3,330 results match your criteria Biosystems[Journal]


Kinetic modelling of compartmentalised reaction networks.

Biosystems 2020 Jul 4:104203. Epub 2020 Jul 4.

Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa. Electronic address:

This paper presents a comprehensive treatment of kinetic modelling of compartmentalised reaction networks in the context of systems biology. There is still a lot of confusion about how to go about constructing compartment models, and many published models are flawed with respect to how they handle compartmentation. The modelling framework described here answers two key questions: Which rate laws should be used to describe the rates of reactions in compartmentalised systems? How should these rate laws be incorporated in the ordinary differential equations (ODEs) that describe the dynamics of the compartmentalised system? The framework rests on the fundamental definition of reaction rate as the number of reaction events per time, which is related to the time derivative of mole amount of reactant or product, an extensive property that is directly proportional to the size of the compartment in which the reaction events occur. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104203DOI Listing

Role of fear in a predator-prey system with ratio-dependent functional response in deterministic and stochastic environment.

Biosystems 2020 Jul 3:104176. Epub 2020 Jul 3.

Department of Mathematics, Indian Institute of Engineering Science and Technology, Shibpur, B. Garden, Howrah, 711103, India. Electronic address:

In this article, we propose and analyse a predator-prey model where apart from direct predation the prey population is affected by the fear induced from predators. The reproduction of the prey population is reduced as a cost of fear. The predator is assumed to consume the prey according to ratio-dependent functional response and is also involved in intra-specific competition due to limited resources of food. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104176DOI Listing

Bisimilar Booleanization of multivalued networks.

Biosystems 2020 Jul 2:104205. Epub 2020 Jul 2.

IBISC - Paris-Saclay University, Univ. Evry, France. Electronic address:

Discrete modelling frameworks of Biological networks can be divided in two distinct categories: Boolean and multivalued. Although multivalued networks are more expressive for qualifying the regulatory behaviours modelled by more than two values, the ability to automatically convert them to Boolean network with an equivalent behaviour breaks down the fundamental borders between the two approaches. Theoretically investigating the conversion process provides relevant insights into bridging the gap between them. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104205DOI Listing

The maximality of circular codes in genes statistically verified.

Biosystems 2020 Jul 2:104201. Epub 2020 Jul 2.

Theoretical Bioinformatics, ICube, CNRS, University of Strasbourg, 300 Boulevard Sébastien Brant, 67400, Illkirch, France. Electronic address:

The maximality of circular codes in genes has 20 preferential trinucleotides in each frame. This combinatorial property is statistically verified in the genes of both bacteria and eukaryotes, and by two approaches computing the trinucleotide occurrence frequencies in the 3 frames at the gene population level (classical method) and at the gene level (recent method). Several remarks explain why the codon usage parameter is unable to identify the circular codes. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104201DOI Listing

A paradigm shift for the Great Bifurcation.

Biosystems 2020 Jun 30:104193. Epub 2020 Jun 30.

GSIS. the Institute for a Global Sustainable Information Society, Steinbrechergasse 15, 1220, Vienna, Austria. Electronic address:

This paper is an attempt to achieve an understanding of the situation the evolution of humanity is confronted with in the age of global challenges. Since global challenges are problems of unprecedented complexity, it is argued that a secular paradigm shift is required away from the overemphasis on allegedly neutral standpoints, on a mechanistic picture of the world and on deductive logics towards accounts of emergence, of systemicity, informationality and conviviality, building upon each other and providing together a transdisciplinary edifice of the sciences, in the end, for, and by the inclusion of, citizens. Viewed from such a combined perspective, the current social evolution is punctuated by a Great Bifurcation similar to bifurcations other emergent systems have been facing. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7326454PMC

Gene regulatory networks in Drosophila early embryonic development as a model for the study of the temporal identity of neuroblasts.

Biosystems 2020 Jun 30:104192. Epub 2020 Jun 30.

I. M. Sechenov Institute of Evolutionary Physiology and Biochemistry Russian Academy of Sciences, 44 Thorez Pr, St.Petersburg, 194223, Russia; Computer Science and CEWIT, SUNY Stony Brook, Stony Brook, 1500 Stony Brook Road, Stony Brook, 11794, NY, USA.

