3,179 results match your criteria BioSystems [Journal]


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

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

Biosystems 2019 Feb 5. 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
February 2019

Quantum biology and human carcinogenesis.

Biosystems 2019 Jan 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
January 2019
8 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

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

Biosystems 2019 Jan 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
January 2019
4 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
1 Read

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
1 Read

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
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Hindmarsh-Rose neuron model with memristors.

Authors:
Usha K Subha P A

Biosystems 2019 Jan 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
January 2019
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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
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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
1 Read

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
1 Read

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
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Modeling 3-D Diffusion Using Queueing Networks.

Biosystems 2018 Dec 27. 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
December 2018
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
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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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https://linkinghub.elsevier.com/retrieve/pii/S03032647183018
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http://dx.doi.org/10.1016/j.biosystems.2018.12.001DOI Listing
February 2019
3 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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https://linkinghub.elsevier.com/retrieve/pii/S03032647183029
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http://dx.doi.org/10.1016/j.biosystems.2018.10.005DOI Listing
November 2018
2 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
1 Read

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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https://linkinghub.elsevier.com/retrieve/pii/S03032647183022
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http://dx.doi.org/10.1016/j.biosystems.2018.11.006DOI Listing
February 2019
2 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
16 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
2 Reads

Mathematical principles and methods of biological surface lubrication with phospholipids bilayers.

Biosystems 2018 Nov 15. 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
November 2018
1 Read

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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https://linkinghub.elsevier.com/retrieve/pii/S03032647183010
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http://dx.doi.org/10.1016/j.biosystems.2018.11.003DOI Listing
January 2019
12 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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https://linkinghub.elsevier.com/retrieve/pii/S03032647183029
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http://dx.doi.org/10.1016/j.biosystems.2018.11.004DOI Listing
March 2019
10 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
6 Reads

Low-density lipoprotein accumulation within the right coronary artery walls for physiological and hypertension conditions.

Biosystems 2019 Mar 1;177:39-43. Epub 2018 Nov 1.

Institute of Physics, University of Silesia, 41-500 Chorzów Katowice, Poland; Silesian Center for Education and Interdisciplinary Research, University of Silesia, 41-500 Chorzów, Poland. Electronic address:

We demonstrate how low-density lipoproteins (LDL) are transported and accumulated through walls of the coronary artery. The result of modeling is a map of the LDL concentration on the patient specific vessel. It identifies places at high risk for plague growth. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.10.017DOI Listing
March 2019
2 Reads

When is altruistic punishment useful in social dilemmas?

Biosystems 2018 Dec 2;174:60-62. Epub 2018 Nov 2.

Faculty of Arts and Design, University of Canberra, Canberra, ACT, Australia.

It is not fully understood how cooperation emerges in a population of individuals with no connections or prior experience with each other. Strategy selection that is purely based on accumulated payoffs promotes free riders who put their self interests above that of any group. How could cooperation persist in these settings? Researchers have posited direct or indirect reciprocity as possible explanations but these theories fail if interactions are not repeated or reputations are ignored. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.10.015DOI Listing
December 2018
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An application of higher order multivariate cumulants in modelling of myoelectrical activity of porcine uterus during early pregnancy.

Biosystems 2019 Jan 2;175:30-38. Epub 2018 Nov 2.

Department of Large Animal Diseases with Clinic, Veterinary Research Centre and Center for Biomedical Research, Faculty of Veterinary Medicine, Warsaw University of Life Sciences (WULS - SGGW), Warsaw, Poland. Electronic address:

The analysis of the uterine contraction have become a general practice in an effort to improve the clinical management of uterine contractions during pregnancy and labour in human beings. The fluctuations in uterine activity may occur without affecting progress of gestation, however the painful and fashion contractions may be the first threat of miscarriage. While pigs were considered as an referential preclinical model, the computational modelling of spontaneous myoelectrical activity of complex systems of porcine myometrium in peri-fertilization period has been proposed. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.10.019DOI Listing
January 2019
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Natural joints: Boundary lubrication and antiphospholipid syndrome (APS).

Biosystems 2019 Mar 31;177:44-47. Epub 2018 Oct 31.

Faculty of Mathematics, Physics and Technical Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-867, Bydgoszcz, Poland.

The paper shows that osteoporosis (OA) changes the SF content and the lipid profile substantially. To estimate the implication of the lipid environment in case the articular cartilage (AC) changes, we measured friction coefficient normal samples, with early and late stages of (OA). During joint inflammation and osteoarthritis, enzymatically activated β-Glycoprotein I is transformed into antibody conformation. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.10.018DOI Listing
March 2019
4 Reads

"Cylindrical worlds" in biology: Does the aggregation strategy give a selective advantage?

Biosystems 2019 Jan 31;175:39-46. Epub 2018 Oct 31.

