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Bio Systems

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https://www.readbyqxmd.com/read/28535929/genetic-coding-and-united-hypercomplex-systems-in-the-models-of-algebraic-biology
#1
REVIEW
Sergey V Petoukhov
Structured alphabets of DNA and RNA in their matrix form of representations are connected with Walsh functions and a new type of systems of multidimensional numbers. This type generalizes systems of complex numbers and hypercomplex numbers, which serve as the basis of mathematical natural sciences and many technologies. The new systems of multi-dimensional numbers have interesting mathematical properties and are called in a general case as "systems of united-hypercomplex numbers" (or briefly "U-hypercomplex numbers")...
May 20, 2017: Bio Systems
https://www.readbyqxmd.com/read/28506827/how-tumor-growth-can-be-influenced-by-delayed-interactions-between-cancer-cells-and-the-microenvironment
#2
Dibakar Ghosh, Subhas Khajanchi, Sylvain Mangiarotti, Fabrice Denis, Syamal K Dana, Christophe Letellier
Although recent advances in oncology emphasized the role of microenvironment in tumor growth, the role of delays for modeling tumor growth is still uncertain. In this paper, we considered a model, describing the interactions of tumor cells with their microenvironment made of immune cells and host cells, in which we inserted, as suggested by the clinicians, two time delays, one in the interactions between tumor cells and immune cells and, one in the action of immune cells on tumor cells. We showed analytically that the singular point associated with the co-existence of the three cell populations loses its stability via a Hopf bifurcation...
May 12, 2017: Bio Systems
https://www.readbyqxmd.com/read/28495292/the-living-organism-strengthening-the-basis
#3
Roland Cazalis, Timoteo Carletti, Ron Cottam
In spite of the considerable amount of literature dedicated to the living organism, it retains its mysteries. One of the most discussed aspects nowadays is whether the term "cognition" can be attributed to all classes of organisms, or whether it only refers to a metaphoric use of one human reality. Our approach consists of retaining the term "cognition" and making it a technical term, in order to propose a generic model. In this way, cognition becomes what finally characterises an organism as an autonomous agent...
May 7, 2017: Bio Systems
https://www.readbyqxmd.com/read/28479110/boredom-begets-creativity-a-solution-to-the-exploitation-exploration-trade-off-in-predictive-coding
#4
Jaime Gomez-Ramirez, Tommaso Costa
Here we investigate whether systems that minimize prediction error e.g. predictive coding, can also show creativity, or on the contrary, prediction error minimization unqualifies for the design of systems that respond in creative ways to non recurrent problems. We argue that there is a key ingredient that has been overlooked by researchers that needs to be incorporated to understand intelligent behavior in biological and technical systems. This ingredient is boredom. We propose a mathematical model based on the Black-Scholes-Merton equation which provides mechanistic insights into the interplay between boredom and prediction pleasure as the key drivers of behavior...
May 4, 2017: Bio Systems
https://www.readbyqxmd.com/read/28465242/in-vitro-molecular-machine-learning-algorithm-via-symmetric-internal-loops-of-dna
#5
Ji-Hoon Lee, Seung Hwan Lee, Christina Baek, Hyosun Chun, Je-Hwan Ryu, Jin-Woo Kim, Russell Deaton, Byoung-Tak Zhang
Programmable biomolecules, such as DNA strands, deoxyribozymes, and restriction enzymes, have been used to solve computational problems, construct large-scale logic circuits, and program simple molecular games. Although studies have shown the potential of molecular computing, the capability of computational learning with DNA molecules, i.e., molecular machine learning, has yet to be experimentally verified. Here, we present a novel molecular learning in vitro model in which symmetric internal loops of double-stranded DNA are exploited to measure the differences between training instances, thus enabling the molecules to learn from small errors...
April 29, 2017: Bio Systems
https://www.readbyqxmd.com/read/28435013/modeling-chagas-disease-in-chile-from-vector-to-congenital-transmission
#6
Mauricio Canals, Dante Cáceres, Sergio Alvarado, Andrea Canals, Pedro E Cattan
Chagaś disease is a human health problem in Latin America. It is highly prevalent in northern Chile between the Arica-Parinacota and Coquimbo regions, with reported incidence of 3-11/100000 inhabitants and mortality of 0.3-0.4/100000. The interruption of vector transmission was reported in 1999 by means of the elimination of the primary vector, Triatoma infestans, from human dwellings, thus the epidemiologic dynamics of this disease should be modified. Here we model the dynamics of Chagaś disease based on previous models for vector and congenital transmission, propose a model that includes both transmission forms and perform simulations...
