Probabilistic verification and analysis of biopathway dynamics
Probabilistic verification and analysis of biopathway dynamics
... PROBABILISTIC VERIFICATION AND ANALYSIS OF BIOPATHWAY DYNAMICS SUCHEENDRA KUMAR PALANIAPPAN (B.Eng, PESIT, India) A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN ... natural and succinct model to work with Consequently, our work concerns the analysis of DBN models of biopathways from a model checking point of view Specifically, we first consider the problem of probabilistic ... share of ups and downs, and they have all added to make the journey very memorable and enjoyable In the process I have had a chance to meet, interact and work with a number of people who have and...
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Verification and analysis of web service composition
... implemented in a series of software tools, to provide verification and analysis support for Web service composition Key words: Web Service, Web Service Composition, Service Orchestration, Service Choreography, ... verification of Web service composition from the perspective of Web service orchestration A challenge to verify Web service composition is that, the highly concurrent nature of Web service orchestration ... Acknowledgement of Published Work Background 2.1 SOA and Web Service Composition 2.1.1 SOA and Web Service 2.1.2 Web Service Composition...
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báo cáo khoa học: "Real-time imaging and analysis of differences in cadmium dynamics in rice cultivars (Oryza sativa) using positron-emitting 107Cd tracer" ppsx
... Real-time imaging and analysis of differences in cadmium dynamics in rice cultivars (Oryza sativa) using positron-emitting 107Cd tracer Satoru Ishikawa1*§, Nobuo ... to grains in typical rice cultivars that differed in grain Cd concentrations We used positron-emitting 107Cd tracer and an innovative imaging technique, the positron-emitting tracer imaging system ... complaints of spinal and leg bone pain, was recognized as a type of chronic toxicity induced by excess Cd contamination of drinking water and cereals (mainly rice) Since then, the contamination of...
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Mathematical and computational analysis of intracelluar dynamics 2
... skin and brain cortex (Feng et al., 20 07; Wang et al., 20 05; Stambolic et al., 20 01; Trotman and Pandolfi, 20 03; Singh et al., 20 02; Tang and Eng, 20 06a, 20 06b) AKT phosphorylation of MDM2 (AKT-MDM2) ... (CI41) and mouse hippocampal 12 neurons (Gottlieb et al., 20 02; Su et al., 20 03; Wang et al., 20 05; Ogawara et al., 20 02; Zhou et al., 20 01; Singh et al., 20 02; Yamaguchi et al., 20 01; Mayo and ... kidney 14 (29 3T and HEK293), human primary keratinocytes cells, mouse fibroblasts (NIH3T3 and MEF) (Gottlieb et al., 20 02; Mayo et al., 20 02; Mayo and Donner, 20 01; Ashcroft et al., 20 02; Ogawara...
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Mathematical and computational analysis of intracelluar dynamics 3
... Sections 3. 3 and 3. 4 Finally, novel systemic behaviors of the system are inferred and predicted from the simulation results (Sections 3. 5 and 3. 6) 34 3. 2 Formulation of kinetic models Figure 3- 1 Kinetic ... p 53] n1 k [ p 53] v3 = j3n1 + [ p 53] n1 v4 = k [PIP 2] k {[PIPT ] − [PIP3]} = j + [PIP 2] j + [PIPT ] − [PIP3] vm = k m [PTEN ][PIP 3] j m + [PIP3] (3- 3) k [ p 53] n2 v5 = v6 = j5n + [ p 53] n2 k [ ... conserved (Figure 3- 7) p53ss AKT*ss [p53ss] [AKTass ] [AKTT ] Figure 3- 7 Model M3: steady-state bifurcation diagrams of p 53 and AKTa The steady state values of p 53 ([p53ss], gray curve) and AKTa ([AKTass],...
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Mathematical and computational analysis of intracelluar dynamics 4
... damped oscillations of p53 and MDM2 protein levels in cell populations of mouse fibroblasts and human breast cancer epithelial MCF-7 cells, following 5Gy of IR The dynamics of the p53-MDM2 oscillator ... populations of human wild-type and Bloom’s syndrome patients’ fibroblast, following induction of DNA damage either by 20 J/m2 of UV radiation or 2.5 Gy of ionizing radiation (IR) ... following: periods of oscillation are to hrs; peaks of MDM2 oscillations lag behind p53 peak for 1.5 to 2.5 hrs; periods of oscillations decrease with increasing IR intensity; and peaks of p53 pulses...
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Mathematical and computational analysis of intracelluar dynamics 5
... (uM) 1 .5 1. 75 0.2 0. 25 0 .5 0. 75 0 .5 1. 25 [AKTT] (uM) 0. 75 1 .5 1. 75 1 .5 1. 75 120 350 D C 110 300 100 90 250 80 200 0. 25 0 .5 0. 75 1. 25 [AKTT] (uM) 1 .5 1. 75 70 0. 25 1. 25 [AKTT] (uM) Figure 5- 24 Oscillation ... Analog and digital forms of p53 oscillations Digital [TP53] 5. 7.2 [p53] uM Analog Tim e Figure 5- 20 Schematic illustration of analog and digital p53 oscillations Time-courses of analog (blue) and ... interval of 0.02 µM For each combination of k0 and j5, a p53 steady-state curve as a function of ρ is computed; k0,basal is set as 0.1 µM/min and j5 is set as 0 .5 µM in the computation of the p53 steady...
