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Academic literature on the topic 'CERNA NETWORK'

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Published: 11 September 2023

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Journal articles on the topic "CERNA NETWORK"

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Qi, Xin, Yuxin Lin, Jiajia Chen, and Bairong Shen. "Decoding competing endogenous RNA networks for cancer biomarker discovery." Briefings in Bioinformatics 21, no. 2 (January 30, 2019): 441–57. http://dx.doi.org/10.1093/bib/bbz006.

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Abstract Crosstalk between competing endogenous RNAs (ceRNAs) is mediated by shared microRNAs (miRNAs) and plays important roles both in normal physiology and tumorigenesis; thus, it is attractive for systems-level decoding of gene regulation. As ceRNA networks link the function of miRNAs with that of transcripts sharing the same miRNA response elements (MREs), e.g. pseudogenes, competing mRNAs, long non-coding RNAs, and circular RNAs, the perturbation of crucial interactions in ceRNA networks may contribute to carcinogenesis by affecting the balance of cellular regulatory system. Therefore, discovering biomarkers that indicate cancer initiation, development, and/or therapeutic responses via reconstructing and analyzing ceRNA networks is of clinical significance. In this review, the regulatory function of ceRNAs in cancer and crucial determinants of ceRNA crosstalk are firstly discussed to gain a global understanding of ceRNA-mediated carcinogenesis. Then, computational and experimental approaches for ceRNA network reconstruction and ceRNA validation, respectively, are described from a systems biology perspective. We focus on strategies for biomarker identification based on analyzing ceRNA networks and highlight the translational applications of ceRNA biomarkers for cancer management. This article will shed light on the significance of miRNA-mediated ceRNA interactions and provide important clues for discovering ceRNA network-based biomarker in cancer biology, thereby accelerating the pace of precision medicine and healthcare for cancer patients.
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Hsiao, Yi-Wen, Lin Wang, and Tzu-Pin Lu. "ceRNAR: An R package for identification and analysis of ceRNA-miRNA triplets." PLOS Computational Biology 18, no. 9 (September 9, 2022): e1010497. http://dx.doi.org/10.1371/journal.pcbi.1010497.

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Competitive endogenous RNA (ceRNA) represents a novel mechanism of gene regulation that controls several biological and pathological processes. Recently, an increasing number of in silico methods have been developed to accelerate the identification of such regulatory events. However, there is still a need for a tool supporting the hypothesis that ceRNA regulatory events only occur at specific miRNA expression levels. To this end, we present an R package, ceRNAR, which allows identification and analysis of ceRNA-miRNA triplets via integration of miRNA and RNA expression data. The ceRNAR package integrates three main steps: (i) identification of ceRNA pairs based on a rank-based correlation between pairs that considers the impact of miRNA and a running sum correlation statistic, (ii) sample clustering based on gene-gene correlation by circular binary segmentation, and (iii) peak merging to identify the most relevant sample patterns. In addition, ceRNAR also provides downstream analyses of identified ceRNA-miRNA triplets, including network analysis, functional annotation, survival analysis, external validation, and integration of different tools. The performance of our proposed approach was validated through simulation studies of different scenarios. Compared with several published tools, ceRNAR was able to identify true ceRNA triplets with high sensitivity, low false-positive rates, and acceptable running time. In real data applications, the ceRNAs common to two lung cancer datasets were identified in both datasets. The bridging miRNA for one of these, the ceRNA for MAP4K3, was identified by ceRNAR as hsa-let-7c-5p. Since similar cancer subtypes do share some biological patterns, these results demonstrated that our proposed algorithm was able to identify potential ceRNA targets in real patients. In summary, ceRNAR offers a novel algorithm and a comprehensive pipeline to identify and analyze ceRNA regulation. The package is implemented in R and is available on GitHub (https://github.com/ywhsiao/ceRNAR).
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Jayarathna, Dulari K., Miguel E. Rentería, Emilie Sauret, Jyotsna Batra, and Neha S. Gandhi. "Identifying Complex lncRNA/Pseudogene–miRNA–mRNA Crosstalk in Hormone-Dependent Cancers." Biology 10, no. 10 (October 9, 2021): 1014. http://dx.doi.org/10.3390/biology10101014.

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The discovery of microRNAs (miRNAs) has fundamentally transformed our understanding of gene regulation. The competing endogenous RNA (ceRNA) hypothesis postulates that messenger RNAs and other RNA transcripts, such as long non-coding RNAs and pseudogenes, can act as natural miRNA sponges. These RNAs influence each other’s expression levels by competing for the same pool of miRNAs through miRNA response elements on their target transcripts, thereby modulating gene expression and protein activity. In recent years, these ceRNA regulatory networks have gained considerable attention in cancer research. Several studies have identified cancer-specific ceRNA networks. Nevertheless, prior bioinformatic analyses have focused on long-non-coding RNA-associated ceRNA networks. Here, we identify an extended ceRNA network (including both long non-coding RNAs and pseudogenes) shared across a group of five hormone-dependent (HD) cancers, i.e., prostate, breast, colon, rectal, and endometrial cancers, using data from The Cancer Genome Atlas (TCGA). We performed a functional enrichment analysis for differentially expressed genes in the shared ceRNA network of HD cancers, followed by a survival analysis to determine their prognostic ability. We identified two long non-coding RNAs, nine genes, and seventy-four miRNAs in the shared ceRNA network across five HD cancers. Among them, two genes and forty-one miRNAs were associated with at least one HD cancer survival. This study is the first to investigate pseudogene-associated ceRNAs across a group of related cancers and highlights the value of this approach to understanding the shared molecular pathogenesis in a group of related diseases.
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Chen, Chen, Li Wang, Qiuju Feng, Qi Liu, Li Wang, and Shuming Huang. "Comprehensive Landscape of Modules-Dysregulated Functions Reveals a Profound Role of ceRNAs in Coronary Heart Disease." Journal of Healthcare Engineering 2022 (March 8, 2022): 1–10. http://dx.doi.org/10.1155/2022/4547413.