Genes belonging to the "gap" and "gap-like" family constitute the best-studied gene regulatory networks (GRNs) in Drosophila embryogenesis. Gap genes are a core of two subnetworks controlling embryonic segmentation: (hunchback, hb; Krüppel, Kr; giant, gt; and knirps, kni) and (hb; Kr; pou-domain, pdm; and, probably, castor, cas). Of particular interest is that (hb, Kr, pdm, cas) also specifies the temporal identity of stem cells, neuroblasts, in Drosophila neurogenesis. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104192DOI Listing

Modelling persistence over generations in biological and cultural evolution based on differential paces of change.

Biosystems 2020 Jun 26:104189. Epub 2020 Jun 26.

CeStatS, Institut de Recherche Mathématique Avancée, Université de Strasbourg, CNRS, Strasbourg, France. Electronic address:

Paces of change are faster in cultural evolution than in biological evolution due to different levels of stability in information storage. This study develops mathematical models to investigate the consequences of differential mutation rates on the ability of groups of information units to survive over many generations. We examined the ability of groups composed of connected units to live on despite the occurrence of deleterious mutations that occur at probabilities ranging from 10 to 10. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104189DOI Listing

Fuzzy-based self organizing aggregation method for swarm robots.

Biosystems 2020 Jun 26:104187. Epub 2020 Jun 26.

Tokat Gaziosmanpaşa Universty, Faculty of Engineering and Architecture, Electric Electronic Engineering Department, Tokat, Turkey.

Fuzzy-based self-organizing aggregation method was suggested in the present study for swarm robots. In the suggested method, Swarm robots evaluate their limited sensor input via rules of fuzzy logic and display aggregation behavior with the suggested aggregation method. In the meantime, swarm robots also have the ability to escape the obstacles in a bounded arena with this method. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104187DOI Listing

A computational approach to validate novel drug targets of gentianine from Swertiya chirayita in Plasmodium falciparum.

Biosystems 2020 Jun 25:104175. Epub 2020 Jun 25.

School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, 751024, Odisha, India.

Gentianine is one of the compounds found in the plant Swertiya chirayita that is known for its antimalarial activity. However, its exact molecular mechanism of action is yet to be understood. In our present study, we applied several computational approaches to filter out and determine possible targets of gentianine in Plasmodium falciparum 3D7. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104175DOI Listing

Mean-reverting neuronal model based on two alternating patterns.

Authors:
Nikita Ratanov

Biosystems 2020 Jun 20:104190. Epub 2020 Jun 20.

Chelyabinsk State University, Br. Kashirinykh str., 129, Chelyabinsk, Russia. Electronic address:

A neuronal action potential model based on the generalised two-state Ornstein-Uhlenbeck process is studied. The model well describes all phases of a neuronal spike cycle, and the intrinsic parameters of the model have clear specification. Laplace transforms of a firing time are obtained explicitly. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104190DOI Listing

Random effects inducing heart pathological dynamics: An approach based on mathematical models.

Biosystems 2020 Jun 17:104177. Epub 2020 Jun 17.

Universidade Federal do Rio de Janeiro, COPPE, Department of Mechanical Engineering, Center for Nonlinear Mechanics, P.O. Box 68.503, 21.941.972, Rio de Janeiro, RJ, Brazil. Electronic address:

This work deals with an investigation of randomness effects on heart rhythm analysis. A mathematical model composed by three-coupled nonlinear oscillators coupled by time-delayed connections is employed for this aim. In this regard, heart rhythm is governed by delayed-differential equations. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104177DOI Listing

GPUPeP: Parallel Enzymatic Numerical P System simulator with a Python-based interface.

Biosystems 2020 Jun 11:104186. Epub 2020 Jun 11.

National Institute of Technology Karnataka, Surathkal, India. Electronic address:

Membrane computing is a computational paradigm inspired by the structure and behavior of a living cell. P Systems are the computing devices that are used to realize membrane computing models. Numerous theoretical studies on many variants of P Systems have shown them to be computationally universal. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104186DOI Listing

The phylogenetic distribution of the glutaminyl-tRNA synthetase and Glu-tRNA amidotransferase in the fundamental lineages would imply that the ancestor of archaea, that of eukaryotes and LUCA were progenotes.

