A new method for the evaluation of vaccine safety based on comprehensive gene expression analysis.
Ontology highlight
ABSTRACT:
SUBMITTER: Momose H
PROVIDER: S-EPMC2896671 | biostudies-literature | 2010
REPOSITORIES: biostudies-literature
Publications
A new method for the evaluation of vaccine safety based on comprehensive gene expression analysis.
Momose Haruka H Mizukami Takuo T Ochiai Masaki M Hamaguchi Isao I Yamaguchi Kazunari K
Journal of biomedicine & biotechnology 20100613
For the past 50 years, quality control and safety tests have been used to evaluate vaccine safety. However, conventional animal safety tests need to be improved in several aspects. For example, the number of test animals used needs to be reduced and the test period shortened. It is, therefore, necessary to develop a new vaccine evaluation system. In this review, we show that gene expression patterns are well correlated to biological responses in vaccinated rats. Our findings and methods using ex ...[more]
Similar Datasets
Project description:In recent years, with the increasingly popular and openness of Geoparks, Environmental safety has become a major concern for sustainable geo-tourism. It is therefore necessary to conduct an environmental safety performance evaluation for promoting geo-tourism development. In order to identify and figure out the factors influencing the tourists' environmental safety perception, an index system was established based on six principles of Crime Prevention Through environment design (CPTED) theory. A Questionnaire was adopted for data collection, and the overall evaluation value and concrete index scores at all levels were obtained via the fuzzy comprehensive analysis and Importance-Performance analysis. Empirical results show that: (1) tourists' perception of environmental safety performance in Shilin Park from high to low was: image and maintenance, Natural Surveillance, territoriality, Access control, Activity support and target hardening; (2) The sub-factors influencing tourists' safety perception mostly include electronic monitoring device, Lighting system, Public safety management, Road layout, environmental sanitation; While attention should be paid on the following aspects including park service center, inter-personal surveillance, surrounding environment, unobstructed view, parking lot, Signpost, for they are considered as high-importance items with relatively poor performance. Based on the analysis, three optimization measures were proposed, including optimizing the layout and design of each space, strengthening the deterrent force of the park and maintaining a good environmental image. This research provides useful suggestions for Geopark decision-makers on determining the priority of Geopark spatial planning and management, as well as achieving the optimal allocation of resources to promote the sustainable development of Geopark.
| S-EPMC8608292 | biostudies-literature
Project description:Water conservation is an important service function of ecosystems. A timely understanding of dynamic changes in the water conservation function is important for the protection and reconstruction of water resources. Based on remote sensing data, meteorological data, land cover data, and the "Technical Criterion for Ecosystem Status Evaluation" issued by the Ministry of Environmental Protection of the People's Republic of China, a comprehensive evaluation system was designed to assess the water conservation function of the Xiongan New Area from 2005 to 2015. The system created from four aspects, including ecological structure, ecological stress, water balance and landscape ecology. The results showed that from 2005 to 2015, the water conservation function of the Xiongan New Area first decreased and then increased, and the overall trend was upward. The increasing areas were mainly concentrated around Baiyangdian and near the grassland. Among all evaluated indicators, the precipitation compliance rate index fluctuated the most from -16.62 in 2010 to 6.70 in 2015. The evapotranspiration index was the largest in 2010 (6.47) and the smallest in 2005 (3.52). The Temperature Vegetation Dryness Index (TVDI) showed that the drought was the severest in 2010 and the least severe in 2015. However, the other indicators remain relatively stable. From the perspective of the spatial distribution, the water conservation function of the Xiongan New Area was gradually enhanced from north to south.
| S-EPMC7482998 | biostudies-literature
Project description:A large number of computational methods have been developed for analyzing differential gene expression in RNA-seq data. We describe a comprehensive evaluation of common methods using the SEQC benchmark dataset and ENCODE data. We consider a number of key features, including normalization, accuracy of differential expression detection and differential expression analysis when one condition has no detectable expression. We find significant differences among the methods, but note that array-based methods adapted to RNA-seq data perform comparably to methods designed for RNA-seq. Our results demonstrate that increasing the number of replicate samples significantly improves detection power over increased sequencing depth.