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Coronary heart disease (CHD) is one of the most common severe cardiovascular diseases. Competitive endogenous RNAs (ceRNA) play critical roles in complex diseases. However, our understanding of the dysregulated functions of ceRNAs in CHD remains limited. Here, we systematically analyzed the alterations of ceRNAs and identified the specific functions based on dysregulated modules from the ceRNA network. A total of 2457 significantly differential expressed genes and 212 differential expressed lncRNAs were identified. We got 76679 regulator relationship between different expression genes and miRNAs and 336 regulator relationship between differential expressed lncRNAs and miRNAs. We constructed the ceRNA network and selected five dysregulated modules. Furthermore, CHD specific functions based on dysregulated modules from the ceRNA network were identified, including histone acetylation, platelet degranulation, cAMP-dependent protein kinase complex, xenobiotic transport and so on. Our results will provide novel insight for a better understanding of the mechanism of ceRNAs and facilitate the identification of novel diagnostic and therapeutic biomarkers in CHD.
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Liang, Ying-Chun, Yu-Peng Wu, Dong-Ning Chen, Shao-Hao Chen, Xiao-Dong Li, Xiong-Lin Sun, Yong Wei, Xu Ning, and Xue-Yi Xue. "Building a Competing Endogenous RNA Network to Find Potential Long Non-Coding RNA Biomarkers for Pheochromocytoma." Cellular Physiology and Biochemistry 51, no. 6 (2018): 2916–24. http://dx.doi.org/10.1159/000496043.

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Background/Aims: Accumulating evidence has shown that long non-coding RNAs (lncRNAs) in competing endogenous RNA (ceRNA) networks play crucial roles in tumor survival and patient prognosis; however, studies investigating ceRNA networks in pheochromocytoma (PCC) are lacking. In this study, we investigated the pathogenesis of PCC and whether lncRNAs acting through ceRNAs networks were associated with prognosis. Methods: A total of 183 PCC samples and 3 control samples from The Cancer Genome Atlas database were analyzed. The Empirical Analysis of Digital Gene Expression Data package in R (edgeR) was used to analyze differentially expressed RNAs. Biological processes and pathways functional enrichment analysis were performed based on the Database for Annotation, Visualization, and Integrated Discovery (DAVID) database. LncRNA/mRNA/miRNA ceRNA network was constructed by Cytoscape v3.0 software based on the differentially expressed RNAs Survival package in R was used to perform survival analysis. Results: In total, 554 differentially expressed lncRNAs, 1775 mRNAs and 40 miRNAs were selected for further analysis. Subsequently, 23 lncRNAs, 22 mRNAs, and 6 miRNAs were included in the constructed ceRNA network. Meanwhile, two of the 23 lncRNAs (C9orf147 and BSN-AS2) were identified as independent predictors of overall survival in PCC patients (P< 0.05). Conclusion: This study improves the understanding of lncRNA-related ceRNA networks in PCC and suggests that the lncRNAs C9orf147 and BSN-AS2 could be independent prognostic biomarkers and potential therapeutic targets for PCC.
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Ye, Hongwei, Yuping Li, Lu Li, Yuhui Huang, Jiahui Wang, and Qin Gao. "Construction of a ceRNA network of regulated ferroptosis in doxorubicin-induced myocardial injury." PeerJ 11 (January 25, 2023): e14767. http://dx.doi.org/10.7717/peerj.14767.

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Background Ferroptosis and long-noncoding RNAs (lncRNAs) play crucial roles in doxorubicin (DOX)-induced myocardial injury (DIMI). Nevertheless, there is no research to construct competing endogenous RNAs (ceRNAs) network between lncRNAs and ferroptosis-related key gene. So our research was designed to screen ferroptosis-related genes from differentially expressed mRNAs in DIMI and construct lncRNAs regulated ferroptosis-related key gene ceRNAs network. Methods The male mice were injected with DOX intraperitoneally to induce myocardial injury, myocardial injury was evaluated by hematoxylin and eosin (HE) staining, and ferroptosis-related protein-glutathione peroxidase 4 (GPx4) protein expression was detected. The differentially expressed lncRNAs and mRNAs were detected by microarray, and the ferroptosis-related genes were screened to construct a protein-protein associations (PPA) network, the highest maximal clique centrality (MCC) score gene were identified by Cytoscape software, miRNAs bound to key genes and lncRNAs bound to miRNAs were predicted; then, the obtained lncRNAs were intersected with differentially expressed lncRNAs detected by microarray. Finally, the lncRNA/miRNA/mRNA ceRNA network of the highest MCC score gene regulating ferroptosis in DIMI was constructed. The expressions of the key components in ceRNA network were detected by qRT-PCR. Results Compared with the control group, in the DOX group, myocardial enzymes and HE staining showed that myocardium structure was changed, and GPx4 protein expression was decreased. The differentially expressed 10,265 lncRNAs and 6,610 mRNAs in the DOX group were detected via microarray. Among them, 114 ferroptosis-related genes were obtained to construct PPA networks, and Becn1 was identified as the key gene. Finally, the ceRNA network including Becn1, three miRNAs and four lncRNAs was constructed by predicting data of the Starbase database. The relative expressions of these components in ceRNA net were up-regulated and consistent with microarray results. Conclusions Based on the microarray detection results and bioinformatics analysis, we screened ferroptosis-related gene Becn1 and constructed the lncRNA/miRNA/mRNA ceRNA network of regulated ferroptosis in DIMI.
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Sheng, Han, Huan Pan, Ming Yao, Longsheng Xu, Jianju Lu, Beibei Liu, Jianfen Shen, and Hui Shen. "Integrated Analysis of Circular RNA-Associated ceRNA Network Reveals Potential circRNA Biomarkers in Human Breast Cancer." Computational and Mathematical Methods in Medicine 2021 (December 20, 2021): 1–16. http://dx.doi.org/10.1155/2021/1732176.