Biosystems 2020 Jun 11:104174. Epub 2020 Jun 11.

The Ionian School, Genetic Code and tRNA Origin Laboratory, Via Roma 19, 67030, Alfedena, L'Aquila, Italy; Institute of Biosciences and Bioresources, National Research Council, Via P. Castellino, 111, 80131, Naples, Italy. Electronic address:

The function of the glutaminyl-tRNA synthetase and Glu-tRNA amidotransferase might be related to the origin of the genetic code because, for example, glutaminyl-tRNA synthetase catalyses the fundamental reaction that makes the genetic code. If the evolutionary stage of the origin of these two enzymes could be unambiguously identified, then the genetic code should still have been originating at that particular evolutionary stage because the fundamental reaction that makes the code itself was still evidently evolving. This would result in that particular evolutionary moment being attributed to the evolutionary stage of the progenote because it would have a relationship between the genotype and the phenotype not yet fully realized because the genetic code was precisely still originating. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104174DOI Listing

Chloroplast history clarified by the criterion of light-harvesting complex.

Biosystems 2020 Jun 10:104173. Epub 2020 Jun 10.

St. Petersburg State University, Department of Microbiology, St. Petersburg, Russia. Electronic address:

Bacterial essence of mitochondria and chloroplasts was initially proclaimed in general outline. Later, the remarkable insight gave way to an elaborate hypothesis. Finally, it took shape of a theory confirmed by molecular biology data. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104173DOI Listing

Natural pyrrolysine-biased translation of stop codons in mitochondrial peptides entirely coded by expanded codons.

Biosystems 2020 Jun 10:104180. Epub 2020 Jun 10.

Aix-Marseille University, IRD, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France. Electronic address:

During the noncanonical deletion transcription, k nucleotides are systematically skipped/deleted after each transcribed trinucleotide producing deletion-RNAs (delRNAs). Peptides matching delRNAs either result from (a) canonical translation of delRNAs; or (b) noncanonical translation of regular transcripts along expanded codons. Only along frame "0" (start site) (a) and (b) produce identical peptides. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104180DOI Listing

Calcium ions tune the beats of cilia and flagella.

Biosystems 2020 Jun 10:104172. Epub 2020 Jun 10.

Faculty of Technical Sciences, University of Novi Sad, Serbia Slobodan Zdravković, Institute of Nuclear Sciences, Vinča, Serbia.

The cytoskeleton of cilia and flagella is so called axoneme a stable cylindrical architecture of nine microtubule doublets. Axoneme performs periodic bending motion by utilizing specific dynein motor family powered by ATP hydrolysis. It is still unclear how this highly organized "ciliary beat" is being initiated and strongly coordinated by the combined action of hundreds dynein motors. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104172DOI Listing

On the use of basic terms eukaryotic cell/eukaryotes/nucleated organisms, on evolutionary views challenged by the discovery of eukaryotic signatures in asgard archaea, and on a new taxon name for eukaryotes.

Biosystems 2020 Jun 10:104178. Epub 2020 Jun 10.

St. Petersburg State University, Department of Microbiology, Vasilyevsky Island, Liniya 16-ya, 29, 199178, St. Petersburg, Russia. Electronic address:

The endosymbiosis theory most widely accepted variant surmises the engulfment of bacterial cell by archaeal cell. For decades, this scenario was reputed to be an unconfirmed hypothesis, and only recently it has obtained an indirect proof in Asgard archaea environmental DNA encoding eukaryotic signatures - actin cytoskeleton, small GTPases, and ESCRT complex. In view of growing interest to this aspect of the endosymbiosis theory, it seemed timely to revisit basic terms eukaryotic cell/eukaryotes/nucleated organisms. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104178DOI Listing

Analysis of the initiation of viral infection under flow conditions with applications to transmission in feed.

Biosystems 2020 Jun 9:104184. Epub 2020 Jun 9.

School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea.

While kinetic models are widely used to describe viral infection at various levels, most of them are focused on temporal aspects and understanding of corresponding spatio-temporal aspects remains limited. In this work, our attention is focused on the initial stage of infection of immobile cells by virus particles ("virions") under flow conditions with diffusion. A practical example of this scenario occurs when humans or animals consume food from virion-containing sources. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7282798PMC

A survey of within-host and between-hosts modelling for antibiotic resistance.

