3,199 results match your criteria Biosystems[Journal]


The key role of the elongation factors in the origin of the organization of the genetic code.

Biosystems 2019 Apr 15. Epub 2019 Apr 15.

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

I suggest a model based on primordial elongation factors able to explain a relevant aspect of the organization of the code itself: why the biosynthetic relationships between amino acids are mainly allocated on the rows of the genetic code. I hypothesize the existence of specific primordial elongation factors able to recognize two aspects of the ancestral aminoacylated-tRNA: the third base of the anticodon and a distinctive recognition sequence, i.e. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.04.009DOI Listing
April 2019
1 Read

The evolution of proteome: from the primeval to the very dawn of LUCA.

Biosystems 2019 Apr 14. Epub 2019 Apr 14.

Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México CDMX, C.P. 04510, Mexico. Electronic address:

The attempt to delineate the essential features that characterized life in its beginnings and the understanding of how those features evolved, represent important scientific challenges. While there have been varied efforts in the elucidation of how the first biomolecules arose from a prebiotic environment, there remains important gaps towards the characterization of the complete repertoire of the Last Universal Common Ancestor (LUCA). We portray a step-wise proteome evolution, by looking at the phenotype encoded by each one of the genetic codes that were appearing along evolution, beginning with the primeval genetic code and then with two intermediate Extended RNA codes, which finally shaped the current Standard Genetic Code (SGC). Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.04.007DOI Listing
April 2019
1 Read

On comparing composition principles of long DNA sequences with those of random ones.

Biosystems 2019 Apr 9. Epub 2019 Apr 9.

Laboratory of biomechanical systems, Russian Academy of Sciences, Moscow, Russia. Electronic address:

The revelation of compositional principles of the organization of long DNA sequences is one of the crucial tasks in the study of biosystems. This paper is devoted to the analysis of compositional differences between real DNA sequences and Markov-like randomly generated similar sequences. We formulate, among other things, a generalization of Chargaff's second rule and verify it empirically on DNA sequences of five model organisms taken from Genbank. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.04.003DOI Listing

Properties of network structures, structure coefficients, and benefit-to-cost ratios.

Authors:
Hendrik Richter

Biosystems 2019 Mar 23;180:88-100. Epub 2019 Mar 23.

HTWK Leipzig University of Applied Sciences, Faculty of Electrical Engineering and Information Technology, Postfach 301166, D-04251 Leipzig, Germany. Electronic address:

In structured populations the spatial arrangement of cooperators and defectors on the interaction graph together with the structure of the graph itself determines the game dynamics and particularly whether or not fixation of cooperation (or defection) is favored. For networks described by regular graphs and for a single cooperator (and a single defector) the question of fixation can be addressed by a single parameter, the structure coefficient. This quantity is invariant with respect to the location of the cooperator on the graph and also does not vary over different networks. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.03.005DOI Listing

RaaMLab: A MATLAB toolbox that generates amino acid groups and reduced amino acid modes.

Biosystems 2019 Mar 21;180:38-45. Epub 2019 Mar 21.

College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China. Electronic address:

Amino acid (AA) classification and its different biophysical and chemical characteristics have been widely applied to analyze and predict the structural, functional, expression and interaction profiles of proteins and peptides. We present RaaMLab, a free and open-source MATLAB toolbox, to facilitate studies on proteins and peptides, to generate AA groups and to extract the structural and physicochemical features of reduced AAs (RedAA). This toolbox offers 4 kinds of databases, including the physicochemical properties of AAs and their groupings, 49 AA classification methods and 5 types of biophysicochemical features of RedAAs. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.03.002DOI Listing

A mathematical model to describe the demographic dynamics of long-lived raptor species.

Biosystems 2019 Mar 15;180:54-62. Epub 2019 Mar 15.

Department of Mathematics, University of Extremadura, Spain; Institute of Advanced Scientific Computation, University of Extremadura, Spain.

Population viability analysis of threatened large and long-lived raptor species has strong limitations due to the restricted demographic information available for these species. In this work, we mathematically model the demographic dynamics of these raptor species through time-indexed branching processes. By assuming the more general non-parametric statistical setting, we determine accurate estimates for the most relevant reproductive parameters involved in the model. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.01.009DOI Listing
March 2019
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Abnormal synchronization patterns in the electrical stimulation-contractile response coupling decrease with noise.