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Circular RNA (circRNA) is closely related to tumorigenesis and cancer progression. Yet, the roles of cancer-specific circRNAs in the circRNA-related ceRNA network of breast cancer (BRCA) remain unclear. The aim of this study was to construct a ceRNA network associated with circRNA and to explore new therapeutic and prognostic targets and biomarkers for breast cancer. We downloaded the circRNA expression profile of BRCA from Gene Expression Omnibus (GEO) microarray datasets and downloaded the miRNA and mRNA expression profiles of BRCA from The Cancer Genome Atlas (TCGA) database. Differentially expressed mRNAs (DEmRNAs), differentially expressed miRNAs (DEmiRNAs), and differentially expressed circRNAs (DEcircRNAs) were identified, and a competitive endogenous RNA (ceRNA) regulatory network was constructed based on circRNA–miRNA pairs and miRNA–mRNA pairs. Gene ontology and pathway enrichment analyses were performed on mRNAs regulated by circRNAs in ceRNA networks. Survival analysis and correlation analysis of all mRNAs and miRNAs in the ceRNA network were performed. A total of 72 DEcircRNAs, 158 DEmiRNAs, and 2762 DE mRNAs were identified. The constructed ceRNA network contains 60 circRNA–miRNA pairs and 140 miRNA–mRNA pairs, including 40 circRNAs, 30 miRNAs, and 100 mRNAs. Functional enrichment indicated that DEmRNAs regulated by DEcircRNAs in ceRNA networks were significantly enriched in the PI3K-Akt signaling pathway, microRNAs in cancer, and proteoglycans in cancer. Survival analysis and correlation analysis of all mRNAs and miRNAs in the ceRNA network showed that 13 mRNAs and 6 miRNAs were significantly associated with overall survival, and 48 miRNA–mRNA interaction pairs had a significant negative correlation. A PPI network was established, and 21 hub genes were determined from the network. This study provides an effective bioinformatics basis for further understanding of the molecular mechanisms and predictions of breast cancer. A better understanding of the circRNA-related ceRNA network in BRCA will help identify potential biomarkers for diagnosis and prognosis.
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Wang, Chao, Kunkai Su, Hanchao Lin, Beini Cen, Shusen Zheng, and Xiao Xu. "Identification and Verification of a Novel MAGI2-AS3/miRNA-374-5p/FOXO1 Network Associated with HBV-Related HCC." Cells 11, no. 21 (November 2, 2022): 3466. http://dx.doi.org/10.3390/cells11213466.

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Background: Hepatocellular carcinoma (HCC) is a very common neoplasm worldwide, and competitive endogenous RNA (ceRNA) plays an important role in the development of HCC. The purpose of this study is to investigate the molecular mechanisms of ceRNAs in HCC. Methods: This study detects potential ceRNAs from HCC through whole genome analysis of lncRNA, miRNA and mRNA expression. We then performed high-throughput sequencing of tissues from five hepatitis B related HCC patients to screen ceRNAs and those screened ceRNAs expressions were verified on tissues from an independent group of six patients. Finally, the function of ceRNAs of interest was illustrated in vitro. Result: Functional and pathway analysis of The Cancer Genome Atlas revealed ceRNA networks. The high-throughput sequencing identified 985 upregulated and 1612 downregulated lncRNAs and 887 upregulated and 1116 downregulated mRNAs in HCC patients. Differentially expressed genes were parallel to cancer-associated processes, comprising 18 upregulated and 35 downregulated significantly enriched pathways including alcoholism and viral carcinogenesis. Among them, a potential ceRNA network was detected and verified in six HCC patients. CeRNAs of the lncRNA MAGI2-AS3/miR-374-5p/FOXO1 pathway were significantly dysregulated in HCC, and validation in vitro showed that FOXO1 is positively regulated by MAGI2-AS3 through the induction of miR-374a/b-5p in HCC cells. In addition, the overexpression of FOXO1 is associated with proliferation, migration, and invasion of HCC cells and increases apoptosis of HCC cells. MiR-374a/b-5p caused an opposite effect by directly suppressing FOXO1 in HCC cells. Conclusion: CeRNA networks were found in HCC and aberrantly expressed ceRNAs of lncRNA MAGI2-AS3/miR-374-5p/FOXO1 plays a crucial role in HCC, assisting in diagnosis and providing a method for treatment.
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An, Biao, Yuan Hu, and Xiao Liang. "Integrated Analysis of the lncRNA-Associated ceRNA Network in Wilms Tumor via TARGET and GEO Databases." Genetics Research 2022 (August 31, 2022): 1–12. http://dx.doi.org/10.1155/2022/2365991.

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Wilms tumor (WT) is the most common genitourinary renal tumor that typically occurs in children under 15 and is thought to be linked to somatic and germline mutations. However, the specific functional role of competing endogenous RNAs (ceRNAs) and their potential implications in WT remain unclear. In this study, we developed an lncRNA-mediated (long noncoding RNA-mediated) ceRNA network via the R packages for WT with expression data obtained from the tumor alterations relevant for genomics-driven therapy (TARGET) database. Unsupervised hierarchical clustering analysis revealed that the WT specimens could be clearly distinguished from healthy specimens with respect to the expression of disordered RNAs. A total of 1,607 differentially expressed (DE) lncRNAs, 116 DE microRNAs (DEmiRNAs), and 3,262 DE messenger RNAs (DEmRNAs) were identified as WT-specific RNAs, and a lncRNA-miRNA-mRNA ceRNA network with 159 DElncRNAs, 18 DEmiRNAs, 131 DEmRNAs, and 792 interactions was constructed. According to the clinical survival data, 12 DElncRNAs, 5 DEmRNAs, and 2 DEmiRNAs were selected from the ceRNA network that could significantly impact the overall survival of WT patients ( P < 0.05 ). Functional enrichment analysis showed that the biological processes and pathways of DEmRNAs, such as cell cycle and virus infection, may be associated with WT. The present study constructed a dysregulated lncRNA-mediated ceRNA network in WT and discovered that lncRNA-mediated ceRNAs may serve as important regulators in WT development and progression. Survival-associated RNAs may serve as new potential biomarkers, suggesting that the constructed ceRNA network in WT might be important for determining optimal therapeutic strategies.
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Ye, Junhong, Jifu Li, and Ping Zhao. "Roles of ncRNAs as ceRNAs in Gastric Cancer." Genes 12, no. 7 (July 2, 2021): 1036. http://dx.doi.org/10.3390/genes12071036.

