Transcription factors (TFs) are proteins that control the transcription of genetic information from DNA to mRNA by binding to specific DNA sequences either on their own or with other proteins as a complex. TFs thus support or suppress the recruitment of the corresponding RNA polymerase. In general, TFs are classified by structure or function. The TF, Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), is expressed in all cell types and tissues. NF-κB signaling and crosstalk are involved in several steps of carcinogenesis including in sequences involving pathogenic stimulus, chronic inflammation, fibrosis, establishment of its remodeling to the precancerous niche (PCN) and transition of a normal cell to a cancer cell. Triggered by various inflammatory cytokines, NF-κB is activated along with other TFs with subsequent stimulation of cell proliferation and inhibition of apoptosis. The involvement of NF-κB in carcinogenesis provides an opportunity to develop anti-NF-κB therapies. The complexity of these interactions requires that we elucidate those aspects of NF-κB interactions that play a role in carcinogenesis, the sequence of events leading to cancer.
{"title":"NF-κB signaling and crosstalk during carcinogenesis","authors":"B. Brücher, F. Lang, I. Jamall","doi":"10.1051/FOPEN/2019010","DOIUrl":"https://doi.org/10.1051/FOPEN/2019010","url":null,"abstract":"Transcription factors (TFs) are proteins that control the transcription of genetic information from DNA to mRNA by binding to specific DNA sequences either on their own or with other proteins as a complex. TFs thus support or suppress the recruitment of the corresponding RNA polymerase. In general, TFs are classified by structure or function. The TF, Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), is expressed in all cell types and tissues. NF-κB signaling and crosstalk are involved in several steps of carcinogenesis including in sequences involving pathogenic stimulus, chronic inflammation, fibrosis, establishment of its remodeling to the precancerous niche (PCN) and transition of a normal cell to a cancer cell. Triggered by various inflammatory cytokines, NF-κB is activated along with other TFs with subsequent stimulation of cell proliferation and inhibition of apoptosis. The involvement of NF-κB in carcinogenesis provides an opportunity to develop anti-NF-κB therapies. The complexity of these interactions requires that we elucidate those aspects of NF-κB interactions that play a role in carcinogenesis, the sequence of events leading to cancer.","PeriodicalId":6841,"journal":{"name":"4open","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74176196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Cordeiro, J. E. García, V. González-López, Sergio L. M. londono
In this paper, we classify by representativeness the elements of a set of complete genomic sequences of Dengue Virus Type 1 (DENV-1), corresponding to the outbreak in Japan during 2014. The set is coming from four regions: Chiba, Hyogo, Shizuoka and Tokyo. We consider this set as composed of independent samples coming from Markovian processes of finite order and finite alphabet. Under the assumption of the existence of a law that prevails in at least 50% of the samples of the set, we identify the sequences governed by the predominant law (see [1, 2]). The rule of classification is based on a local metric between samples, which tends to zero when we compare sequences of identical law and tends to infinity when comparing sequences with different laws. We found that the order of representativeness, from highest to lowest and according to the origin of the sequences is: Tokyo, Chiba, Hyogo, and Shizuoka. When comparing the Japanese sequences with their contemporaries from Asia, we find that the less representative sequence (from Shizuoka) is positioned in groups considerably far away from that which includes the sequences from the other regions in Japan, this offers evidence to suppose that the outbreak in Japan could be produced by more than one type of DENV-1.