Biosystems 2019 Mar 15;180:63-70. Epub 2019 Mar 15.

Centro de Investigación y de Estudios Advanzados del Instituto Politécnico Nacional (IPN), Vía del Conocimiento 201, Parque de Investigación e Innovación Tecnológica, 66600, Apodaca, NL, Mexico. Electronic address:

Synchronization theory predicts that if an oscillator interacts with a rhythmical external force, then it should react to a rhythmical force by adjusting its frequency. Furthermore, noise is present in nature, and it affects the nervous and cardiovascular systems. In this paper, we analyze the heart as an oscillator, where noisy periodic electrical stimulation can be regarded as an external forcing. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.03.004DOI Listing
March 2019
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Evolution of hierarchy in bacterial metabolic networks.

Biosystems 2019 Mar 13;180:71-78. Epub 2019 Mar 13.

Department of Biology, Stanford University, Stanford, CA 94305, USA. Electronic address:

Flow hierarchy is a useful way to characterize the movement of information and matter throughout a network. Hierarchical network organizations are shown to arise when there is a cost of maintaining links in the network. A similar constraint exists in metabolic networks, where costs come from reduced efficiency of nonspecific enzymes or from producing unnecessary enzymes. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.02.012DOI Listing

A model of molecular vector machine of proteins.

Authors:
Vladimir Karasev

Biosystems 2019 Mar 13;180:7-18. Epub 2019 Mar 13.

St. Petersburg State Electrotechnical University, Prof. Popov str. 5, 197376, St. Petersburg, Russia. Electronic address:

Based on the analysis of NH⋯OC bond region of the proteins pentafragments using the quantum chemistry representations, a group of 20 vectors of action has been isolated. These vectors of action are reconstructed by a group of 20 side chains of amino acids being the irreducible representations of vectors. As a result, a model of molecular vector machine of proteins (MVM) has been proposed. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.02.001DOI Listing
March 2019
4 Reads

Temperature effects on neuronal firing rates and tonic-to-bursting transitions.

Biosystems 2019 Mar 9;180:1-6. Epub 2019 Mar 9.

Department of Physics, Illinois State University, Normal, IL 61790, USA; School of Biological Sciences, Illinois State University, Normal, IL 61790, USA. Electronic address:

Temperature fluctuations can affect neurological processes at a variety of levels, with the overall output that higher temperatures in general increase neuronal activity. While variations in firing rates can happen with the neuronal system maintaining its homeostatic firing pattern of tonic firing, or bursting, changes in firing rates can also be associated with transitions between the two patterns of firing. Our computer simulations suggest a possible mechanism directly related to the shortening of the duration of the action potential for higher firing rates with temperature increase. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.03.003DOI Listing
March 2019
6 Reads

A mathematical investigation on the active substance pulsatory release from a solution-charged liposome.

Biosystems 2019 May 6;179:48-54. Epub 2019 Mar 6.

Department of Mathematical Modeling in Life Sciences, Institute of Mathematical Statistics and Applied Mathematics, Calea 13 Septembrie, nr. 13, Bucharest, Romania; Department of Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, Spl. Independentei nr. 91-95, Bucharest, Romania. Electronic address:

We adopt a model in which the time evolution of a solution-charged liposome with selective permeability is seen as a sequence of two-stage cycles. In the first stage the lipid vesicle with a certain input concentration of the active substance is swelling up in an osmotic process until it reaches a size that one pore is formed on its surface. The second stage follows, where the vesicle content is partially eliminated through the pore to induce a decrease of the vesicle volume up to its original size. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.03.001DOI Listing
May 2019
6 Reads

Supercritical and subcritical Hopf-bifurcations in a two-delayed prey-predator system with density-dependent mortality of predator and strong Allee effect in prey.

Biosystems 2019 Mar 7;180:19-37. Epub 2019 Mar 7.

Department of Electronics and Electrical Communication Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India. Electronic address:

One of the possible ways to visualize the effect of intra- and inter-species synergistic and antagonistic interactions in a natural ecosystem is the detailed analysis of the underlying prey-predator model, and the subsequent analytical findings may provide a definite justification towards the species coexistence, which often maintains biodiversity in nature. Here, our central motivation is to understand the combined effect of the Allee threshold and intra-species competition on the evolution of interacting species, which often experience delays in evolution due to its complex ecological and physiological processes. Therefore, in the present paper, we extensively analyze the stability of a two-delayed prey-predator system in the presence of strong Allee effects in prey and intra-species competition in predator. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.02.011DOI Listing
March 2019
2 Reads

Fault detection and therapeutic intervention in gene regulatory networks using SAT solvers.