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Although ignored in the past, with the recent deepening of research, significant progress has been made in the field of non-coding RNAs (ncRNAs). Accumulating evidence has revealed that microRNA (miRNA) response elements regulate RNA. Long ncRNAs, circular RNAs, pseudogenes, miRNAs, and messenger RNAs (mRNAs) form a competitive endogenous RNA (ceRNA) network that plays an essential role in cancer and cardiovascular, neurodegenerative, and autoimmune diseases. Gastric cancer (GC) is one of the most common cancers, with a high degree of malignancy. Considerable progress has been made in understanding the molecular mechanism and treatment of GC, but GC’s mortality rate is still high. Studies have shown a complex ceRNA crosstalk mechanism in GC. lncRNAs, circRNAs, and pseudogenes can interact with miRNAs to affect mRNA transcription. The study of the involvement of ceRNA in GC could improve our understanding of GC and lead to the identification of potential effective therapeutic targets. The research strategy for ceRNA is mainly to screen the different miRNAs, lncRNAs, circRNAs, pseudogenes, and mRNAs in each sample through microarray or sequencing technology, predict the ceRNA regulatory network, and, finally, conduct functional research on ceRNA. In this review, we briefly discuss the proposal and development of the ceRNA hypothesis and the biological function and principle of ceRNAs in GC, and briefly introduce the role of ncRNAs in the GC’s ceRNA network.
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Dissertations / Theses on the topic "CERNA NETWORK"

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Cavalazzi, Marco Carlo. "Enterprise Social Networks: The Case of CERN." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2016. http://amslaurea.unibo.it/11560/.

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Social networks are commonly seen as a global trend that allows users to search and contact others with similar interests, write a post, reply, like or share content, create groups and organize events. This said, there is much more that can be done to exploit the full potential of social media. In order to improve the business, providing employees, customers and partners the best tools to cooperate and gain value from the whole community, many organizations are taking the matter in their own hands, using Enterprise Social Networks. Close analysis of case studies and comprehensive statistics shows why it is important to pursue this path. At CERN, the European Organization for Nuclear Research, where the number of employees, students and volunteers that everyday work in partnership both on site and through the network reaches the thousands, a new kind of platform has been deployed, able to exploit the social knowledge of the personnel. The thesis will describe the case study of CERN to understand not only why it is essential to become a social organization but also how a social environment can be developed. The last chapters will focus on examining my work on the platform, considering a mobile responsive design, realized to make the environment adapt to any screen size, an integrated resource planning tool, which gives the scientists the mean to easily manage the everyday work on the particle accelerators, and the platform’s Application Programming Interface, which allows anyone with the right credentials to include content from the enterprise social network into a personal or departmental webpage, giving everyone an even easier way to participate.
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Riksem, Hans-Even Ramsevik. "Design and Implementation of an Efficient, Reliable and Safe Work-Package Database System at CERN." Thesis, Norges teknisk-naturvitenskapelige universitet, Institutt for telematikk, 2010. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-12175.

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The Activity Coordination Tool (ACT) is a web application designed to automate theplanning and coordination of work packages. In the CMS experiment at CERN it isimportant that work packages in the underground facilities are properly planned inorder to not jeopardize time schedules, equipments, budgets and safety. The subjectof this thesis is the development of the database schema used by the ACT application.The schema has been developed from scratch in order to best fit the needs of CMS andto cover all aspects of the planning and coordination process not found in other CERNdatabases.Models and diagrams of the database schema are based on a step by step descriptionof the work package process. This step by step description was used to organize thedata, to make the data and data relationships consistency, and to make the databasestructure flexible for extensions in the future. These models would eventually be usedto implement the schema in the CMS online database.Another database at CERN has many similarities with the ACT database. These twodatabases will eventually merge due to common interest, and the ACT database schemaneeded therefore to resemble some tables in this database in order to facilitate themerging. Some problems with network traversal and security needs to be solved beforethese two databases can be merged.The architecture and usage of the database schema can affect the database performancebut it doesn’t contribute to the reliability of the databases system. The hardware andsoftware components making up the database system itself are usually the main contributorsto this. The CMS online network work hard to keep the performance and reliabilityof their database system as good as possible. Everything from disks to networkconnections is redundant. In addition to component redundancy are features providedby Oracle used to improve performance. The amount of server redundancy does howeverseem a bit exaggerated, and the performance could be slightly improved if otherOracle features were used.
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Papadopoulos, S. "Optical network design, modelling and performance evaluation for the upgraded LHC at CERN." Thesis, University College London (University of London), 2013. http://discovery.ucl.ac.uk/1390672/.

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This thesis considers how advances in optical network and optoelectronic technologies may be utilised in particle physics applications. The research is carried out within a certain framework; CERN's Large Hadron Collider (LHC) upgrade. The focus is on the upgrade of the "last-tier" data links, those residing between the last information-processing stage and the accelerator. For that purpose, different network architectures, based on the Passive Optical Network (PON) architectural paradigm, are designed and evaluated. Firstly, a Time-Division Multiplexed (TDM) PON targeting timing, trigger and control applications is designed. The bi-directional, point-to-multipoint nature of the architecture leads to infrastructure efficiency increase. A custom protocol is developed and implemented using FPGAs. It is experimentally verified that the network design can deliver significantly higher data rate than the current infrastructure and meet the stringent latency requirements of the targeted application. Consequently, the design of a network that can be utilised to transmit all types of information at the upgraded LHC, the High-Luminosity LHC (HL-LHC) is discussed. The most challenging requirement is that of the high upstream data rate. As WDM offers virtual point-to-point connectivity, the possibility of using a Wavelength-Division Multiplexed (WDM) PON is theoretically investigated. The shortcomings of this solution are identified; these include high cost and complexity, therefore a simpler architecture is designed. This is also based on the PON paradigm and features the use of Reflective Electroabsorption Modulators (REAM) at the front-end (close to the particle collision point). Its performance is experimentally investigated and shown to meet the requirements of a unified architecture at the HL-LHC from a networking perspective. Finally, since the radiation resistance of optoelectronic components used at the front-end is of major importance, the REAM radiation hardness is experimentally investigated. Their radiation resistance limits are established, while new insights into the radiation damage mechanism are gained.
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Lippitsch, Angelika [Verfasser]. "A Deformation Analysis Method for the Metrological ATLAS Cavern Network at CERN / Angelika Lippitsch." Aachen : Shaker, 2007. http://d-nb.info/1166511103/34.