| S-EPMC4054597 | biostudies-literature
Project description:This study focuses on a safety evaluation method for underground gas storage. Gas storage is usually constructed underground in complex environments, and the service life of such facilities is limited. To ensure the secure and long-term operation of gas storage facilities, safety evaluation has become the focus of management. The present paper provides an effective method for safety evaluation. An index system was established as the foundation of the analysis for this evaluation, and the matter-element extension method was applied to obtain a quantitative evaluation result. For the weight values of each index in the matter-element extension method, this paper presents a comprehensive weight computation method based on vague sets and entropy. By application of this method, the safety level of a gas storage facility in the Jintan salt mines (in Jiangsu, China) was calculated, and the evaluation result was 4.6433, which meant the safety level was V and the underground gas storage was slightly at risk. It indicated that the influence on the overall safety and tightness of this gas storage could be ignored in the operation process, but the frequency of regular monitoring should be increased. The defective indexes were also obtained, such as salt rock cohesion, the roof thickness, the volume contraction ratio, the interlayer content, the height of the casing shoe and the adjacent cavity pressure difference, which need to be monitored and modified. This paper evaluated the safety of the underground gas storage from a unique perspective. It is expected that the results of this research will contribute to the maintenance and operational decisions, and provide a reference for management in the energy industry.
| S-EPMC7211865 | biostudies-literature
Project description:A more accurate prognosis for non-small-cell lung cancer (NSCLC) patients could aid in the identification of patients at high risk for recurrence. Many NSCLC mRNA expression signatures claiming to be prognostic have been reported in the literature. The goal of this study was to identify the most promising mRNA prognostic signatures in NSCLC for further prospective clinical validation.We carried out a systematic review and meta-analysis of published mRNA prognostic signatures for resected NSCLC. The prognostic performance of each signature was evaluated via a meta-analysis of 1927 early stage NSCLC patients collected from 15 studies using three evaluation metrics (hazard ratios, concordance scores, and time-dependent receiver-operating characteristic curves). The performance of each signature was then evaluated against 100 random signatures. The prognostic power independent of clinical risk factors was assessed by multivariate Cox models.Through a literature search, we identified 42 lung cancer prognostic signatures derived from genome-wide expression profiling analysis. Based on meta-analysis, 25 signatures were prognostic for survival after adjusting for clinical risk factors and 18 signatures carried out significantly better than random signatures. When analyzing histology types separately, 17 signatures and 8 signatures are prognostic for adenocarcinoma and squamous cell lung cancer, respectively. Despite little overlap among published gene signatures, the top-performing signatures are highly concordant in predicted patient outcomes.Based on this large-scale meta-analysis, we identified a set of mRNA expression prognostic signatures appropriate for further validation in prospective clinical studies.
| S-EPMC5834090 | biostudies-other
Project description:An online evaluation method of coal mine comprehensive level based on Fuzzy Comprehensive Evaluation method (FCE) is proposed. Firstly, following the principles of fairness, systematicness and hierarchy, taking research and development, production, sales, finance, safety and management as the first level indicators, a set of multi-level evaluation indicator system of coal mine comprehensive level combining objective and subjective evaluation indicators is established. Secondly, according to the characteristics of the indicator system, the specific process of FCE of coal mine comprehensive level is given. Then, taking SQL Server as the database management system and C#.NET as the development language, a set of B/S structure online evaluation system of coal mine comprehensive level based on FCE is designed and developed. Finally, the proposed method is applied to Coal group PM for test. The application shows that the method proposed can provide an efficient and convenient online evaluation platform to evaluate the comprehensive level of coal mines for the Coal group, and the horizontal and longitudinal comparison of the evaluation results can urge the coal mines to maintain their advantages and avoid their disadvantages, which is of some significance for improving the overall competitiveness of the Coal group.
| S-EPMC8366963 | biostudies-literature
Project description:BACKGROUND: Clustering-based methods on gene-expression analysis have been shown to be useful in biomedical applications such as cancer subtype discovery. Among them, Matrix factorization (MF) is advantageous for clustering gene expression patterns from DNA microarray experiments, as it efficiently reduces the dimension of gene expression data. Although several MF methods have been proposed for clustering gene expression patterns, a systematic evaluation has not been reported yet. RESULTS: Here we evaluated the clustering performance of orthogonal and non-orthogonal MFs by a total of nine measurements for performance in four gene expression datasets and one well-known dataset for clustering. Specifically, we employed a non-orthogonal MF algorithm, BSNMF (Bi-directional Sparse Non-negative Matrix Factorization), that applies bi-directional sparseness constraints superimposed on non-negative constraints, comprising a few dominantly co-expressed genes and samples together. Non-orthogonal MFs tended to show better clustering-quality and prediction-accuracy indices than orthogonal MFs as well as a traditional method, K-means. Moreover, BSNMF showed improved performance in these measurements. Non-orthogonal MFs including BSNMF showed also good performance in the functional enrichment test using Gene Ontology terms and biological pathways. CONCLUSIONS: In conclusion, the clustering performance of orthogonal and non-orthogonal MFs was appropriately evaluated for clustering microarray data by comprehensive measurements. This study showed that non-orthogonal MFs have better performance than orthogonal MFs and K-means for clustering microarray data.