Biosystems 2020 Jun 7;196:104182. Epub 2020 Jun 7.

Instituto de Matemáticas, UNAM, Unidad Juriquilla, Blvd. Juriquilla 3001, Juriquilla, Queretaro, 76230, Mexico; Frankfurt Institute for Advanced Studies, Ruth-Moufang-Strasse 1, 60438, Frankfurt am Main, Germany. Electronic address:

Antibiotic resistance is a global public health problem which has the attention of many stakeholders including clinicians, the pharmaceutical industry, researchers and policy makers. Despite the existence of many studies, control of resistance transmission has become a rather daunting task as the mechanisms underlying resistance evolution and development are not fully known. Here, we discuss the mechanisms underlying antibiotic resistance development, explore some treatment strategies used in the fight against antibiotic resistance and consider recent findings on collateral susceptibilities amongst antibiotic classes. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104182DOI Listing

Human evolution is biological & technological evolution.

Authors:
Adrian Bejan

Biosystems 2020 May 31:104156. Epub 2020 May 31.

Duke University, Durham, NC, 27708-0300, USA. Electronic address:

Abstract. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104156DOI Listing

Sociotype and cultural evolution the acceleration of cultural change alongside industrial revolutions.

Biosystems 2020 May 30:104170. Epub 2020 May 30.

Bioinformation and Systems Biology Group, Aragon Health Sciences Institute (IACS), 50009, Zaragoza, Spain; Department of Economic Statistics, University of Zaragoza, 50006, Zaragoza, Spain. Electronic address:

The present work explores, from the vantage point of the sociotype, the dramatic acceleration of cultural change alongside the successive industrial revolutions, particularly in the ongoing information era. Developed within the genotype-phenotype-sociotype conceptual triad, the sociotype means the average social environment that is adaptively demanded by the "social brain" of each individual. For there is a regularity of social interaction, centered on social bonding and talking time, which has been developed as an adaptive trait, evolutionarily rooted, related to the substantial size increase of human groups. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104170DOI Listing

French flag gradients and Turing reaction-diffusion versus differentiation waves as models of morphogenesis.

Biosystems 2020 May 30:104169. Epub 2020 May 30.

Department of Mathematical Sciences, Georgia Southern University, Statesboro, GA, USA. Electronic address:

The Turing reaction-diffusion model and the French Flag Model are widely accepted in the field of development as the best models for explaining embryogenesis. Virtually all current attempts to understand cell differentiation in embryos begin and end with the assumption that some combination of these two models works. The result may become a bias in embryogenesis in assuming the problem has been solved by these two-chemical substance-based models. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104169DOI Listing

The bacterial roots of the new autocracies: An essay on "Biopolitics".

Authors:
Howard Bloom

Biosystems 2020 May 30:104168. Epub 2020 May 30.

A new wave of autocratic nationalisms has at least ten nations in its grip, and growing. Does this new impulse of authoritarianism have roots in a deep evolutionary past? The answer goes back to two algorithms roughly 3.85 billion years old. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104168DOI Listing

Psychological 'double-slit experiment' in decision making: Quantum versus classical.

Biosystems 2020 May 30:104171. Epub 2020 May 30.

International Center for Mathematical Modeling in Physics, Engineering, Economics, and Cognitive Science, Linnaeus University, 351 95, Växjö, Sweden; National Research University for Information Technology, Mechanics and Optics (ITMO), Department, St. Petersburg, 197101, Russia.

This paper is devoted to justification of the application of quantum probability theory to problems of cognition, psychology, and decision making. Such applications are heavily based on quantum-like representation of interference of events that is formalized with complex probability amplitudes ("mental wave functions") and the Born rule for calculation of probability. In this paper, we present universal mathematical formalization of interference of events based on the calculus of intensities of interacting processes. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104171DOI Listing

Freedom and evolution in the dynamics of social systems.

Authors:
Adrian Bejan

Biosystems 2020 May 25:104158. Epub 2020 May 25.