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Silva, Leandro Pereira da. "Leannet : uma arquitetura que utiliza o contexto da cena para melhorar o reconhecimento de objetos." Pontif?cia Universidade Cat?lica do Rio Grande do Sul, 2018. http://tede2.pucrs.br/tede2/handle/tede/8168.

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Computer vision is the science that aims to give computers the capability of see- ing the world around them. Among its tasks, object recognition intends to classify objects and to identify where each object is in a given image. As objects tend to occur in particular environments, their contextual association can be useful to improve the object recognition task. To address the contextual awareness on object recognition task, the proposed ap- proach performs the identification of the scene context separately from the identification of the object, fusing both information in order to improve the object detection. In order to do so, we propose a novel architecture composed of two convolutional neural networks running in parallel: one for object identification and the other to the identification of the context where the object is located. Finally, the information of the two-streams architecture is concatenated to perform the object classification. The evaluation is performed using PASCAL VOC 2007 and MS COCO public datasets, by comparing the performance of our proposed approach with architectures that do not use the scene context to perform the classification of the ob- jects. Results show that our approach is able to raise in-context object scores, and reduces out-of-context objects scores.
A vis?o computacional ? a ci?ncia que permite fornecer aos computadores a ca- pacidade de verem o mundo em sua volta. Entre as tarefas, o reconhecimento de objetos pretende classificar objetos e identificar a posi??o onde cada objeto est? em uma imagem. Como objetos costumam ocorrer em ambientes particulares, a utiliza??o de seus contex- tos pode ser vantajosa para melhorar a tarefa de reconhecimento de objetos. Para utilizar o contexto na tarefa de reconhecimento de objetos, a abordagem proposta realiza a iden- tifica??o do contexto da cena separadamente da identifica??o do objeto, fundindo ambas informa??es para a melhora da detec??o do objeto. Para tanto, propomos uma nova arquite- tura composta de duas redes neurais convolucionais em paralelo: uma para a identifica??o do objeto e outra para a identifica??o do contexto no qual o objeto est? inserido. Por fim, a informa??o de ambas as redes ? concatenada para realizar a classifica??o do objeto. Ava- liamos a arquitetura proposta com os datasets p?blicos PASCAL VOC 2007 e o MS COCO, comparando o desempenho da abordagem proposta com abordagens que n?o utilizam o contexto. Os resultados mostram que nossa abordagem ? capaz de aumentar a probabili- dade de classifica??o para objetos que est?o em contexto e reduzir para objetos que est?o fora de contexto.
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Fraticelli, Chiara. "Λc reconstruction with artificial neural networks." Bachelor's thesis, Alma Mater Studiorum - Università di Bologna, 2020. http://amslaurea.unibo.it/19985/.

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Il rivelatore ALICE studia collisioni di ioni pesanti ultrarelativistici in modo da creare e di conseguenza studiare lo stato della materia chiamato plasma di quark e gluoni. Questo obiettivo risulta difficoltoso data la sua vita breve, quindi facciamo riferimento a misure indirette per la prova della sua esistenza. In questa tesi abbiamo sfruttato tecniche di machine learning per studiare il decadimento del barione charmato Λc per dedurre alcune sue proprietà. In particolare abbiamo usato il metodo delle reti neurali per ricavare tutte le informazioni possibili con la tecninca di un'analisi multivariata.
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Pimentel, Ana Cristina de Lima. "A Rede Cegonha em cena: algumas controvérsias sobre uma corrente de cuidados especiais." Universidade do Estado do Rio de Janeiro, 2014. http://www.bdtd.uerj.br/tde_busca/arquivo.php?codArquivo=7056.

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
A Rede Cegonha foi uma iniciativa pública governamental instituída em 2011 com o foco na atenção à saúde materna e infantil. Surgiu enquanto uma promessa de campanha e foi constituída oficialmente no mandato de Dilma Rousseff que a caracterizaria como uma corrente de cuidados especiais. O processo de constituição desta agenda política foi perpassado por controvérsias que evidenciavam diferenças sobre o que seria uma agenda pública de saúde voltada para as mulheres, além de divergências sobre o como se construir uma política de saúde na área da mulher. Assim, em torno destas controvérsias a própria concepção de saúde da mulher e saúde reprodutiva estavam em debate. A perspectiva de configuração da política é compreendida dinamicamente, desnaturalizando a própria concepção de Estado, abandonando o pressuposto de sua universalidade. Assim, observar a dinâmica de constituição da Rede Cegonha, entendendo-a enquanto um processo aberto. De outro modo, as controvérsias também funcionaram como uma entrada no estudo da própria política, funcionando como um forjar estranho. Os adversários contribuem para a desconstrução de verdades, assim, práticas e crenças são colocadas em análise. Para esta finalidade alguns procedimentos metodológicos foram escolhidos. O primeiro deles foi a pesquisa em dois blogs que se destacaram por acolher e divulgar opiniões sobre a Rede Cegonha. Também foram realizadas entrevistas a atores-chave e realizada leituras de documentos oficiais da política. A trajetória de constituição da política é narrada em dois pontos. O primeiro construído a partir da fala daqueles que contribuíram na sua formulação e/ou execução da política. O segundo a partir de uma fala que a confronta. Ambas apresentações serão cotejadas pelos documentos públicos oficiais. O processo de constituição da Rede Cegonha foi perpassado por controvérsias sobre diferentes concepções de políticas de saúde reprodutiva. Novos sujeitos políticos se articularam a partir destas controvérsias, tal seja, movimentos pro-vida, movimentos pela humanização do parto, blogueiras maternistas, movimentos feministas se posicionaram neste processo.
Rede Cegonha was a government public initiative established in 2011 with the focus on attention to maternal and child health. Emerged as a campaign promise and was officially incorporated in the Rousseffs mandate that would characterize as "stream of special care". The process of formation of this policy agenda was permeated by controversies which exhibited differences on what would be a public health agenda focused on women, as well as disagreements over how to make health policy in the area of women. Thus, these controversies surrounding the conception of women's health and reproductive health were debated. The prospect of policy configuration is dynamically understood, by denaturalizing the concept of the State, abandoning the assumption of universality of the State. Thus observe the dynamics of constitution of Rede Cegonha, understanding it as an open process . On the other hand, disputes also functioned as an entry in the study of politics itself, acting as a forge " weird." Opponents contribute to the deconstruction of truths , thus practices and beliefs are put into analysis. For this purpose some methodological procedures were chosen . The first was the research on two blogs that stood out to welcome and disseminate opinions about Rede Cegonha. Interviews were also carried out to key stakeholders and held readings of official policy documents. The trajectory this policy is told in two points. The first was constructed from the speech of those who contributed to its formulation and or implementation of policy. The second from a speech that confronts. Both presentations will be complemented by the official public documents. The process of establishment of the Rede Cegonha was permeated by controversies about different conceptions of reproductive health policies. New political subjects were articulated from these controversies, this is, pro-life movements, movements for the humanization of birth, Mom Bloguers, feminist movements have positioned themselves in the process.
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Haas, Stefan. "The IEEE 1355 Standard : developments, performance and application in high energy physics." Thesis, University of Liverpool, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.367130.