{"title":"Classification of autochthonous dengue virus type 1 strains circulating in Japan in 2014","authors":"M. Cordeiro, J. E. García, V. González-López, Sergio L. M. londono","doi":"10.1051/FOPEN/2019018","DOIUrl":"https://doi.org/10.1051/FOPEN/2019018","url":null,"abstract":"In this paper, we classify by representativeness the elements of a set of complete genomic sequences of Dengue Virus Type 1 (DENV-1), corresponding to the outbreak in Japan during 2014. The set is coming from four regions: Chiba, Hyogo, Shizuoka and Tokyo. We consider this set as composed of independent samples coming from Markovian processes of finite order and finite alphabet. Under the assumption of the existence of a law that prevails in at least 50% of the samples of the set, we identify the sequences governed by the predominant law (see [1, 2]). The rule of classification is based on a local metric between samples, which tends to zero when we compare sequences of identical law and tends to infinity when comparing sequences with different laws. We found that the order of representativeness, from highest to lowest and according to the origin of the sequences is: Tokyo, Chiba, Hyogo, and Shizuoka. When comparing the Japanese sequences with their contemporaries from Asia, we find that the less representative sequence (from Shizuoka) is positioned in groups considerably far away from that which includes the sequences from the other regions in Japan, this offers evidence to suppose that the outbreak in Japan could be produced by more than one type of DENV-1.","PeriodicalId":6841,"journal":{"name":"4open","volume":"100 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85171689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Let G be a primitive strongly regular graph G such that the regularity is less than half of the order of G and A its matrix of adjacency, and let 𝒜 be the real Euclidean Jordan algebra of real symmetric matrices of order n spanned by the identity matrix of order n and the natural powers of A with the usual Jordan product of two symmetric matrices of order n and with the inner product of two matrices being the trace of their Jordan product. Next the spectra of two Hadamard series of 𝒜 associated to A2 is analysed to establish some conditions over the spectra and over the parameters of G.
{"title":"Euclidean Jordan algebras and some conditions over the spectra of a strongly regular graph","authors":"L. Vieira","doi":"10.1051/FOPEN/2019017","DOIUrl":"https://doi.org/10.1051/FOPEN/2019017","url":null,"abstract":"Let G be a primitive strongly regular graph G such that the regularity is less than half of the order of G and A its matrix of adjacency, and let 𝒜 be the real Euclidean Jordan algebra of real symmetric matrices of order n spanned by the identity matrix of order n and the natural powers of A with the usual Jordan product of two symmetric matrices of order n and with the inner product of two matrices being the trace of their Jordan product. Next the spectra of two Hadamard series of 𝒜 associated to A2 is analysed to establish some conditions over the spectra and over the parameters of G.","PeriodicalId":6841,"journal":{"name":"4open","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78548671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Balidis, I. Papadopoulou, Dimitris Malandris, Z. Zachariadis, Dimitrios Sakellaris, T. Vakalis, S. Asteriadis, P. Tranos, E. Loukovitis, M. Poulos, Z. Gatzioufas, G. Anogeianakis
Introduction: Refractive Surgery (RS), has advanced immensely in the last decades, utilizing methods and techniques that fulfill stringent criteria for safety, efficacy, cost-effectiveness, and predictability of the refractive outcome. Still, a non-negligible percentage of RS require corrective retreatment. In addition, surgeons should be able to advise their patients, beforehand, as to the probability that corrective RS will be necessary. The present article addresses these issues with regard to myopia and explores the use of Neural Networks as a solution to the problem of the prediction of the RS outcome. Methods: We used a computerized query to select patients who underwent RS with any of the available surgical techniques (PRK, LASEK, Epi-LASIK, LASIK) between January 2010 and July 2017 and we investigated 13 factors which are related to RS. The data were normalized by forcing the weights used in the forward and backward propagations to be binary; each integer was represented by a 12-bit serial code, so that following this preprocessing stage, the vector of the data values of all 13 parameters was encoded in a binary vector of 1 × (13 × 12) = 1 × 156 size. Following the preprocessing stage, eight independent Learning Vector Quantization (LVQ) networks were created in random way using the function Ivqnet of Matlab, each one of them responding to one query with (0 retreat class) or (1 correct class). The results of the eight LVQs were then averaged to permit a best estimate of the network’s performance while a voting procedure by the neural nets was used to arrive at the outcome Results: Our algorithm was able to predict in a statistically significant way (as evidenced by Cohen’s Kappa test result of 0.7595) the need for retreatment after initial RS with good sensitivity (0.8756) and specificity (0.9286). Conclusion: The results permit us to be optimistic about the future of using neural networks for the prediction of the outcome and, eventually, the planning of RS.