Duke University, Durham, NC, 27708-0300, USA. Electronic address:

This is a review of recent work on how the physics of evolution accounts for the origin, changes and future of social systems. Evolution means the changes (spatial, temporal) that happen with discernible direction in time. Changes are everywhere because physical features of 'freedom to change' are in every moving and flowing system. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104158DOI Listing

A search for the physical basis of the genetic code.

Biosystems 2020 May 4:104148. Epub 2020 May 4.

Department of Physics, University of Alberta, Edmonton, AB, T6G 2E1, Canada; Department of Oncology, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada; DIMEAS, Politecnico di Torino, Turin, Italy. Electronic address:

DNA contains the genetic code, which provides complete information about the synthesis of proteins in every living cell. Each gene encodes for a corresponding protein but most of the DNA sequence is non-coding. In addition to this non-coding part of the DNA, there is another redundancy, namely a multiplicity of DNA triplets (codons) corresponding to code for a given amino acid. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104148DOI Listing

TMTCPT: The Tree Method based on the Taxonomic Categorization and the Phylogenetic Tree for fine-grained categorization.

Biosystems 2020 Apr 28:104137. Epub 2020 Apr 28.

Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran.

Fine-grained categorization is one of the most challenging problems in machine vision. Recently, the presented methods have been based on convolutional neural networks, increasing the accuracy of classification very significantly. Inspired by these methods, we offer a new framework for fine-grained categorization. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104137DOI Listing

Stochastic models coupling gene expression and partitioning in cell division in Escherichia coli.

Biosystems 2020 Jun 28;193-194:104154. Epub 2020 Apr 28.

Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, 33014, Tampere, Finland. Electronic address:

Regulation of future RNA and protein numbers is a key process by which cells continuously best fit the environment. In bacteria, RNA and proteins exist in small numbers and their regulatory processes are stochastic. Consequently, there is cell-to-cell variability in these numbers, even between sister cells. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104154DOI Listing

Three types of logical structure resulting from the trilemma of free will, determinism and locality.

Biosystems 2020 Apr 28;195:104151. Epub 2020 Apr 28.

Centre for Unconventional Computing, University of West England, Coldharbour Ln., Stoke Gilfford, Bristol, BS16 QY, United Kingdom.

How can one defend free will against determinism? Since quantum mechanics entails non-locality, it enables the co-existence of free will and determinism. Is non-locality in cognition possible, or must quantum mechanics be rejected? Here, we define free will, determinism and locality in terms of a binary relation between objects and representations, and we verify that the three concepts constitute a trilemma. We also show that non-locality in cognition is naturally found in decision making without any assumption of quantum mechanics. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104151DOI Listing

libsbmljs-Enabling web-based SBML tools.

Biosystems 2020 Apr 24;195:104150. Epub 2020 Apr 24.

Department of Bioengineering, University of Washington, Box 355061, Seattle, WA 98195-5061, United States of America.

The SBML standard is used in a number of online repositories for storing systems biology models, yet there is currently no Web-capable JavaScript library that can read and write the SBML format. This is a severe limitation since the Web has become a universal means of software distribution, and the graphical capabilities of modern web browsers offer a powerful means for building rich, interactive applications. Also, there is a growing developer population specialized in web technologies that is poised to take advantage of the universality of the web to build the next generation of tools in systems biology and other fields. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104150DOI Listing

Inferring population statistics of receptor neurons sensitivities and firing-rates from general functional requirements.

Authors:
Carlo Fulvi Mari

Biosystems 2020 Jun 23;193-194:104153. Epub 2020 Apr 23.

On the basis of the evident ability of neuronal olfactory systems to evaluate the intensity of an odorous stimulus and at the same time also recognise the identity of the odorant over a large range of concentrations, a few biologically-realistic hypotheses on some of the underlying neural processes are made. In particular, it is assumed that the receptor neurons mean firing-rate scale monotonically with odorant intensity, and that the receptor sensitivities range widely across odorants and receptor neurons hence leading to highly distributed representations of the stimuli. The mathematical implementation of the phenomenological postulates allows for inferring explicit functional relationships between some measurable quantities. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104153DOI Listing

Probability of change in life: Amino acid changes in single nucleotide substitutions.

Biosystems 2020 Jun 4;193-194:104135. Epub 2020 Apr 4.