Biosystems 2019 May 2;179:55-62. Epub 2019 Mar 2.

Indian Institute of Technology, Kharagpur, India. Electronic address:

Random somatic mutations disrupt homeostasis of the cell resulting in various undesirable phenotypes including proliferation. One of the most important questions in systems medicine research is the therapeutic intervention design, which requires the knowledge of these mutations. A single or multiple mutations can occur in the diseases like cancer. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.02.013DOI Listing
May 2019
2 Reads

Indication of quantum mechanical electron transport in human substantia nigra tissue from conductive atomic force microscopy analysis.

Biosystems 2019 May 28;179:30-38. Epub 2019 Feb 28.

4512 Beverly Drive, 75205, Dallas, TX, United States. Electronic address:

Neuromelanin and ferritin in dopamine neurons of the substantia nigra have a distribution and density that is similar to disordered arrays of quantum dots in photovoltaic devices, which have been experimentally shown to conduct electric energy using quantum mechanical electron transport mechanisms. Conductive atomic force microscopy tests were performed on human substantia nigra tissue at room temperature, to determine whether evidence of electron transport is present. The test results presented here provide evidence of quantum mechanical electron transport from ferritin and neuromelanin at levels that may be sufficient to cause or contribute to generation of action potentials. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.02.003DOI Listing
May 2019
5 Reads

Guaranteed satisficing and finite regret: Analysis of a cognitive satisficing value function.

Biosystems 2019 Feb 27;180:46-53. Epub 2019 Feb 27.

School of Science and Engineering, Tokyo Denki University, Ishizaka, Hatoyama, Hiki, Saitama 350-0394, Japan; Dwango Artificial Intelligence Laboratory, 5-24-5 Hongo, Bunkyo, Tokyo 113-0033, Japan. Electronic address:

As reinforcement learning algorithms are being applied to increasingly complicated and realistic tasks, it is becoming increasingly difficult to solve such problems within a practical time frame. Hence, we focus on a satisficing strategy that looks for an action whose value is above the aspiration level (analogous to the break-even point), rather than the optimal action. In this paper, we introduce a simple mathematical model called risk-sensitive satisficing (RS) that implements a satisficing strategy by integrating risk-averse and risk-prone attitudes under the greedy policy. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.02.009DOI Listing
February 2019
2 Reads

Analysis of an evolutionary algorithm for complex fuzzy cognitive map learning based on graph theory metrics and output concepts.

Biosystems 2019 May 24;179:39-47. Epub 2019 Feb 24.

Kielce University of Technology, al. Tysiąclecia Państwa Polskiego 7, 25-314 Kielce, Poland.

The fuzzy cognitive map (FCM) is an effective tool for modeling dynamic decision support systems. It describes the analyzed phenomenon in the form of key concepts and the causal connections between them. The main aspects of the building of the FCM model are: concepts selection, determining the output concepts, criterion selection, and determining the relationships between concepts. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.02.010DOI Listing
May 2019
2 Reads

Gene grouping strategy for network modeling from a small time-series dataset: An illustrative analysis of human organogenesis.

Authors:
Kiyohiro Maeda

Biosystems 2019 May 21;179:24-29. Epub 2019 Feb 21.

Imaging Technology Center, Fujifilm Corporation, 798 Miyanodai, Kaisei-machi, Ashigarakami-gun, Kanagawa, 258-8538, Japan. Electronic address:

Several algorithms have been proposed for modeling a gene regulatory network from a time-series expression dataset, but these have been used in relatively few studies because experimental cost often restricts the number of sampling time points to less than that of genes by more than one order of magnitude. In order to reduce the number of parameters for network modeling, we propose a method for grouping genes by both temporal expression pattern and biological function, modeling interactions between the gene groups by a dynamic Bayesian network approach. Results from applying the method to a gene expression dataset on human organogenesis demonstrate that more biologically plausible results can be obtained by modeling an interaction network for groups of genes than by modeling that for single genes. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.02.008DOI Listing
May 2019
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Spatiotemporal models in biology and the health sciences.

Biosystems 2019 May 19;179:15-16. Epub 2019 Feb 19.

Institute of Mathematics and Physics, UTP University of Science and Technology, PL-85796 Bydgoszcz, Poland.