| S-EPMC3278848 | biostudies-other
Project description:Non-muscle invasive bladder cancer (NMIBC) patients often have fewer treatment options, and suffer the progression of disease due to mechanisms that are not clear, as well as due to its diversity. This study was designed to explore the molecular mechanism of bladder cancer through an RNA-seq. In addition to conventional analyses, we also simplified the network through modularization using the WGCNA algorithm, with the help of the topological overlapping matrix and hierarchical cluster tree, which are based on the PPI network of STRING. Furthermore, the hub genes were confirmed through survival analyses in the independent cohorts (n = 431). Among them, 15 genes were significantly associated with poor prognosis. Finally, we validated the results at mRNA and protein level using qRT-PCR, IHC and western blotting. Taken together, our research is important for the prediction, as well as the prospective clinical development of drug targets and biomarkers.
| S-EPMC6604748 | biostudies-literature
Project description:BackgroundDiabetic nephropathy (DN) is the major complication of diabetes mellitus, and leading cause of end-stage renal disease. The underlying molecular mechanism of DN is not yet completely clear. The aim of this study was to analyze a DN microarray dataset using weighted gene co-expression network analysis (WGCNA) algorithm for better understanding of DN pathogenesis and exploring key genes in the disease progression.MethodsThe identified differentially expressed genes (DEGs) in DN dataset GSE47183 were introduced to WGCNA algorithm to construct co-expression modules. STRING database was used for construction of Protein-protein interaction (PPI) networks of the genes in all modules and the hub genes were identified considering both the degree centrality in the PPI networks and the ranked lists of weighted networks. Gene ontology and Reactome pathway enrichment analyses were performed on each module to understand their involvement in the biological processes and pathways. Following validation of the hub genes in another DN dataset (GSE96804), their up-stream regulators, including microRNAs and transcription factors were predicted and a regulatory network comprising of all these molecules was constructed.ResultsAfter normalization and analysis of the dataset, 2475 significant DEGs were identified and clustered into six different co-expression modules by WGCNA algorithm. Then, DEGs of each module were subjected to functional enrichment analyses and PPI network constructions. Metabolic processes, cell cycle control, and apoptosis were among the top enriched terms. In the next step, 23 hub genes were identified among the modules in genes and five of them, including FN1, SLC2A2, FABP1, EHHADH and PIPOX were validated in another DN dataset. In the regulatory network, FN1 was the most affected hub gene and mir-27a and REAL were recognized as two main upstream-regulators of the hub genes.ConclusionsThe identified hub genes from the hearts of co-expression modules could widen our understanding of the DN development and might be of targets of future investigations, exploring their therapeutic potentials for treatment of this complicated disease.
| S-EPMC8252307 | biostudies-literature
Project description:BackgroundThe recent advances in next generation sequencing technology have made the sequencing of RNA (i.e., RNA-Seq) an extemely popular approach for gene expression analysis. Identification of significant differential expression represents a crucial initial step in these analyses, on which most subsequent inferences of biological functions are built. Yet, for identification of these subsequently analysed genes, most studies use an additional minimal threshold of differential expression that is not captured by the applied statistical procedures.ResultsHere we introduce a new analysis approach, ABSSeq, which uses a negative binomal distribution to model absolute expression differences between conditions, taking into account variations across genes and samples as well as magnitude of differences. In comparison to alternative methods, ABSSeq shows higher performance on controling type I error rate and at least a similar ability to correctly identify differentially expressed genes.ConclusionsABSSeq specifically considers the overall magnitude of expression differences, which enhances the power in detecting truly differentially expressed genes by reducing false positives at both very low and high expression level. In addition, ABSSeq offers to calculate shrinkage of fold change to facilitate gene ranking and effective outlier detection.
| S-EPMC4973090 | biostudies-literature