Pub Date : 2015-07-13DOI: 10.1109/LLS.2015.2449511
Jing Su, M. A. Henson
A critical decision in the mammalian cell cycle is whether to pass through the restriction point (R-point) or enter the cell cycle. In this letter, we modeled the decision-making system of the mammalian cell cycle entry and the simulated circadian regulation of the R-point driven by external epithelial growth factor (EGF) patterns. Our conceptual model replicated key signaling behaviors observed experimentally, suggesting that the proposed network captured the essential system features. The model revealed the dramatic importance of the EGF dynamics on promoting cell proliferation, showed that the EGF signal duration was more important than the signal strength for driving cells past the R-point, and suggested that the loss of circadian control of the cell cycle entry could be associated with cancer development.
{"title":"Circadian Gating of the Mammalian Cell Cycle Restriction Point: A Mathematical Analysis","authors":"Jing Su, M. A. Henson","doi":"10.1109/LLS.2015.2449511","DOIUrl":"https://doi.org/10.1109/LLS.2015.2449511","url":null,"abstract":"A critical decision in the mammalian cell cycle is whether to pass through the restriction point (R-point) or enter the cell cycle. In this letter, we modeled the decision-making system of the mammalian cell cycle entry and the simulated circadian regulation of the R-point driven by external epithelial growth factor (EGF) patterns. Our conceptual model replicated key signaling behaviors observed experimentally, suggesting that the proposed network captured the essential system features. The model revealed the dramatic importance of the EGF dynamics on promoting cell proliferation, showed that the EGF signal duration was more important than the signal strength for driving cells past the R-point, and suggested that the loss of circadian control of the cell cycle entry could be associated with cancer development.","PeriodicalId":87271,"journal":{"name":"IEEE life sciences letters","volume":"1 1","pages":"11-14"},"PeriodicalIF":0.0,"publicationDate":"2015-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/LLS.2015.2449511","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"62509608","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}
Pub Date : 2015-06-30DOI: 10.1109/LLS.2015.2451291
Burook Misganaw, M. Vidyasagar
In multiclass machine learning problems, one needs to distinguish between the nominal labels that do not have any natural ordering and the ordinal labels that are ordered. Ordinal labels are pervasive in biology, and some examples are given here. In this note, we point out the importance of making use of the order information when it is inherent to the problem. We demonstrate that algorithms that use this additional information outperform the algorithms that do not, on a case study of assigning one of four labels to the ovarian cancer patients on the basis of their time of progression-free survival. As an aside, it is also pointed out that the algorithms that make use of ordering information require fewer data normalizations. This aspect is important in biological applications, where data are plagued by variations in platforms and protocols, batch effects, and so on.
{"title":"Exploiting Ordinal Class Structure in Multiclass Classification: Application to Ovarian Cancer","authors":"Burook Misganaw, M. Vidyasagar","doi":"10.1109/LLS.2015.2451291","DOIUrl":"https://doi.org/10.1109/LLS.2015.2451291","url":null,"abstract":"In multiclass machine learning problems, one needs to distinguish between the nominal labels that do not have any natural ordering and the ordinal labels that are ordered. Ordinal labels are pervasive in biology, and some examples are given here. In this note, we point out the importance of making use of the order information when it is inherent to the problem. We demonstrate that algorithms that use this additional information outperform the algorithms that do not, on a case study of assigning one of four labels to the ovarian cancer patients on the basis of their time of progression-free survival. As an aside, it is also pointed out that the algorithms that make use of ordering information require fewer data normalizations. This aspect is important in biological applications, where data are plagued by variations in platforms and protocols, batch effects, and so on.","PeriodicalId":87271,"journal":{"name":"IEEE life sciences letters","volume":"1 1","pages":"15-18"},"PeriodicalIF":0.0,"publicationDate":"2015-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/LLS.2015.2451291","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"62509637","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}
Pub Date : 2015-06-30DOI: 10.1109/LLS.2015.2451291
Burook Misganaw;Mathukumalli Vidyasagar
In multiclass machine learning problems, one needs to distinguish between the nominal labels that do not have any natural ordering and the ordinal labels that are ordered. Ordinal labels are pervasive in biology, and some examples are given here. In this note, we point out the importance of making use of the order information when it is inherent to the problem. We demonstrate that algorithms that use this additional information outperform the algorithms that do not, on a case study of assigning one of four labels to the ovarian cancer patients on the basis of their time of progression-free survival. As an aside, it is also pointed out that the algorithms that make use of ordering information require fewer data normalizations. This aspect is important in biological applications, where data are plagued by variations in platforms and protocols, batch effects, and so on.
