Modeling of the quantum entangled state transfer protocol in the cell microtubules
Biosystems. 2023 Dec 10;235:105100. doi: 10.1016/j.biosystems.2023.105100. Online ahead of print.ABSTRACTIn the work based on the quantum gates representation, the modeling of the quantum entangled state transfer protocol in the cell microtubules is carried out. It has been proved that considered data transmission can be determined as a mechanism that ensures the transfer of information through a quantum channel in microtubule tryptophans chain. The influence of external factors on the formation of entangled states is investigated. It is shown that the influence of the external environment has an ambiguous character and ca...
Source: Biosystems - December 10, 2023 Category: Biotechnology Authors: Sergey E Shirmovsky Source Type: research
Modeling of the quantum entangled state transfer protocol in the cell microtubules
Biosystems. 2023 Dec 10;235:105100. doi: 10.1016/j.biosystems.2023.105100. Online ahead of print.ABSTRACTIn the work based on the quantum gates representation, the modeling of the quantum entangled state transfer protocol in the cell microtubules is carried out. It has been proved that considered data transmission can be determined as a mechanism that ensures the transfer of information through a quantum channel in microtubule tryptophans chain. The influence of external factors on the formation of entangled states is investigated. It is shown that the influence of the external environment has an ambiguous character and ca...
Source: Biosystems - December 10, 2023 Category: Biotechnology Authors: Sergey E Shirmovsky Source Type: research
Modeling of the quantum entangled state transfer protocol in the cell microtubules
Biosystems. 2023 Dec 8:105100. doi: 10.1016/j.biosystems.2023.105100. Online ahead of print.ABSTRACTIn the work based on the quantum gates representation, the modeling of the quantum entangled state transfer protocol in the cell microtubules is carried out. It has been proved that considered data transmission can be determined as a mechanism that ensures the transfer of information through a quantum channel in microtubule tryptophans chain. The influence of external factors on the formation of entangled states is investigated. It is shown that the influence of the external environment has an ambiguous character and can con...
Source: Biosystems - December 10, 2023 Category: Biotechnology Authors: S Eh Shirmovsky Source Type: research
PTEN expression can be used as a switch between senescence and apoptosis in breast cancer cells according to a logical model of the G2/M checkpoint
Biosystems. 2023 Dec 6:105097. doi: 10.1016/j.biosystems.2023.105097. Online ahead of print.ABSTRACTWorldwide, the second-highest mortality rate is caused by breast cancer (BC). The most studied BC cell line is MCF-7 because it exhibits strong consistency with clinical cases and is a good system for analyzing tumors with functional estrogen receptors (ER-positive cancers). In this paper, we introduce the first theoretical method for describing PTEN-loss-induced cellular senescence (PICS), which is an increase in cellular senescence caused by PTEN knockout, utilizing a logical model of the G2/M checkpoint. We predict that P...
Source: Biosystems - December 8, 2023 Category: Biotechnology Authors: Yolanda M B Marcello Daner A Silveira Shantanu Gupta Jos é Carlos M Mombach Source Type: research
SetQuence & amp; SetOmic: Deep set transformers for whole genome and exome tumour analysis
Biosystems. 2023 Dec 6:105095. doi: 10.1016/j.biosystems.2023.105095. Online ahead of print.ABSTRACTIn oncology, Deep Learning has shown great potential to personalise tasks such as tumour type classification, based on per-patient omics data-sets. Being high dimensional, incorporation of such data in one model is a challenge, often leading to one-dimensional studies and, therefore, information loss. Instead, we first propose relying on non-fixed sets of whole genome or whole exome variant-associated sequences, which can be used for supervised learning of oncology-relevant tasks by our Set Transformer based Deep Neural Netw...
Source: Biosystems - December 8, 2023 Category: Biotechnology Authors: Neringa Jurenaite Daniel Le ón-Periñán Veronika Donath Sunna Torge Ren é Jäkel Source Type: research
PTEN expression can be used as a switch between senescence and apoptosis in breast cancer cells according to a logical model of the G2/M checkpoint
Biosystems. 2023 Dec 6:105097. doi: 10.1016/j.biosystems.2023.105097. Online ahead of print.ABSTRACTWorldwide, the second-highest mortality rate is caused by breast cancer (BC). The most studied BC cell line is MCF-7 because it exhibits strong consistency with clinical cases and is a good system for analyzing tumors with functional estrogen receptors (ER-positive cancers). In this paper, we introduce the first theoretical method for describing PTEN-loss-induced cellular senescence (PICS), which is an increase in cellular senescence caused by PTEN knockout, utilizing a logical model of the G2/M checkpoint. We predict that P...
Source: Biosystems - December 8, 2023 Category: Biotechnology Authors: Yolanda M B Marcello Daner A Silveira Shantanu Gupta Jos é Carlos M Mombach Source Type: research
SetQuence & amp; SetOmic: Deep set transformers for whole genome and exome tumour analysis
Biosystems. 2023 Dec 6:105095. doi: 10.1016/j.biosystems.2023.105095. Online ahead of print.ABSTRACTIn oncology, Deep Learning has shown great potential to personalise tasks such as tumour type classification, based on per-patient omics data-sets. Being high dimensional, incorporation of such data in one model is a challenge, often leading to one-dimensional studies and, therefore, information loss. Instead, we first propose relying on non-fixed sets of whole genome or whole exome variant-associated sequences, which can be used for supervised learning of oncology-relevant tasks by our Set Transformer based Deep Neural Netw...