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Sidebo, Edvin. "Charged particle distributions and robustness of the neural network pixel clustering in ATLAS." Licentiate thesis, KTH, Partikel- och astropartikelfysik, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-190858.

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This thesis contains a study of the robustness of the artificial neural network used in the ATLAS track reconstruction algorithm as a tool to recover tracks in dense environments. Different variations, motivated by potential discrepancies between data and simulation, are performed to the neural network’s input while monitoring the corresponding change in the output. Within reasonable variation magnitudes, the neural networks prove to be robust to most variations. In addition, a measurement of charged particle distributions is summarised. This is one of the first such measurements carried out for proton-proton colli- sions at √s = 13 TeV, limited to a phase space defined by transverse momentum pT > 100 MeV and absolute pseudorapidity |η| < 2.5. Tracks are corrected for de- tector inefficiencies and unfolded to particle-level. The result is compared to the prediction of different models. Overall, the EPOS and Pythia 8 A2 models show the best agreement with the data.
Spår från elektriskt laddade partiklar rekonstrueras i ATLAS genom att kombinera mätningar från de innersta subdetektorerna. I de extrema miljöer som skapas i proton-proton-kollisionerna i Large Hadron Collider vid CERN är det av yttersta vikt att algoritmen för att rekonstruera spår är högpresterande. Uppgiften är särskilt svår i partikelrika miljöer där flera partiklar färdas nära varandra, åtskilda av avstånd jämförbara med storleken på detektorns utläsningselement. Ett artificiellt neuralt nätverk används i algoritmen för att klassificera mätdata från pixeldetektorn, belägen närmast interaktionspunkten, för att lyckas identifiera spår i partikelrika miljöer som annars hade gått förlorade. I denna avhandling utreds det neurala nätverkets stabilitet. Dess känslighet studeras genom att manuellt manipulera dess indata och därefter utvärdera dess resultat. Nätverket tränas med simulerad data. Variationerna i indata är utformade för att undersöka skillnader mellan data och simulering, orsakade av osäkerheter i simuleringsmodellen eller osäkerheter i pixeldetektorns kalibrering. Av de undersökta variationerna har en osäkerhet i skalan eller utläsningströskeln för pixeldetektorns kalibrering den största effekten på nätverkets resultat. Andra variationer har en betydligt mindre påverkan. Avhandlingen presenterar också en studie av distributioner av elektriskt laddade partiklar producerade i proton-proton-kollisioner. Det är en av de första studierna av partikeldistributioner för Large Hadron Colliders andra körning med mass-centrum-energi √s = 13 TeV. Mätningen är begränsad till fasrymden definierad av en transversell rörelsemängd pT > 100 MeV, och absolut rapiditet |η| < 2.5. Spår av partiklar rekonstrueras och korrigeras för detektorns ineffektiviteter för att presenteras på partikelnivå. Dessa jämförs sedan med förutsägelser från olika modeller. Modellerna EPOS och Pythia 8 A2 är generellt de som bäst överensstämmer med data. Författaren har undersökt partiklar som migrerar in och ut ur fasrymden. Andelen spår associerade till partiklar som migrerat utifrån uppskattas med simulerad data, till som mest 10% nära fasrymdens gränser. Osäkerheten på denna andel uppskattas till att vara som mest 4.5%, huvudsakligen orsakad av osäkerheten på mängden material i de innersta subdetektorerna.

QC 20160817

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Surappa-Narayanappa, Ananth Prakash. "The evolution, modifications and interactions of proteins and RNAs." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/269851.

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Proteins and RNAs are two of the most versatile macromolecules that carry out almost all functions within living organisms. In this thesis I have explored evolutionary and regulatory aspects of proteins and RNAs by studying their structures, modifications and interactions. In the first chapter of my thesis I investigate domain atrophy, a term I coined to describe large-scale deletions of core structural elements within protein domains. By looking into truncated domain boundaries across several domain families using Pfam, I was able to identify rare cases of domains that showed atrophy. Given that even point mutations can be deleterious, it is surprising that proteins can tolerate such large-scale deletions. Some of the structures of atrophied domains show novel protein-protein interaction interfaces that appear to compensate and stabilise their folds. Protein-protein interactions are largely influenced by the surface and charge complementarity, while RNA-RNA interactions are governed by base-pair complementarity; both interaction types are inherently different and these differences might be observed in their interaction networks. Based on this hypothesis I have explored the protein-protein, RNA-protein and the RNA-RNA interaction networks of yeast in the second chapter. By analysing the three networks I found no major differences in their network properties, which indicates an underlying uniformity in their interactomes despite their individual differences. In the third chapter I focus on RNA-protein interactions by investigating post-translational modifications (PTMs) in RNA-binding proteins (RBPs). By comparing occurrences of PTMs, I observe that RBPs significantly undergo more PTMs than non-RBPs. I also found that within RBPs, PTMs are more frequently targeted at regions that directly interact with RNA compared to regions that do not. Moreover disorderedness and amino acid composition were not observed to significantly influence the differential PTMs observed between RBPs and nonRBPs. The results point to a direct regulatory role of PTMs in RNA-protein interactions of RBPs. In the last chapter, I explore regulatory RNA-RNA interactions. Using differential expression data of mRNAs and lncRNAs from mouse models of hereditary hemochromatosis, I investigated competing regulatory interactions between mRNA, lncRNA and miRNA. A mutual interaction network was created from the predicted miRNA interaction sites on mRNAs and lncRNAs to identify regulatory RNAs in the disease. I also observed interesting relations between the sense-antisense mRNA-lncRNA pairs that indicate mutual regulation of expression levels through a yet unknown mechanism.
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Books on the topic "CERNA NETWORK"

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1994, Altherr Tanguy d., Aurenche P, Veneziano G, and Sorba P, eds. From thermal field theory to neural networks: A day to remember Tanguy Altherr, Cern, 4 November 1994. Singapore: World Scientific, 1996.