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http://dx.doi.org/10.1016/j.biosystems.2019.02.006DOI Listing

Computational modeling and analysis of the impacts of sleep deprivation on glucose stimulated insulin secretion.

Biosystems 2019 May 18;179:1-14. Epub 2019 Feb 18.

Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Islamabad, Pakistan.

Circadian clock is an exquisite internal biological clock functioning in all living organisms. Lifestyle changes such as shift work or frequent travelling might result in malfunctioning of the central and consequently the peripheral clocks leading to different metabolic disorders. Disruptions in β cell clock have been found to be a potential reason behind β cell failure that makes a person prone towards developing type 2 diabetes (T2DM). Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.02.005DOI Listing

Fundamental, Quantitative Traits of the "Sociotype".

Biosystems 2019 Feb 16;180:79-87. Epub 2019 Feb 16.

Bioinformation Group. Aragon Institute of Health Science (IACS)/Aragon Health Research Institute (IIS Aragón). 50009 Zaragoza, Spain. Electronic address:

In whatever domain of life, from cells to organisms to societies, communicative exchanges underlie the formation and maintenance, and decay, of the emerging collective structures. It can be clearly seen in the human social world. The different classes of social bonds in a complex society revolve around, and are intimately related with, the communicative relationships that every individual entertains-essentially via face-to-face conversation. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.02.007DOI Listing
February 2019

Plant leaf computing.

Authors:
Andrew Adamatzky

Biosystems 2019 Feb 12. Epub 2019 Feb 12.

Unconventional Computing Laboratory, University of the West of England, Bristol BS16 1QY, UK. Electronic address:

Action potentials are multi-functional signals in plants. While most plant cells are conductive, and electrically coupled with each other, the action potentials are channelled faster along the plants' vascular network. Conductivity of the networks is geometrically constrained, thus allow for selective propagation and interaction between the impulses. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.02.004DOI Listing
February 2019
4 Reads

Multiplicative noise is beneficial for the transmission of sensory signals in simple neuron models.

Biosystems 2019 Apr 5;178:25-31. Epub 2019 Feb 5.

Bernstein Center for Computational Neuroscience Berlin, Philippstr. 13, Haus 2, 10115 Berlin, Germany. Electronic address:

We study simple integrate-and-fire type models with multiplicative noise and consider the transmission of a weak and slow signal, i.e. a signal that evokes a small modulation of the instantaneous firing rate on time scales that are much larger than the membrane time scale and the mean interspike interval. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.02.002DOI Listing
April 2019
1 Read

Quantum biology and human carcinogenesis.

Biosystems 2019 Apr 26;178:16-24. Epub 2019 Jan 26.

Geisinger Commonwealth School of Medicine, 525 Pine Street, Scranton, PA 18509, USA. Electronic address:

Quantum-mediated effects have been observed in biological systems. We have previously discussed basis-dependent quantum selection as a mechanism for directed adaptive mutation, a process in which selective pressure specifically induces mutation in those genes involved in the adaptive response. Tumor progression in cancer easily lends itself to the adaptive evolutionary perspective, as the Darwinian combination of heritable variations together with selection of the better proliferating variants are believed to play a major role in multistep carcinogenesis. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S03032647183043
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http://dx.doi.org/10.1016/j.biosystems.2019.01.010DOI Listing
April 2019
16 Reads

Biological computation and the foundations of biological organization: The legacy of the journal BioSystems.

Biosystems 2019 Feb;176:A1

Department of Biology Memorial University of Newfoundland St. John's, NL, A1B3X9, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.biosystems.2018.12.002DOI Listing
February 2019
3 Reads

Avian model to mitigate gut-derived immune response and oxidative stress during heat.

Biosystems 2019 Apr 16;178:10-15. Epub 2019 Jan 16.

University of Molise, Department of Agricultural, Environmental and Food Sciences, Via F. de Sanctis snc, 86100, Campobasso, Italy.

The tissue injury at the early stages of the heat stress response triggers release of inflammatory and oxidative agents from intestinal content into the milieu of the body. Intestinal homeostasis (i.e. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S03032647183032
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http://dx.doi.org/10.1016/j.biosystems.2019.01.007DOI Listing
April 2019
7 Reads

Patchy spread patterns in three-species bistable systems with facultative mutualism.

Biosystems 2019 Mar 17;177:24-33. Epub 2019 Jan 17.

Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Boulevard Juriquilla 3001, 73230, Querétaro Mexico.

A three-species population system under a facultative mutualistic relationship of one of the species is studied. The considered interactions are as follows: facultative between the first species and the second species, obligatory mutualism between the second species and the first one, and the third species is a predator of the first species. For this purpose, we extend the model proposed by Morozov et al. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.01.008DOI Listing
March 2019
2 Reads

Retrocausal regulation for the onset of a reaction cycle.

Authors:
Koichiro Matsuno

Biosystems 2019 Mar 14;177:1-4. Epub 2019 Jan 14.

Nagaoka University of Technology, Nagaoka 940-2188, Japan.

The emergence of a reaction cycle in a mixture of reacting molecules may require naturalized regulation of the constituent material elements. One source of naturalized regulation could be sought in updating the constituent elements through exchanging with those available from the outside under the conditions of unidirectional heat flow. One physical vehicle for implementing constant material exchange could be a durable reaction cycle serving as a necessary precursor to the phenomenon called life. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.01.006DOI Listing
March 2019
8 Reads

Effects of complementary loop composition in truncated R3C ligase ribozymes on kiss switch activation.

Biosystems 2019 Mar 11;177:9-15. Epub 2019 Jan 11.

Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan. Electronic address:

The formation of a kissing-loop through the introduction of complementary 7-membered loops is known to dramatically increase the activity of truncated R3C ligase ribozymes that otherwise display reduced activity. Restoration of activity is thought to result from kissing complex formation-induced rearrangement of two molecules with complementary loops. By combining two types of R3C ligase ribozyme mutants,  and , the influence of loop composition on ligation activity was investigated. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.01.004DOI Listing
March 2019
1 Read

Hindmarsh-Rose neuron model with memristors.

Authors:
Usha K Subha P A

Biosystems 2019 Apr 9;178:1-9. Epub 2019 Jan 9.

Department of Physics, Farook College, University of Calicut, Kerala 673632, India. Electronic address:

We analyze single and coupled Hindmarsh-Rose neurons in the presence of a time varying electromagnetic field which results from the exchange of ions across the membrane. Memristors are used to model the relation between magnetic flux of the electromagnetic field and the membrane potential of interacting neurons. The bifurcation analysis of Hindmarsh-Rose neurons has been carried out by varying the modulation intensity of induced current on the membrane potential. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.01.005DOI Listing
April 2019
3 Reads

Outbreaks of the measles in the Dutch Bible Belt and in other places - New prospects for a 1000 year old virus.

Biosystems 2019 Mar 4;177:16-23. Epub 2019 Jan 4.

Dept. of Physics, East Carolina University, Greenville, NC 27858, USA; Faculty of Mechanical Engineering and Institute of Mathematics and Physics, University of Technology and Life Sciences, 85-796 Bydgoszcz, Poland.

In the Netherlands there has been nationwide vaccination against the measles since 1977. However, a tight-knit community of a few hundred thousand orthodox protestants in the "Dutch Bible Belt" refuses the vaccine. Within this community of orthodox protestants there has been an outbreak of the measles with roughly 2500 reported cases about every twelve years. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.01.003DOI Listing
March 2019
2 Reads

On (sub)mesoscopic scale peculiarities of diffusion driven growth in an active matter confined space, and related (bio)material realizations.

Authors:
Adam Gadomski

Biosystems 2019 Feb 3;176:56-58. Epub 2019 Jan 3.

Department of Modeling of Physicochemical Processes, Institute of Mathematics and Physics, UTP University of Science and Technology, Kaliskiego 7, PL-85796, Bydgoszcz, Poland. Electronic address:

Diffusion in a confined space becomes an extremely important problem with many versatile applications, ranging from biomedical to biotechnological, and involving functional and smart (bio)materials. In this study, we have shown that the well-known Mullins-Sekerka approach to morphological stability of the diffusional non-ideal sphere's growth, for which a confinement factor disappears, is a firm starting point for further questions. It has two modifications and/or extensions for which the confinement factor is involved readily and becomes (in)finite firstly for microscale (or micrometer scale) involving biomatter packing phenomena. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.01.002DOI Listing
February 2019
3 Reads

Biomechanical properties of 3D-printed bone models.

Biosystems 2019 Feb 3;176:52-55. Epub 2019 Jan 3.