April 20, 2017: Bio Systems
https://www.readbyqxmd.com/read/28428118/on-plant-roots-logical-gates
#7
Andrew Adamatzky, Georgios Ch Sirakoulis, Genaro J Martínez, Frantisek Baluška, Stefano Mancuso
Theoretical constructs of logical gates implemented with plant roots are morphological computing asynchronous devices. Values of Boolean variables are represented by plant roots. A presence of a plant root at a given site symbolises the logical True, an absence the logical False. Logical functions are calculated via interaction between roots. Two types of two-inputs-two-outputs gates are proposed: a gate 〈x, y〉→〈xy, x+y〉 where root apexes are guided by gravity and a gate 〈x,y〉→〈x¯y,x〉 where root apexes are guided by humidity...
April 17, 2017: Bio Systems
https://www.readbyqxmd.com/read/28428117/cellular-non-linear-network-model-of-microbial-fuel-cell
#8
Michail-Antisthenis Tsompanas, Andrew Adamatzky, Ioannis Ieropoulos, Neil Phillips, Georgios Ch Sirakoulis, John Greenman
A cellular non-linear network (CNN) is a uniform regular array of locally connected continuous-state machines, or nodes, which update their states simultaneously in discrete time. A microbial fuel cell (MFC) is an electro-chemical reactor using the metabolism of bacteria to drive an electrical current. In a CNN model of the MFC, each node takes a vector of states which represent geometrical characteristics of the cell, like the electrodes or impermeable borders, and quantify measurable properties like bacterial population, charges produced and hydrogen ion concentrations...
April 17, 2017: Bio Systems
https://www.readbyqxmd.com/read/28410875/particle-sorting-by-paramecium-cilia-arrays
#9
Richard Mayne, James G H Whiting, Gabrielle Wheway, Chris Melhuish, Andrew Adamatzky
Motile cilia are cell-surface organelles whose purposes, in ciliated protists and certain ciliated metazoan epithelia, include generating fluid flow, sensing and substance uptake. Certain properties of cilia arrays, such as beating synchronisation and manipulation of external proximate particulate matter, are considered emergent, but remain incompletely characterised despite these phenomena having being the subject of extensive modelling. This study constitutes a laboratory experimental characterisation of one of the emergent properties of motile cilia: manipulation of adjacent particulates...
April 12, 2017: Bio Systems
https://www.readbyqxmd.com/read/28392341/computational-complexity-of-algorithms-for-sequence-comparison-short-read-assembly-and-genome-alignment
#10
REVIEW
Shakuntala Baichoo, Christos A Ouzounis
A multitude of algorithms for sequence comparison, short-read assembly and whole-genome alignment have been developed in the general context of molecular biology, to support technology development for high-throughput sequencing, numerous applications in genome biology and fundamental research on comparative genomics. The computational complexity of these algorithms has been previously reported in original research papers, yet this often neglected property has not been reviewed previously in a systematic manner and for a wider audience...
April 6, 2017: Bio Systems
https://www.readbyqxmd.com/read/28385591/optimal-control-problems-of-mosquito-borne-disease-subject-to-changes-in-feeding-behavior-of-aedes-mosquitoes
#11
M A Masud, Byul Nim Kim, Yongkuk Kim
Dengue viruses (DENV) are transmitted to humans by the bite of Aedes mosquitoes. It is known that dengue virus infection in Aedes aegypti female mosquitoes makes a change in the feeding behavior of the infected mosquitoes. In this study, using the forces of infection, we incorporated the effect of changes in the feeding behavior of mosquitoes into the standard vector-borne SIR-SI model. It has been proved that both a single-strain model and a two-strain model exhibit forward bifurcations. Moreover, optimal implementations of control with specific prevention measures for dengue transmission are analyzed...
April 3, 2017: Bio Systems
https://www.readbyqxmd.com/read/28377182/a-biophysical-approach-to-cancer-dynamics-quantum-chaos-and-energy-turbulence
#12
REVIEW
Abicumaran Uthamacumaran
Cancer is a term used to define a collective set of rapidly evolving cells with immortalized replication, altered epimetabolomes and patterns of longevity. Identifying a common signaling cascade to target all cancers has been a major obstacle in medicine. A quantum dynamic framework has been established to explain mutation theory, biological energy landscapes, cell communication patterns and the cancer interactome under the influence of quantum chaos. Quantum tunneling in mutagenesis, vacuum energy field dynamics, and cytoskeletal networks in tumor morphogenesis have revealed the applicability for description of cancer dynamics, which is discussed with a brief account of endogenous hallucinogens, bioelectromagnetism and water fluctuations...
April 2, 2017: Bio Systems
https://www.readbyqxmd.com/read/28344109/phylogenomic-proximity-and-metabolic-discrepancy-of-methanosarcina-mazei-go1-across-methanosarcinal-genomes
#13
M Bharathi, P Chellapandi
Methanosarcina mazei Go1 is a heterotrophic methanogenic archaean contributing a significant role in global methane cycling and biomethanation process. Phylogenomic relatedness and metabolic discrepancy of this genome were described herein by comparing its whole genome sequence, intergenomic distance, genome function, synteny homologs and origin of replication, and marker genes with very closely related genomes, Methanosarcina acetivorans and Methanosarcina barkeri. Phylogenomic analysis of this study revealed that genome functional feature and metabolic core of M...