{"title":"Using neural networks to predict the outcome of refractive surgery for myopia","authors":"M. Balidis, I. Papadopoulou, Dimitris Malandris, Z. Zachariadis, Dimitrios Sakellaris, T. Vakalis, S. Asteriadis, P. Tranos, E. Loukovitis, M. Poulos, Z. Gatzioufas, G. Anogeianakis","doi":"10.1051/fopen/2019024","DOIUrl":"https://doi.org/10.1051/fopen/2019024","url":null,"abstract":"Introduction: Refractive Surgery (RS), has advanced immensely in the last decades, utilizing methods and techniques that fulfill stringent criteria for safety, efficacy, cost-effectiveness, and predictability of the refractive outcome. Still, a non-negligible percentage of RS require corrective retreatment. In addition, surgeons should be able to advise their patients, beforehand, as to the probability that corrective RS will be necessary. The present article addresses these issues with regard to myopia and explores the use of Neural Networks as a solution to the problem of the prediction of the RS outcome. Methods: We used a computerized query to select patients who underwent RS with any of the available surgical techniques (PRK, LASEK, Epi-LASIK, LASIK) between January 2010 and July 2017 and we investigated 13 factors which are related to RS. The data were normalized by forcing the weights used in the forward and backward propagations to be binary; each integer was represented by a 12-bit serial code, so that following this preprocessing stage, the vector of the data values of all 13 parameters was encoded in a binary vector of 1 × (13 × 12) = 1 × 156 size. Following the preprocessing stage, eight independent Learning Vector Quantization (LVQ) networks were created in random way using the function Ivqnet of Matlab, each one of them responding to one query with (0 retreat class) or (1 correct class). The results of the eight LVQs were then averaged to permit a best estimate of the network’s performance while a voting procedure by the neural nets was used to arrive at the outcome Results: Our algorithm was able to predict in a statistically significant way (as evidenced by Cohen’s Kappa test result of 0.7595) the need for retreatment after initial RS with good sensitivity (0.8756) and specificity (0.9286). Conclusion: The results permit us to be optimistic about the future of using neural networks for the prediction of the outcome and, eventually, the planning of RS.","PeriodicalId":6841,"journal":{"name":"4open","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87303699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The work proposes a new general nonlinear mathematical model describing the social process of two-level assimilation taking into account quadratic members of self-restriction of population growth of three sides. In the case of constant coefficients of the model, the first integral of a three-dimensional dynamic system has been found, which in the phase space of solutions is a cone. The three-dimensional dynamic system is reduced to two-dimensional and with the help of the Bendixon’s criterion the theorem of existence in the first quarter of the phase plane of the closed integral trajectory is proved. Thus, conditions on model parameters are found that do not fully assimilate the third side.
{"title":"Research of a three-dimensional nonlinear dynamic system describing the process of two-level assimilation","authors":"T. Chilachava, G. Pochkhua","doi":"10.1051/fopen/2020008","DOIUrl":"https://doi.org/10.1051/fopen/2020008","url":null,"abstract":"The work proposes a new general nonlinear mathematical model describing the social process of two-level assimilation taking into account quadratic members of self-restriction of population growth of three sides. In the case of constant coefficients of the model, the first integral of a three-dimensional dynamic system has been found, which in the phase space of solutions is a cone. The three-dimensional dynamic system is reduced to two-dimensional and with the help of the Bendixon’s criterion the theorem of existence in the first quarter of the phase plane of the closed integral trajectory is proved. Thus, conditions on model parameters are found that do not fully assimilate the third side.","PeriodicalId":6841,"journal":{"name":"4open","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83021941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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