Faculty of Mechanical Engineering, UTP University of Science and Technology in Bydgoszcz, Poland. Electronic address:

Bone lesions resulting from large traumas or cancer resections can be successfully treated by directly using synthetic materials or in combination with tissue engineering methods (hybrid). Synthetic or hybrid materials combined with bone tissue's natural ability for regeneration and biological adaptation to the directions of loading, allow for full recovery of its biological functions. Increasing interest in new production methods or various types of regenerative membranes and shaped scaffolds means that methods such as additive manufacturing can significantly accelerate the preparation of constructs used in the further biological adaptation of natural tissue. Read More

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http://dx.doi.org/10.1016/j.biosystems.2019.01.001DOI Listing
February 2019
1 Read

Gene expression cancer classification using modified K-Nearest Neighbors technique.

Biosystems 2019 Feb 3;176:41-51. Epub 2019 Jan 3.

Computers and Systems Department, Faculty of Engineering, Mansoura University, Mansoura, Egypt. Electronic address:

Gene expression microarray classification is a crucial research field as it has been employed in cancer prediction and diagnosis systems. Gene expression data are composed of dozens of samples characterized by thousands of genes. Hence, an accurate and effective classification of such samples is a challenge. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.12.009DOI Listing
February 2019
1 Read

Normal diffusion in a medium connected to a subdiffusive medium with absorption.

Biosystems 2019 Mar 3;177:5-8. Epub 2019 Jan 3.

Department of Radiological Informatics and Statistics, Medical University of Gdańsk, ul. Tuwima 15, 80-210 Gdańsk, Poland.

We present a model of diffusion in a system consisting of a medium A, in which normal diffusion occurs, connected to a subdiffusive medium B in which absorption of diffusing particles may take place. Diffusion in B is described by the subdiffusion-absorption equation with a fractional time derivative. Solutions to equations are obtained for a specific boundary condition at the border between media. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.12.008DOI Listing
March 2019
2 Reads

Thinking as a quantum phenomenon.

Authors:
Alexey V Melkikh

Biosystems 2019 Feb 31;176:32-40. Epub 2018 Dec 31.

Ural Federal University, Yekaterinburg, 620002, Mira str. 19, Russia. Electronic address:

In this study, a model is constructed in which the formation of new synaptic contacts and the tuning of synaptic weights are mediated by quantum nonlocal interactions. The interaction between biologically important molecules in the brain can be the basis of the quantum metalanguage, which controls the behavior of humans and animals. The dynamics of biologically important molecules must include their topological properties. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.12.007DOI Listing
February 2019
1 Read

Modeling 3-D diffusion using queueing networks.

Biosystems 2019 May 27;179:17-23. Epub 2018 Dec 27.

University of Nebraska-Lincoln, 2714 South, 60th Street, 68106, Omaha, NE, United States.

The objective of this paper is to propose and then validate a new method for simulating molecular diffusion in a 3-D environment. Diffusion governing principles of Brownian motion have been discovered by Einstein and Smoluchowski. In a classical approach, diffusion is modeled using partial differential equations. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.12.006DOI Listing
May 2019
2 Reads

The distribution of information for sEMG signals in the rectal cancer treatment process.

Biosystems 2019 Feb 19;176:13-16. Epub 2018 Dec 19.

Division of Computational Physics and Electronics, Institute of Physics, Silesian Centre for Education and Interdisciplinary Research, University of Silesia in Katowice, Poland. Electronic address:

The electrical activity of external anal sphincter can be registered with surface electromyography. This signals are known to be highly complex and nonlinear. This work aims in characterisation of the information carried in the signals by harvesting the concept of information entropy. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.12.004DOI Listing
February 2019
2 Reads

Articular cartilage. Strong adsorption and cohesion of phospholipids with the quaternary ammonium cations providing satisfactory lubrication of natural joints.

Biosystems 2019 Feb 19;176:27-31. Epub 2018 Dec 19.

Tribochemistry Consulting, Salt Lake City, UT, 84117, USA; University of Economy, Biotribology Laboratory, Garbary 2, 85-229, Bydgoszcz, Poland. Electronic address:

Much evidence supports the hypothesis that surface-active phospholipid (SAPL) molecules on articular cartilage (AC) adsorbed to negatively-charged proteoglycan matrix form phospholipid (membrane), are negatively charged surface (-PO) and hydrophilic. In Hills cartilage model (1984) phospholipids adsorbed to cartilage surface act as boundary lubricants making the surface extremely hydrophobic. Hydrophobic surface of AC has gained no support in all experimental facts presented in this paper and the current literature showing that AC is amphoteric and hydrophilic with the negatively charged surface (-PO). Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.12.005DOI Listing
February 2019
2 Reads

Evolutionary acquisition of complex traits in artificial epigenetic networks.