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Lazar, Jonathan. Understanding web credibility: A synthesis of the research literature. Hanover: Now Publishers, 2007.

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From Thermal Field Theory to Neural Networks: A Day to Remember Tanguy Altherr : Cern 4 November 1994. World Scientific Pub Co Inc, 1996.

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Lazar, Jonathan. Understanding Web Credibility: A Synthesis of the Research Literature. Now Publishers, 2007.

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Book chapters on the topic "CERNA NETWORK"

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Wan, Xiangyuan, and Ziwen Li. "Computational Identification of ceRNA and Reconstruction of ceRNA Regulatory Network Based on RNA-seq and Small RNA-seq Data in Plants." In Modeling Transcriptional Regulation, 261–75. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1534-8_17.

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Guo, Jiaxin, Yize Liu, Fu Li, Rong Qin, Langlang Zhang, Chao Gao, and Xiaohong He. "Screening of Key Genes in Retinoblastoma and Construction of ceRNA Regulatory Network." In Biomedical and Computational Biology, 147–68. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-25191-7_12.

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Hulboj, Milosz Marian, and Ryszard Erazm Jurga. "CERN Investigation of Network Behaviour and Anomaly Detection." In Lecture Notes in Computer Science, 353–54. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-04342-0_21.

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Lopez-Miguel, Ignacio D., Borja Fernández Adiego, Faiq Ghawash, and Enrique Blanco Viñuela. "Verification of Neural Networks Meets PLC Code: An LHC Cooling Tower Control System at CERN." In Engineering Applications of Neural Networks, 420–32. Cham: Springer Nature Switzerland, 2023. http://dx.doi.org/10.1007/978-3-031-34204-2_35.

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Cano, Juan-Carlos, Dongkyun Kim, and Pietro Manzoni. "CERA: Cluster-Based Energy Saving Algorithm to Coordinate Routing in Short-Range Wireless Networks." In Information Networking, 306–15. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-540-45235-5_30.

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Brolli, Tiziana. "Il canis ingens, il Capricorno e l’aragosta nella Cena Trimalchionis." In Antichistica. Venice: Fondazione Università Ca’ Foscari, 2021. http://dx.doi.org/10.30687/978-88-6969-557-5/008.

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This paper focuses on the exegesis of some Petronian animals. As for the chained dog, the painted one (29.1) and the one in the flesh (64.7-9 and 72.7-9), we recognise both a dense network of epic references to the catabasis of Aeneas and ironic allusions to Seneca and to the popular tradition. Besides that, in our opinion, the epic language used to describe the fall of Ascyltus and Encolpius into the fishpond (72.7) emphasises the game between art and life which pervades the Cena. In the second part we defend the manuscript reading super capricornum locustam marinam (35.4).
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Xie, Iris. "Interactive IR in Web Search Engine Environments." In Interactive Information Retrieval in Digital Environments, 83–115. IGI Global, 2008. http://dx.doi.org/10.4018/978-1-59904-240-4.ch004.

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Tim Berners-Lee wrote the initial proposal for the World Wide Web in 1989, and developed it online in 1991 by using a hypertext model (Berners-Lee, 1989, 1996). The World Wide Web was developed to allow people to collaborate on projects; it began at CERN, the European Particle Physics Laboratory in Geneva, Switzerland, and expanded across nations and disciplines. Berners-Lee (1996) defined the components of the Web: the boundless information world, the address system (URI), a network protocol (HTTP), a markup language (HTML), a body of data, and the client-server architecture of the Web. The creation in 1993 of Mosaic, a graphic Web interface that was the precursor of Netscape, enabled millions of people to easily access the Web. Since then, the increase in Web resources has been phenomenal, and Web search engines are the essential tools for navigating those Web resources.
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De Lucca, Valeria. "The Teatro Colonna (1682–1686)." In The Politics of Princely Entertainment, 234–77. Oxford University Press, 2020. http://dx.doi.org/10.1093/oso/9780190631130.003.0008.

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This chapter considers the years following Lorenzo Onofrio Colonna’s return to Rome in 1681 together with his son Filippo II and his new bride, the young Spanish noblewoman Lorenza de la Cerda. As part of his strategy to affirm his newly acquired political and social power as a former Viceroy over the other aristocratic Roman families, Lorenzo Onofrio commissioned the building of a new theater in his palace. This chapter takes a new look at the ways in which the networks of relationships Lorenzo Onofrio had built over the years made his theater one of the most important stages in the Italian peninsula for the circulation of repertory between Vienna, Venice, Rome, and Naples, as well as of singers. Behind some of the most spectacular productions of the Teatro Colonna was a team of extraordinary architects and men of theaters under the leadership of Filippo Acciaioli and Carlo Fontana.
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Bellucci, A., A. Malizia, and P. Diaz. "The Anatomy of Web 2.0." In Quality and Communicability for Interactive Hypermedia Systems, 36–63. IGI Global, 2010. http://dx.doi.org/10.4018/978-1-61520-763-3.ch003.