Source: Biosystems - December 8, 2023 Category: Biotechnology Authors: Neringa Jurenaite Daniel Le ón-Periñán Veronika Donath Sunna Torge Ren é Jäkel Source Type: research
A computational method for small molecule-RNA binding sites identification by utilizing position specificity and complex network information
Biosystems. 2023 Dec 5;235:105094. doi: 10.1016/j.biosystems.2023.105094. Online ahead of print.ABSTRACTSome computational methods have been given for small molecule-RNA binding site identification due to that it plays a significant role in revealing biology function researches. However, it is still challenging to design an accurate model, especially for MCC. We designed a feature extraction technology from two aspects (position specificity and complex network information). Specifically, complex network was employed to express the space topological structure and sequence position information for improving prediction effect...
Source: Biosystems - December 6, 2023 Category: Biotechnology Authors: Lichao Zhang Kang Xiao Liang Kong Source Type: research
Kinetics of cancer metastasis
Biosystems. 2023 Dec 4:105098. doi: 10.1016/j.biosystems.2023.105098. Online ahead of print.ABSTRACTThe formation of metastases during cancer is now considered to be induced by migrating metastatic stem cells (MetSCs) in preexisting niches or niches induced by MetSCs or tumor-derived exosomes (TDEs). I propose and compare two simplest generic models describing these two scenarios. The number of tumours is predicted (i) to increase exponentially in the case of preexisting niches and (ii) to diverge during a finite time interval in the case of induced niches. The latter prediction is novel and of interest because rapid colla...
Source: Biosystems - December 6, 2023 Category: Biotechnology Authors: Vladimir P Zhdanov Source Type: research
A computational method for small molecule-RNA binding sites identification by utilizing position specificity and complex network information
Biosystems. 2023 Dec 4:105094. doi: 10.1016/j.biosystems.2023.105094. Online ahead of print.ABSTRACTSome computational methods have been given for small molecule-RNA binding site identification due to that it plays a significant role in revealing biology function researches. However, it is still challenging to design an accurate model, especially for MCC. We designed a feature extraction technology from two aspects (position specificity and complex network information). Specifically, complex network was employed to express the space topological structure and sequence position information for improving prediction effect. Th...
Source: Biosystems - December 6, 2023 Category: Biotechnology Authors: Lichao Zhang Kang Xiao Liang Kong Source Type: research
Kinetics of cancer metastasis
Biosystems. 2023 Dec 4:105098. doi: 10.1016/j.biosystems.2023.105098. Online ahead of print.ABSTRACTThe formation of metastases during cancer is now considered to be induced by migrating metastatic stem cells (MetSCs) in preexisting niches or niches induced by MetSCs or tumor-derived exosomes (TDEs). I propose and compare two simplest generic models describing these two scenarios. The number of tumours is predicted (i) to increase exponentially in the case of preexisting niches and (ii) to diverge during a finite time interval in the case of induced niches. The latter prediction is novel and of interest because rapid colla...
Source: Biosystems - December 6, 2023 Category: Biotechnology Authors: Vladimir P Zhdanov Source Type: research
A computational method for small molecule-RNA binding sites identification by utilizing position specificity and complex network information
Biosystems. 2023 Dec 4:105094. doi: 10.1016/j.biosystems.2023.105094. Online ahead of print.ABSTRACTSome computational methods have been given for small molecule-RNA binding site identification due to that it plays a significant role in revealing biology function researches. However, it is still challenging to design an accurate model, especially for MCC. We designed a feature extraction technology from two aspects (position specificity and complex network information). Specifically, complex network was employed to express the space topological structure and sequence position information for improving prediction effect. Th...
Source: Biosystems - December 6, 2023 Category: Biotechnology Authors: Lichao Zhang Kang Xiao Liang Kong Source Type: research
Kinetics of cancer metastasis
Biosystems. 2023 Dec 4:105098. doi: 10.1016/j.biosystems.2023.105098. Online ahead of print.ABSTRACTThe formation of metastases during cancer is now considered to be induced by migrating metastatic stem cells (MetSCs) in preexisting niches or niches induced by MetSCs or tumor-derived exosomes (TDEs). I propose and compare two simplest generic models describing these two scenarios. The number of tumours is predicted (i) to increase exponentially in the case of preexisting niches and (ii) to diverge during a finite time interval in the case of induced niches. The latter prediction is novel and of interest because rapid colla...
Source: Biosystems - December 6, 2023 Category: Biotechnology Authors: Vladimir P Zhdanov Source Type: research
Identification of common factors among fibrosarcoma, rhabdomyosarcoma, and osteosarcoma by network analysis
In conclusion, the common DEGs identified in this study have been shown to play significant and multiple roles in various other cancers based on the literature review, indicating their significance.PMID:38052344 | DOI:10.1016/j.biosystems.2023.105093 (Source: Biosystems)
Source: Biosystems - December 5, 2023 Category: Biotechnology Authors: Mehran Radak Nakisa Ghamari Hossein Fallahi Source Type: research
Animal design advantage from the analogy between friction and body heat loss
Biosystems. 2023 Dec 2:105096. doi: 10.1016/j.biosystems.2023.105096. Online ahead of print.ABSTRACTWhen a fluid accelerates as it sweeps a solid surface there are two consequences: the friction and the heat transfer (thermal contact) between fluid and solid increase simultaneously. This is known as the universal analogy between fluid friction and heat transfer. In thermal engineering these two effects are problematic because improved thermal contact is beneficial, and increased friction (i.e., pumping power) is detrimental to overall performance. In the present article we question whether the 'analogy' between these confl...
Source: Biosystems - December 4, 2023 Category: Biotechnology Authors: Adrian Bejan Jordan D Charles Source Type: research