Biosystems 2019 Feb 14;176:17-26. Epub 2018 Dec 14.

School of Mathematical and Computer Sciences, Heriot-Watt University, UK.

How complex traits arise within organisms over evolutionary time is an important question that has relevance both to the understanding of biological systems and to the design of bio-inspired computing systems. This paper investigates the process of acquiring complex traits within epiNet, a recurrent connectionist architecture capable of adapting its topology during execution. Inspired by the biological processes of gene regulation and epigenetics, epiNet captures biological organisms' ability to alter their regulatory topologies according to environmental stimulus. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.12.001DOI Listing
February 2019
4 Reads

Morphogenetic processes as data: Quantitative structure in the Drosophila eye imaginal disc.

Biosystems 2018 Nov 25;173:256-265. Epub 2018 Oct 25.

Gulf Specimen Marine Laboratory & Aquarium, 222 Clark Drive, Panacea, FL, 32346, USA; C.S. Mott Center for Human Growth & Development, Department of Obstetrics & Gynecology, Wayne State University, 275 E. Hancock, Detroit, MI, 48201, USA. Electronic address:

We can improve our understanding of biological processes through the use of computational and mathematical modeling. One such morphogenetic process (ommatidia formation in the Drosophila eye imaginal disc) provides us with an opportunity to demonstrate the power of this approach. We use a high-resolution image that catches the spatially- and temporally-dependent process of ommatidia formation in the act. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.10.005DOI Listing
November 2018
3 Reads

Acquisition and reconstruction of 4D surfaces of axolotl embryos with the flipping stage robotic microscope.

Biosystems 2018 Nov 25;173:214-220. Epub 2018 Oct 25.

Computational And Physical Systems (CAPS) Group, Department of Virtual Technology and Design, University of Idaho, Moscow, ID, 83844-2481, USA. Electronic address:

We have designed and constructed a Flipping Stage for a light microscope that can view the whole exterior surface of a 2 mm diameter developing axolotl salamander embryo. It works by rapidly inverting the bottom-heavy embryo, imaging it as it rights itself. The images are then montaged to reconstruct the whole 3D surface versus time, for a full 4D record of the surface. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.10.006DOI Listing
November 2018
2 Reads

Gallstone formation as an example of the two-step space confined aggregation process.

Authors:
Jacek Siódmiak

Biosystems 2019 Feb 12;176:1-5. Epub 2018 Dec 12.

Institute of Mathematics and Physics, UTP University of Science and Technology, Al. Prof. S. Kaliskiego 7, 85-796 Bydgoszcz, Poland. Electronic address:

Gallstone disease and in particular its cholesterol type is one of the most common diseases of the digestive system. More than 10% of the population is affected by this disease and in the case of Native Indians of Peru and Chile this rate reaches as much as 100%. While the disease is well-researched from a medical point of view, the two-step mechanism of formation of gallstones is not well studied. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.12.003DOI Listing
February 2019
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An integrated parametric model for MT self-assembly formation analysis.

Biosystems 2019 Feb 6;176:6-12. Epub 2018 Dec 6.

Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA. Electronic address:

Self-assembly is a ubiquitous, naturally occurring, robust process in many living organisms. Microtubule (MT), a self-organization system assemble itself into functional units by attaching to cellular structures. Modeling microtubule self-organization is of interest as microtubule forms a network of protein filaments that is critical to many processes in eukaryotic cells. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.11.006DOI Listing
February 2019
3 Reads

m-CALP - Yet another way of generating handwritten data through evolution for pattern recognition.

Biosystems 2019 Jan 6;175:24-29. Epub 2018 Dec 6.

Department of Computer Science, FAST-NUCES, Faisal Town, Lahore, Pakistan. Electronic address:

Recently a cellular automata learning and prediction (CALP) model was proposed that used evolution to generate handwritten data for pattern recognition. However, the proposed method by CALP was mechanical and not intuitive, as it did not consider the degree of image deformation that takes place during evolution. The problem with this approach is that it evolved handwritten shapes to a completely different form. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.11.007DOI Listing
January 2019
2 Reads

Optimal control applied to a temperature dependent schistosomiasis model.