{"title":"Exploiting Ordinal Class Structure in Multiclass Classification: Application to Ovarian Cancer","authors":"Burook Misganaw;Mathukumalli Vidyasagar","doi":"10.1109/LLS.2015.2451291","DOIUrl":"https://doi.org/10.1109/LLS.2015.2451291","url":null,"abstract":"In multiclass machine learning problems, one needs to distinguish between the nominal labels that do not have any natural ordering and the ordinal labels that are ordered. Ordinal labels are pervasive in biology, and some examples are given here. In this note, we point out the importance of making use of the order information when it is inherent to the problem. We demonstrate that algorithms that use this additional information outperform the algorithms that do not, on a case study of assigning one of four labels to the ovarian cancer patients on the basis of their time of progression-free survival. As an aside, it is also pointed out that the algorithms that make use of ordering information require fewer data normalizations. This aspect is important in biological applications, where data are plagued by variations in platforms and protocols, batch effects, and so on.","PeriodicalId":87271,"journal":{"name":"IEEE life sciences letters","volume":"1 1","pages":"15-18"},"PeriodicalIF":0.0,"publicationDate":"2015-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/LLS.2015.2451291","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49908372","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}
Pub Date : 2015-06-16DOI: 10.1109/LLS.2015.2446211
Ana Sofia Rufino Ferreira;Justin Hsia;Murat Arcak
We propose a lateral inhibition system and analyze contrasting patterns of gene expression. The system consists of a set of compartments interconnected by channels. Each compartment contains a colony of cells that produce diffusible molecules to be detected by the neighboring colonies. Each cell is equipped with an inhibitory circuit that reduces its production when the detected signal is sufficiently strong. We characterize the parameter range in which steady-state patterns emerge.
{"title":"A Compartmental Lateral Inhibition System to Generate Contrasting Patterns","authors":"Ana Sofia Rufino Ferreira;Justin Hsia;Murat Arcak","doi":"10.1109/LLS.2015.2446211","DOIUrl":"https://doi.org/10.1109/LLS.2015.2446211","url":null,"abstract":"We propose a lateral inhibition system and analyze contrasting patterns of gene expression. The system consists of a set of compartments interconnected by channels. Each compartment contains a colony of cells that produce diffusible molecules to be detected by the neighboring colonies. Each cell is equipped with an inhibitory circuit that reduces its production when the detected signal is sufficiently strong. We characterize the parameter range in which steady-state patterns emerge.","PeriodicalId":87271,"journal":{"name":"IEEE life sciences letters","volume":"1 1","pages":"7-10"},"PeriodicalIF":0.0,"publicationDate":"2015-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/LLS.2015.2446211","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49908370","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}
Pub Date : 2015-06-16DOI: 10.1109/LLS.2015.2446211
Ana Sofia Rufino Ferreira, Justin Hsia, M. Arcak
We propose a lateral inhibition system and analyze contrasting patterns of gene expression. The system consists of a set of compartments interconnected by channels. Each compartment contains a colony of cells that produce diffusible molecules to be detected by the neighboring colonies. Each cell is equipped with an inhibitory circuit that reduces its production when the detected signal is sufficiently strong. We characterize the parameter range in which steady-state patterns emerge.
{"title":"A Compartmental Lateral Inhibition System to Generate Contrasting Patterns","authors":"Ana Sofia Rufino Ferreira, Justin Hsia, M. Arcak","doi":"10.1109/LLS.2015.2446211","DOIUrl":"https://doi.org/10.1109/LLS.2015.2446211","url":null,"abstract":"We propose a lateral inhibition system and analyze contrasting patterns of gene expression. The system consists of a set of compartments interconnected by channels. Each compartment contains a colony of cells that produce diffusible molecules to be detected by the neighboring colonies. Each cell is equipped with an inhibitory circuit that reduces its production when the detected signal is sufficiently strong. We characterize the parameter range in which steady-state patterns emerge.","PeriodicalId":87271,"journal":{"name":"IEEE life sciences letters","volume":"1 1","pages":"7-10"},"PeriodicalIF":0.0,"publicationDate":"2015-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/LLS.2015.2446211","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"62509598","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}
Pub Date : 2015-06-04DOI: 10.1109/LLS.2015.2439498
John H. Abel;Lukas A. Widmer;Peter C. St. John;Jörg Stelling;Francis J. Doyle
In the mammalian suprachiasmatic nucleus (SCN), a population of noisy cell-autonomous oscillators synchronizes to generate robust circadian rhythms at the organism level. Within these cells, two isoforms of Cryptochrome, Cry1