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Mathematical and computational analysis of intracelluar dynamics 6
... 53 55 57 59 61 63 65 67 69 71 73 75 77 79 Figure 6- 1B Percentage length of each exonic region relative to its flanking intronic region To illustrate the fact that the exonic region of the dystrophin ... in Figure 6- 1 121 1,000,000 N u m b e r o f b a s e p a irs 100,000 10,000 1,000 100 10 1 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 Exon 43 45 47 49 51 53 55 57 59 61 63 65 67 69 71 73 75 ... (Pramono et al., 19 96; Matsuo, 19 96; Matsuo and Takeshima, 2005; Wilton and Fletcher, 2005a, 2005b; Wilton et al., 2007; AartsmaRus et al., 2002, 2004, 2005, 20 06; van Deutekom and van Ommen, 2003;...
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Mathematical and computational analysis of intracelluar dynamics 7
... 0 .7 0 .7 0 .7 0.6 0.6 0.6 0.5 0.5 0.5 0.4 0.4 0.4 0.3 0.3 0.3 0.2 0.2 0.2 0.1 0.1 0 90 92 94 96 98 100 102 104 106 108 0.1 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 19 20 21 22 23 24 25 26 27 ... only 17% of target sites of (+) AONs had one or more clusters, they were manifested in 52% of target sites of (++) AONs Set B also exhibited similar trends: 71 %, 70 % and 80% of target sites of (–) ... 5th-percentile of L3 scores of (++) AON target sites (Appendix A-18) On the other hand, target sites of h45AON5 and h46AON4 graded as (+) and target sites of h51AON29, h55AON5 and h77AON2 graded...
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Mathematical and computational analysis of intracelluar dynamics 8
... systematically in place of current trial -and- error means, which could reduce the cost and waiting time of therapy In conclusion, the use of models has greatly aided in the understanding of the two intracellular ... dynamics between the two steady states of the system leads to the understanding of how cells regulate the switch between cell survival and death Interestingly, bistability between apoptotic and ... exhibit oscillatory dynamics under certain conditions The role of these oscillations of intracellular p53 protein levels upon DNA damage in cell survival and death in the context of the p53-AKT network...
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Mathematical and computational analysis of intracelluar dynamics 9
... specific and other known or unknown details of the regulation of p53 and AKT In particular, different forms of p53 are ignored to reduce the number of variables and unknown mechanistic and kinetic ... genetic diseases Examples of such 163 genes are beta-globin gene in thalassemia (Suwanmanee et al., 2002; Gorman et al., 2000; Sazani and Kole, 2003; Dominski and Kole, 199 3) and OA1 gene in ocular ... algorithm, the accuracy of the model is limited by the accuracy of such algorithms However, the use of vast numbers of predicted secondary structures that averaged 44,582 of them per exon (Appendix...
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Mathematical and computational analysis of intracelluar dynamics
... system A system- level understanding of the biological process and elucidating of the systems behaviors can then be obtained from the insights of such analyses The dynamics of two intracellular processes ... not a standalone process Analyses show that dynamics of co-transcriptional binding accessibilities of AON target sites could statistically correlate with efficacy and efficiency of 94% of previously ... physiologies and make novel predictions by analyzing intracellular dynamics based on the known interactions among intracellular components using mathematical and computational models Examples of intracellular...
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Review and analysis of renewable energy perspectives in Serbia
... of International Business and Cooperation, 2009 [17] Ministry of Energy and Mining Renewable Energy in Serbia Ministry of Energy and Mining, 2009 [18] Statistical Office of the Republic of Serbia ... Republic of Serbia Strategy of development of energy industry of Republic of Serbia until 2015, draft report, 2005 [6] EPS – Electric Power Industry of Serbia, Ministry of Energy and Mining of the ... of Serbia, Statistical Office of the Republik of Serbia [16] Larive Serbia Croatia, Serbia and Bosnia-Herzegovina - Renewable energy The Dutch Ministry of Economic Affairs, EVD – The Agency of...
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E-Recruiting Categories and Analysis of Fortune 100 Career Web Sites
... the company size and the characteristics of the career Web sites Each of the Fortune 100 companies’ Web sites was visited to determine the content of the corporate career Web sites Table shows ... Number of Companies 19 20 24 12 A Content Analysis of Fortune 100 Career Web Sites In this section, we analyze e-recruiting practices of the Fortune 100 companies Data were collected from the career ... content analysis of the Fortune 100 companies’ career Web sites All the Fortune 100 companies practice e-recruiting However, the content analysis indicates that most of them need to develop better e-recruiting...
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Đo kiểm đánh giá can nhiễu mạng truyền hình cáp The Measurement and Analysis of the effect of interference in Television Cable network
... quan mạng truyền hình cáp, đo kiểm đánh giá can nhiễu mạng truyền hình cáp, tình hình triển khai truyền hình cáp cấc tỉnh duyên hải phía bắc Việt Nam Nghiên cứu ảnh hƣởng can nhiễu mạng truyền hình ... nhận xét mạng A 2.1 Truyền hình cáp EG B 2.2 Truyền hình cáp ALPHA C 2.3 Truyền hình cáp Minh Trí D 2.4 Truyền hình cáp Thái Bình E 2.5 Truyền hình cáp Nam Định F 2.6 Truyền hình cáp Hải Phòng III ... ĐO XÁC ĐỊNH CAN NHIỄU TỪ MẠNG TRUYỀN HÌNH CÁP A 3.1 Một số can nhiễu điển hình 1) 3.1.1 Can nhiễu truyền hình cáp EG – Hải phòng gây cho mạng dùng riêng Công ty Việt Phương - Hiện tƣợng can nhiễu: ...
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