Biosystems 2019 Jan 3;175:47-56. Epub 2018 Dec 3.

School of Life Sciences, College of Agriculture, Engineering and Science, Westville Campus, University of KwaZulu-Natal, Durban, South Africa.

Schistosomiasis, the most common water-borne infection worldwide, continues to pose a serious public health challenge in developing nations and to travellers who visit these endemic regions. We apply optimal control on a temperature dependent schistosomiasis model. Our optimal control aims to minimize the pre-patent and patent human population at minimal costs. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.11.008DOI Listing
January 2019
25 Reads

Mathematical model for plant-insect interaction with dynamic response to PAD4-BIK1 interaction and effect of BIK1 inhibition.

Biosystems 2019 Jan 24;175:11-23. Epub 2018 Nov 24.

Department of Computer Science, Jamia Millia Islamia, New Delhi, 110025, India. Electronic address:

Plant-insect interaction system is a widely studied model of the ecosystem. Numerical understanding of this counter system has developed from initial analogy based approach with a predator-prey model to its recent mathematical interpretation including plant immunity concept. In current work, we propose an extension to this model, including molecular interactions behind the plant defense system and its effect on ecological behaviour. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.11.005DOI Listing
January 2019
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Mathematical principles and methods of biological surface lubrication with phospholipids bilayers.

Biosystems 2019 Apr 15;178:32-40. Epub 2018 Nov 15.

Gdynia Maritime University, Morska 81-87, 81-225 Gdynia, Poland. Electronic address:

This paper presents a mini-review of investigations performed by the authors in the field of hydrodynamic theory of lubrication of biological systems and synthetic processing of results to indicate the influence of biologically live material properties on biological liquid viscosity variations. The goal of the presented study was to demonstrate a new principle of a general mathematical theory applied to the mechanism of hydrodynamic lubrication of human joint cartilage surfaces with phospholipids bilayer and to indicate analytical solutions of hydrodynamic pressure, temperature and bio-fluid velocity components. Moreover, 3D variations of dynamic synovial fluid viscosity are assessed, particularly its variations across the entire film thickness. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.11.002DOI Listing
April 2019
3 Reads

Elucidating effects of reaction rates on dynamics of the lac circuit in Escherichia coli.

Biosystems 2019 Jan 14;175:1-10. Epub 2018 Nov 14.

College of Engineering, Swansea University, Swansea, United Kingdom.

Gene expression is regulated by a complex transcriptional network. It is of interest to quantify uncertainty of not knowing accurately reaction rates of underlying biochemical reactions, and to understand how they affect gene expression. Assuming a kinetic model of the lac circuit in Escherichia coli, regardless of how many reactions are involved in transcription regulation, transcription rate is shown to be the most important parameter affecting steady state production of mRNA and protein in the cell. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.11.003DOI Listing
January 2019
18 Reads

Perfect anomalous transport of subdiffusive cargos by molecular motors in viscoelastic cytosol.

Authors:
Igor Goychuk

Biosystems 2019 Mar 9;177:56-65. Epub 2018 Nov 9.

Institute for Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam-Golm, Germany. Electronic address:

Multiple experiments show that various submicron particles such as magnetosomes, RNA messengers, viruses, and even much smaller nanoparticles such as globular proteins diffuse anomalously slow in viscoelastic cytosol of living cells. Hence, their sufficiently fast directional transport by molecular motors such as kinesins is crucial for the cell operation. It has been shown recently that the traditional flashing Brownian ratchet models of molecular motors are capable to describe both normal and anomalous transport of such subdiffusing cargos by molecular motors with a very high efficiency. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.11.004DOI Listing
March 2019
15 Reads

Spacial models of malfunctioned protein complexes help to elucidate signal transduction critical for insulin release.

Biosystems 2019 Mar 3;177:48-55. Epub 2018 Nov 3.

Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland. Electronic address:

Mutations in gene KCNJ11 encoding the Kir6.2 subunit of the ATP-sensitive potassium channel (KATP), a representative of a quite complex biosystem, may affect insulin release from pancreatic beta-cells. Both gain and loss of channel activity are observed, which lead to varied clinical phenotypes ranging from neonatal diabetes to congenital hyperinsulinism. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.11.001DOI Listing
March 2019
9 Reads