactive Cas9 protein for transcription repression and activation, respectively. While CRISPRi and CRISPRa have tremendous potential to systematically investigate gene function in bacteria, few programs are specifically tailored to identify guides in draft bacterial genomes genomewide. Furthermore, few programs offer open-source code with flexible design parameters for bacterial targeting. To address these limitations, we created GuideFinder, a customizable, user-friendly program that can design guides for any annotated bacterial genome. GuideFinder designs guides from NGG protospacer-adjacent motif (PAM) sites for any number of genes by the use of an annotated genome and FASTA file input by the user. Guides are filtered according to user-defined design parameters and removed if they contain any off-target matches. Iteration with lowered parameter thresholds allows the program to design guides for genes that did not produce guides with the more stringent parameters, one of several features unique to GuideFinder. GuideFinder can also identify paired guides for targeting multiplicity, whose validity we tested experimentally. GuideFinder has been tested on a variety of diverse bacterial genomes, finding guides for 95% of genes on average. Moreover, guides designed by the program are functionally useful—focusing on CRISPRi as a potential application—as demonstrated by essential gene knockdown in two staphylococcal species. Through the large-scale generation of guides, this open-access software will improve accessibility to CRISPR/Cas studies of a variety of bacterial species. IMPORTANCE With the explosion in our understanding of human and environmental microbial diversity, corresponding efforts to understand gene function in these organisms are strongly needed. CRISPR/Cas9 technology has revolutionized interrogation of gene function in a wide variety of model organisms. Efficient CRISPR guide design is required for systematic gene targeting. However, existing tools are not adapted for the broad needs of microbial targeting, which include extraordinary species and subspecies genetic diversity, the overwhelming majority of which is characterized by draft genomes. In addition, flexibility in guide design parameters is important to consider the wide range of factors that can affect guide efficacy, many of which can be species and strain specific. We designed GuideFinder, a customizable, user-friendly program that addresses the limitations of existing software and that can design guides for any annotated bacterial genome with numerous features that facilitate guide design in a wide variety of microorganisms.

scholarly journals Comparison of Prediction Methods for Axial Strength of Grouted Connections with Shear Keys

2020 ◽  
Vol 10 (6) ◽  
pp. 1942
Author(s):  
You Xianhui ◽  
Wu Zhaoqi ◽  
Chen Zehao
Keyword(s):  
Health And Safety ◽  
Prediction Method ◽  
American Petroleum Institute ◽  
Experimental Results ◽  
Offshore Wind ◽  
Prediction Methods ◽  
Compression Tests ◽  
Axial Strength ◽  
Wide Range ◽  
Shear Keys

Grouted connections are commonly used in marine engineering, especially on oil platforms, cross-sea bridges, and offshore wind power turbines. The prediction methods for axial carrying capacity of grouted connections with shear keys and their application ranges in current codes were analyzed in this paper. The calculated results by using different codes were compared based on a practical grouted connection between steel piles and the jacket foundation of a wind turbine. The research team conducted axial compression tests on seven specimens, collected a wide range of experimental results to establish a database, and finally compared the standard calculation results with the experimental results. The study indicates that the axial strength of grouted connections predicted by different methods is distinct. The calculation formula of the British Health and Safety Executive (HSE, 2002) has obvious limitations; specifically, with increased shear keys, strength is overestimated, resulting in insecure design outcome of structures. The results calculated by the Norwegian Det Norske Veritas (DNV, 2013) are generally consistent with the experimental results, in which the reduction effect of multiple shear keys was considered. The prediction method of the American Petroleum Institute (API, 2007), which undervalues the bearing performance of connections, is excessively conservative. The method of the combined Norwegian and German Det Norske Veritas–Germanischer Lloyd (DNV-GL, 2016) has wider applicability and is safe, reliable, and economical.

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