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In the last 20 years we have assisted to the birth and growth of the World Wide Web. It rapidly changed from a tool conceived for scientists at CERN, into a global information network, populated by billions of users. Currently, we are experiencing another change within the Web paradigm, where the Web is viewed as a read/write tool enhancing users’ collaboration and participation in information creation, consuming and sharing. Web 2.0, intended as a second step in the Web’s evolution, is a complex topic and therefore it is difficult to clearly define it. It concerns viewing the Web as a platform for the development of Rich Internet Applications that go beyond the page metaphor of Web 1.0. It lies on the ideas of 1) users’ participation; 2) users production of content and; 3) data remixability, so that Web applications and services can be employed as social tools allowing mass users collaboration and information sharing. The authors describe in this chapter, the main concepts behind the Web 2.0 paradigm, together with the technological aspects and design patterns that demonstrate this new way to use and perceive the Web. In second stance, they highlight future directions and research trends which are leading to the next Web’s evolution phase: the Social Semantic Web.
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Becker, Richard C., and Frederick A. Spencer. "Historical Perspectives in Hemostasis, Coagulation, and Fibrinolysis: A Foundation for Understanding Thrombotic Disorders and Developing Effective Treatment." In Fibrinolytic and Antithrombotic Therapy. Oxford University Press, 2006. http://dx.doi.org/10.1093/oso/9780195155648.003.0005.

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Hemostasis, the prompt cessation of bleeding at a site of vascular injury, is among the most fundamental physiologic and teleologically vital defense mechanisms in nature. Without a functionally intact hemostatic mechanism, death could ensue rapidly even after minor traumas associated with everyday life. In mammalian blood coagulation, regulated by a complex network of integrated biochemical events, five protease factors (f ) (fIIa [thrombin], fVIIa, fIXa, fXa, and protein C) interact with five cofactors (tissue factor, f VIIIa, fVa, thrombomodulin, and protein S) to regulate the generation of fibrin (Davidson et al., 2003). Although each component of the mammalian coagulation network has unique functional properties, available data based on gene organizations, protein structure, and sequence analysis suggest that it may have resulted from the reduplication and diversification of two gene structures over 400 million years ago. A vitamin K–dependent serine protease is composed of a γ-carboxylated glutamic acid (GLA) epidermal growth factor-like (EGF) 1–EGF 2-serine protease domain structure common to fVII, fIX, fX, and protein C, and the A1-A2-B-AB-C1-C2 domain structure common to fV and fVIII. Prothrombin is also a vitamin K–dependent serine protease; however, it contains kringle domains rather than EGF domains (suggesting a replacement during gene duplication and shuffling). Analyses of active site function amino acid residues reveal distinguishing characteristics of thrombin from other serine proteases, supporting its position as the ancestral blood enzyme (Krem and Cera, 2002; McLysaght et al., 2002). The rapid transformation of fluid blood to a gel-like substance (clot) has been a topic of great interest to scientists, physicians, and philosophers since the days of Plato and Aristotle ( Jewett, 1892; Lee, 1952). However, it was not until the beginning of the 18th century that blood clotting (coagulation) was appreciated as a means to stem blood loss from wounds (hemostasis) (Petit, 1731). As with other areas of science, the microscope played a pivotal role in the understanding of coagulation. In the mid-17th century, Marcello Malpighi separated the individual components of a blood clot into fibers, cells, and serum (Forester, 1956).
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Conference papers on the topic "CERNA NETWORK"

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Pellegrino, R., F. Ticconi, B. Skawran, M. Castoldi, P. Schirmacher, I. Costa, and T. Longerich. "LINC00152 drives a ceRNA network in human hepatocellular carcinoma." In 36. Jahrestagung der Deutschen Arbeitsgemeinschaft zum Studium der Leber. Georg Thieme Verlag KG, 2020. http://dx.doi.org/10.1055/s-0039-3402246.

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K. Biwott, Felix, Nini Rao, Changlong Dong, and Fenglin Gao. "Construction of Dysregulated lncRNA-Associated ceRNA Network in Atrial Fibrillation." In ICBBT '21: 2021 13th International Conference on Bioinformatics and Biomedical Technology. New York, NY, USA: ACM, 2021. http://dx.doi.org/10.1145/3473258.3473278.

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Chen, Dayuan, Fan Chen, Peng Guo, and Hongbo Chen. "LncRNA LINC00665 affected gastric cancer through Mir-9-5p according to CeRNA network analysis." In Second International Conference on Biomedical and Intelligent Systems (IC-BIS2023), edited by Ming Chen and Gangmin Ning. SPIE, 2023. http://dx.doi.org/10.1117/12.2687538.

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Frank, Pablo, and Jose Incera. "A Neural Network Based Test Bed for Evaluating the Quality of Video Streams in IP Networks." In 2006 Electronics, Robotics and Automotive Mechanics Conference. IEEE, 2006. http://dx.doi.org/10.1109/cerma.2006.7.

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Ibánez, Susana Rivera, Raúl Aquino Santos, Victor Rangel Licea, Arthur Edwards Block, and Miguel Ángel García Ruiz. "Hybrid WiFi-WiMAX Network Routing Protocol." In 2008 Electronics, Robotics and Automotive Mechanics Conference (CERMA). IEEE, 2008. http://dx.doi.org/10.1109/cerma.2008.24.

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Alarcón-Paredes, Antonio, and Amadeo-José Argüelles-Cruz. "CAINN - Weightless Alpha-Beta Neural Network." In 2008 Electronics, Robotics and Automotive Mechanics Conference (CERMA). IEEE, 2008. http://dx.doi.org/10.1109/cerma.2008.94.

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Perez, Jose P., Jorge A. Gonzalez, Rogelio Soto, and Joel Perez. "Trajectory Tracking of Complex Dynamical Network for Delayed Recurrent Neural Network via Control V-Stability." In 2010 IEEE Electronics, Robotics and Automotive Mechanics Conference (CERMA). IEEE, 2010. http://dx.doi.org/10.1109/cerma.2010.9.

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Rodriguez, Nibaldo, and Claudio Cubillos. "Orthogonal Neural Network Based Predistortion for OFDM Systems." In Electronics, Robotics and Automotive Mechanics Conference (CERMA 2007). IEEE, 2007. http://dx.doi.org/10.1109/cerma.2007.4367690.

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Ponce, Hiram, and Pedro Ponce. "Artificial Organic Networks." In 2011 IEEE Electronics, Robotics and Automotive Mechanics Conference (CERMA). IEEE, 2011. http://dx.doi.org/10.1109/cerma.2011.12.

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Shoaie, M. A., S. Meroli, S. Machado, and D. Ricci. "Evolving trends in CERN optical fibre infrastructure." In 2017 19th International Conference on Transparent Optical Networks (ICTON). IEEE, 2017. http://dx.doi.org/10.1109/icton.2017.8024940.

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