Antibody & Product Development Lab, BII, A(∗)STAR, 138671, Singapore; P53 Laboratory, A(∗)STAR, Singapore; Experimental Drug Development Centre, A(∗)STAR, Singapore. Electronic address:

Mutations underpin the processes in life, be it beneficial or detrimental. While mutations are assumed to be random in the bereft of selection pressures, the genetic code has underlying computable probabilities in amino acid phenotypic changes. With a wide range of implications including drug resistance, understanding amino acid changes is important. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104135DOI Listing

On Boolean gates in fungal colony.

Biosystems 2020 Jun 4;193-194:104138. Epub 2020 Apr 4.

Unconventional Computing Laboratory, UWE, Bristol, UK; Department of Applied Sciences, UWE, Bristol, UK.

A fungal colony maintains its integrity via flow of cytoplasm along mycelium network. This flow, together with possible coordination of mycelium tips propagation, is controlled by calcium waves and associated waves of electrical potential changes. We propose that these excitation waves can be employed to implement a computation in the mycelium networks. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104138DOI Listing

Optimality of circular codes versus the genetic code after frameshift errors.

Biosystems 2020 Apr 3:104134. Epub 2020 Apr 3.

Department of Computer Science, ICube, CNRS, University of Strasbourg, Strasbourg, France. Electronic address:

The standard genetic code (SGC) describes how 64 trinucleotides (codons) encode 20 amino acids and the stop translation signal. Biochemical and statistical studies have shown that the standard genetic code is optimized to reduce the impact of errors caused by incorporation of wrong amino acids during translation. This is achieved by mapping codons that differ by only one nucleotide to the same amino acid or one with similar biochemical properties, so that if misincorporation occurs, the structure and function of the translated protein remain relatively unaltered. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104134DOI Listing

A centrality based multi-objective approach to disease gene association.

Biosystems 2020 Jun 31;193-194:104133. Epub 2020 Mar 31.

Computer Science Department, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada. Electronic address:

Disease Gene Association finds genes that are involved in the presentation of a given genetic disease. We present a hybrid approach which implements a multi-objective genetic algorithm, where input consists of centrality measures based on various relational biological evidence types merged into a complex network. Multiple objective settings and parameters are studied including the development of a new exchange methodology, safe dealer-based crossover. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104133DOI Listing

Shuffling type of biological evolution based on horizontal gene transfer and the biosphere gene pool hypothesis.

Biosystems 2020 Jun 26;193-194:104131. Epub 2020 Mar 26.

Gulf Specimen Marine Laboratory, Panacea, FL, 32346, United States; C.S. Mott Center for Human Growth & Development, Department of Obstetrics & Gynecology, Wayne State University, Detroit, MI, United States. Electronic address:

Widespread horizontal gene transfer (HGT) may appear a significant factor that accelerates biological evolution. Here we look at HGT primarily from the point of view of prokaryote clones, which we take as the descendants of a single cell, all of whom have exactly the same nucleotide sequence. Any novelty that emerges as a random mutation, creating a new clone, could either disappear before its first HGT, or survive for a period and be transferred to another clone. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104131DOI Listing

Entropy, externality and human evolution.

Biosystems 2020 May 12;191-192:104130. Epub 2020 Mar 12.

International Center for Mathematical Modeling, Linnaeus University, Växjö, Sweden.

Considering biosphere as a closed thermodynamical system, inside it, biological organisms may be considered as open thermodynamical systems exchanging energy and matter with ecosystem. Making appeal to non-equilibrium thermodynamics, anthropology, biology, sociology and cliodynamics, we discuss, from an interdisciplinary stance, some main moments of human evolution from either the phylogenetic and the ontogenetic standpoint, highlighting the crucial bifurcation which saw the rising of the modern societies with respect to primitive ones. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104130DOI Listing

Using activity time windows and logical representation to reduce the complexity of biological network models: G1/S checkpoint pathway with DNA damage.

Biosystems 2020 May 9;191-192:104128. Epub 2020 Mar 9.

Complex Systems, Big Data and Informatics Initiative (CSBII), Lincoln University, Christchurch, New Zealand. Electronic address:

Biological systems are difficult to understand complex systems. Scientists continue to create models to simulate biological systems but these models are complex too; for this reason, new reduction methods to simplify complex biological models into simpler ones are increasingly needed. In this paper, we present a way of reducing complex quantitative (continuous) models into logical models based on time windows of system activity and logical (Boolean) models. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104128DOI Listing

Representing life: A natural philosophical project.