March 23, 2017: Bio Systems
https://www.readbyqxmd.com/read/28300609/a-binary-representation-of-the-genetic-code
#14
Louis R Nemzer
This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA bases is assigned a unique 2-bit identifier, so that the 64 triplet codons are each indexed by a 6-bit label. The ordering of the bits reflects the hierarchical organization manifested by the DNA replication/repair and tRNA translation systems. In this system, transition and transversion mutations are naturally expressed as binary operations, and the severities of the different point mutations can be analyzed...
March 12, 2017: Bio Systems
https://www.readbyqxmd.com/read/28263840/a-mathematical-model-predicting-host-mitochondrial-pyruvate-transporter-activity-to-be-a-critical-regulator-of-mycobacterium-tuberculosis-pathogenicity
#15
Parul Mehrotra, Kanury V S Rao, Samrat Chatterjee
Modulation of host metabolic machinery by Mycobacterium tuberculosis is a well established phenomenon. In our earlier study (Mehrotra et al., 2014), we observed a marked increase in acetyl-CoA levels in cells bearing virulent M. tuberculosis infections compared to host cells harbouring avirulent infections. The difference was observed inspite of similar levels of total host cellular pyruvate in both infection types. The present study aimed in capturing the cause for such a phenomenon that defines the pathogenicity of M...
March 2, 2017: Bio Systems
https://www.readbyqxmd.com/read/28254369/applying-attractor-dynamics-to-infer-gene-regulatory-interactions-involved-in-cellular-differentiation
#16
Ahmadreza Ghaffarizadeh, Gregory J Podgorski, Nicholas S Flann
The dynamics of gene regulatory networks (GRNs) guide cellular differentiation. Determining the ways regulatory genes control expression of their targets is essential to understand and control cellular differentiation. The way a regulatory gene controls its target can be expressed as a gene regulatory function. Manual derivation of these regulatory functions is slow, error-prone and difficult to update as new information arises. Automating this process is a significant challenge and the subject of intensive effort...
February 28, 2017: Bio Systems
https://www.readbyqxmd.com/read/28238940/dynamic-landscape-models-of-coevolutionary-games
#17
Hendrik Richter
Players of coevolutionary games may update not only their strategies but also their networks of interaction. Based on interpreting the payoff of players as fitness, dynamic landscape models are proposed. The modeling procedure is carried out for Prisoner's Dilemma (PD) and Snowdrift (SD) games that both use either birth-death (BD) or death-birth (DB) strategy updating. The main focus is on using dynamic fitness landscapes as a mathematical model of coevolutionary game dynamics. Hence, an alternative tool for analyzing coevolutionary games becomes available, and landscape measures such as modality, ruggedness and information content can be computed and analyzed...
February 24, 2017: Bio Systems
https://www.readbyqxmd.com/read/28238939/temporary-removal-unitary-circular-code-motifs-in-genomes-of-eukaryotes
#18
Karim El Soufi, Christian J Michel
The publisher regrets that this article has been temporarily removed. A replacement will appear as soon as possible in which the reason for the removal of the article will be specified, or the article will be reinstated. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
February 24, 2017: Bio Systems
https://www.readbyqxmd.com/read/28174135/a-system-of-recurrent-neural-networks-for-modularising-parameterising-and-dynamic-analysis-of-cell-signalling-networks
#19
S Samarasinghe, H Ling
In this paper, we show how to extend our previously proposed novel continuous time Recurrent Neural Networks (RNN) approach that retains the advantage of continuous dynamics offered by Ordinary Differential Equations (ODE) while enabling parameter estimation through adaptation, to larger signalling networks using a modular approach. Specifically, the signalling network is decomposed into several sub-models based on important temporal events in the network. Each sub-model is represented by the proposed RNN and trained using data generated from the corresponding ODE model...
February 4, 2017: Bio Systems
https://www.readbyqxmd.com/read/28167098/what-if-houses-were-powered-by-milk
#20
Neil Phillips, Andrew Adamatzky, Richard Mayne
Living architectures and green energy are hot topics of the applied sciences. They aim to develop buildings that co-live with their environment and co-habit with people they house. An ultimate goal would be to make every block in a building capable of producing energy. We present results of scoping, and somewhat illustrative, experiments on generating electrical energy in modified aerated concrete blocks. These blocks are commonly used in modern building industry and therefore make an ideal candidate for 'inbuilt' microbial bio-reactors...
February 3, 2017: Bio Systems
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