Biosystems 2020 May 28;191-192:104127. Epub 2020 Feb 28.

The Living Systems Project, Dept. of Electronics and Informatics, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050, Brussels, Belgium.

We address multi-levelled organization as a vital aspect of any characterization of Nature, and propose that a model-hierarchical description is fitting for a Natural Philosophical point of view. An important aspect is that the different organizational levels in a model hierarchy are partially isolated and autonomous, partially communicating across the entire scale assembly. Of particular interest are the complex interfaces between levels, and the manner in which these may be transited by a generic form of quantum error correction. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104127DOI Listing

A percolation model of natural selection.

Biosystems 2020 Jun 22;193-194:104120. Epub 2020 Feb 22.

Department of Biophysics, Faculty of Physics, M.V.Lomonosov Moscow State University. Moscow, 119991, Russia. Electronic address:

A new approach has been proposed and developed: the selection of optimal variants in the evolutionary mutation flow is considered as an analogue of a percolation filter. Interaction of mutations in a series of generations and random processes of drift determine the collective behavior of nodes (individuals - carriers and converters of mutations) and bonds (mutations) in the space of percolation lattice. It is shown that the choice of the development trajectory at the population level depends on the spectrum of supporting and prohibiting mutations under the influence of conjugate deterministic and random factors. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104120DOI Listing

Breaking down calcium timing in heterogenous cells populations.

Biosystems 2020 May 19;191-192:104117. Epub 2020 Feb 19.

Unit of Nonlinear Physics and Mathematical Modeling, Department of Engineering, Campus Bio-Medico University of Rome, Via A. del Portillo 21, 00128, Rome, Italy; International Center for Relativistic Astrophysics Network - ICRANet, Piazza della Repubblica 10, Pescara, 65122, Italy. Electronic address:

Calcium controls a large number of cellular processes at different scales. Decades of studies have pointed out the importance of calcium signaling in regulating differentiation, apoptosis, mitosis and functions such as secretion, muscle contraction and memory. The space-time structure of calcium signaling is central to this complex regulation. Read More

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Deamination gradients within codons after 1<->2 position swap predict amino acid hydrophobicity and parallel β-sheet conformational preference.

Biosystems 2020 May 18;191-192:104116. Epub 2020 Feb 18.

Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, F-38700, La Tronche, France; The National Natural History Collections, The Hebrew University of Jerusalem, 91404, Jerusalem, Israel. Electronic address:

Deaminations C->T and A->G are frequent mutations producing nucleotide content gradients across genomes proportional to singlestrandedness during replication/transcription. Hence, within single codons, deamination risks increase from first to third codon positions, while second codon positions are functionally most crucial. Here genetic codes are analyzed assuming that after anticodons protected codons from deaminations, first and second codon positions swapped (N2N1N3->N1N2N3), with lowest deamination risks for N2 in presumed primitive N2N1N3 codons. Read More

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Using lattice SIS epidemiological model with clustered treatment to investigate epidemic control.

Biosystems 2020 May 15;191-192:104119. Epub 2020 Feb 15.

School of Mathematics and Statistics, Laboratory of Applied Mathematics and Complex Systems, Center for Data Science, Lanzhou University, Lanzhou 730000, PR China. Electronic address:

In epidemic control, how the size of treatment blocks influences the disease is a very interesting problem. Here, we construct an SIS model with spatially clustered treatment blocks using cellular automata and pair approximation to investigate the disease control and optimal arrangement of treatment blocks. On a same treatment intensity, the treatment blocks are built randomly and the individuals in the treatment blocks are cured in the next interval. Read More

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Multi-parameter exploration of dynamics of regulatory networks.

Authors:
Tomáš Gedeon

Biosystems 2020 Apr 10;190:104113. Epub 2020 Feb 10.

Department of Mathematical Sciences, Montana State University, Bozeman, MT 59715, United States of America. Electronic address:

Over the last twenty years advances in systems biology have changed our views on microbial communities and promise to revolutionize treatment of human diseases. In almost all scientific breakthroughs since time of Newton, mathematical modeling has played a prominent role. Regulatory networks emerged as preferred descriptors of how abundances of molecular species depend on each other. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7082111PMC

Softness-based adaptive mesh refinement algorithm for soft tissue deformation.

Biosystems 2020 May 7;191-192:104103. Epub 2020 Feb 7.

College of Physics and Information Engineering, Fuzhou University, Fuzhou, 350108, China. Electronic address:

Soft tissue and organ modeling is the most critical function of any virtual surgical system. This study proposes a softness-based adaptive mesh refinement algorithm to simultaneously ensure realistic and real-time soft tissue simulation. The algorithm was constructed to consider that in a virtual surgery scenario, the surgical sites involve large deformation and thus require high simulation precision, whereas the nonsurgical sites involve small deformations and thus require low simulation precision. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104103DOI Listing
May 2020
1.548 Impact Factor

Computational modelling and optimal control of measles epidemic in human population.

Biosystems 2020 Apr 7;190:104102. Epub 2020 Feb 7.

Faculty of Military Science, Stellenbosch University, Cape Town, South Africa. Electronic address:

Measles is an awfully contagious acute viral infection. It can be fatal, causing cough, red eyes, followed by a fever and skin rash with signs of respiratory infection. In this paper, we propose and analyze a model describing the transmission dynamics of a measles epidemic in the human population using the stability theory of differential equations. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104102DOI Listing

In pursuit of the framework behind the biosphere: S-curves, self-assembly and the genetic entropy paradox.

Authors:
Keith R Skene

Biosystems 2020 Apr 4;190:104101. Epub 2020 Feb 4.

Biosphere Research Institute, Letham, Angus, DD8 2PY, UK. Electronic address:

The origins, evolution and functioning of the Biosphere have occupied humankind for as long as recorded history has existed. In this paper we examine the claims of thermodynamics to be the framework within which we can understand the evolution, functioning and development of the Biosphere, exploring the evidence from ecology, molecular science and evolutionary biology, and particularly focussing upon the maximum entropy production principle (MEPP), and its explanatory potential in terms of many of the logistic relationships found within the Biosphere. We introduce the genetic entropy paradox, where the DNA increases in terms of internal information entropy, as the genetic code is continuously randomized through mutation, and yet this leads to increasing external entropy production, as increasingly more complicated structures and functions are produced in the form of new protein morphologies and metabolic pathways (again determined by the bioenergetic context). Read More

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Extended Bayesian inference incorporating symmetry bias.

Biosystems 2020 Apr 4;190:104104. Epub 2020 Feb 4.

Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.

We start by proposing a causal induction model that incorporates symmetry bias. This model has two parameters that control the strength of symmetry bias and includes conditional probability and conventional models of causal induction as special cases. We calculated the determination coefficients between assessments by participants in eight types of causal induction experiments and the estimated values using the proposed model. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104104DOI Listing

The semantic theory of language.

Biosystems 2020 Apr 22;190:104100. Epub 2020 Jan 22.

Dipartimento di Morfologia ed Embriologia, Via Fossato di Mortara 64a, 44121, Ferrara, Italy. Electronic address:

Traditional linguistics was based on the idea that language is an activity that links sounds and meaning, an idea that has been referred to as 'the code view of language' because codes are the most familiar processes that generate meaning. Ever since the work of Noam Chomsky, however, this view has been increasingly replaced by 'the syntax view of language', the idea that children learn a language because they have an innate mechanism that allows them to grasp the syntax of whatever language they grow up with. This innate mechanism has been given various names - first Universal Grammar, then Language Acquisition Device (LAD), and finally Faculty of Language - but despite decades of research attempts there still is no evidence that such a device actually exists. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104100DOI Listing

Bifurcation analysis of a modular model of embryonic kidney development.

Biosystems 2020 Mar 11;189:104099. Epub 2020 Jan 11.

Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran; Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran. Electronic address:

Many biological processes show switching behaviors in response to parameter changes. Although numerous surveys have been conducted on bifurcations in biological systems, they commonly focus on over-represented parts of signaling cascades, known as motifs, ignoring the multi-motif structure of biological systems and the communication links between these building blocks. In this paper, a method is proposed which partitions molecular interactions to modules based on a control theory point of view. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104099DOI Listing