Functional Morphology and Biomechanics, Zoological Institute, Kiel University, Am Botanischen Garten, 1-9, 24118, Kiel, Germany.

Tree trunks and other cylindrical objects, where aggregated insects live, represent a very specific world for predator-prey interactions, which must differ from the situation on a 2D plane. In the present paper, in order to gain a better understanding of the specificity of predator-prey interaction in a cylindrical space, we applied a theoretical approach. Here we introduce a numerical model that allows us to test the effect of different interaction properties between predator and aggregated prey on the plane (2D) and on a cylinder (3D), taking into consideration different abilities of predators to visually detect the prey in these two types of space. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S03032647183027
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http://dx.doi.org/10.1016/j.biosystems.2018.10.016DOI Listing
January 2019
3 Reads

Evolutionary conservation and functional implications of circular code motifs in eukaryotic genomes.

Biosystems 2019 Jan 24;175:57-74. Epub 2018 Oct 24.

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

A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses (Michel, 2015, 2017; Arquès and Michel, 1996). This set X has an interesting mathematical property, since X is a maximal C self-complementary trinucleotide circular code (Arquès and Michel, 1996). Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the reading frame in genes. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S03032647183031
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http://dx.doi.org/10.1016/j.biosystems.2018.10.014DOI Listing
January 2019
9 Reads

Morphomechanical rules of embryonic development.

Authors:
Lev V Beloussov

Biosystems 2018 Nov 16;173:10-17. Epub 2018 Oct 16.

Department of Embryology, Faculty of Biology, Moscow State University; Moscow 119992, Russia. Electronic address:

We start by comparing two explicatory approaches, which we call law-centered and "instructivistic". Although the latter dominates in modern biology, we find it inappropriate for treating developmental problems, especially those related to morphogenesis. As an example of a law-centered approach we suggest a simple morphomechanical rule based upon the idea of the hyper-restoration of mechanical stresses. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.10.012DOI Listing
November 2018
1 Read

Morphomechanical reactions and mechanically stressed structures in amphibian embryos, as related to gastrulation and axial organs formation.

Biosystems 2018 Nov 12;173:18-25. Epub 2018 Oct 12.

Department of Embryology, Faculty of Biology, Moscow State University, Moscow 119992, Russia.

Reactions of embryonic tissues to a distributed and concentrated stretching are described and compared with the mechanics of the normal gastrulation movements. A role of mechanically stressed dynamic cell structures in the gastrulation, demarcation of notochord borders and in providing proportionality of the axial rudiments is demonstrated. A morphomechanical scheme of amphibian gastrulation is presented. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.10.011DOI Listing
November 2018
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The publications of embryologist Lev V. Beloussov.

Authors:
Richard Gordon

Biosystems 2018 Nov 12;173:4-6. Epub 2018 Oct 12.

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:

A list of papers and books of the late Lev V. Beloussov was compiled and is available in Word and EndNote Supplements. The breadth of his work is briefly described. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.10.013DOI Listing
November 2018
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Professor Lev Beloussov and the birth of morphomechanics.

Biosystems 2018 Nov 10;173:26-35. Epub 2018 Oct 10.

Lomonossov Moscow State University, Faculty of Biology, Department of Embryology, 119991, Moscow, Leninskie Gory, 1-12, Russia; Federal State Budgetary Research Institution "Institute of Experimental Medicine", Department of Experimental Physiology, 197376, St Petersburg, Akad. Pavlova Str 12, Russia. Electronic address:

The first explanations of the mechanisms of development of living organisms were proposed in antiquity. At that time two competing ideas existed, about the strict determination of embryonic structures (we call it the "Hippocrates line") and about the possible formation of structures from the unstructured condition ("Aristotle line"). We can trace the opposition between the "Hippocrates line" and "Aristotle line" from antiquity till the present time. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.10.010DOI Listing
November 2018
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Dynamic maternal gradients and morphogenetic networks in Drosophila early embryo.

Biosystems 2018 Nov 10;173:207-213. Epub 2018 Oct 10.

Mathematical Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, Polytekhnicheskaya 29, 195251, St. Petersburg, Russia. Electronic address:

Here, we review the latest publications on dynamics and interpretation of morphogen gradients in Drosophila early embryo. The instructive cues provided by these gradients are further interpreted by target genes to enable correct cell fate specification. Moreover, recent studies point on the dynamic and active input from gradients themselves. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.10.009DOI Listing
November 2018
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A guide to gene regulatory network inference for obtaining predictive solutions: Underlying assumptions and fundamental biological and data constraints.

Biosystems 2018 Dec 9;174:37-48. Epub 2018 Oct 9.

Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.

The study of biological systems at a system level has become a reality due to the increasing powerful computational approaches able to handle increasingly larger datasets. Uncovering the dynamic nature of gene regulatory networks in order to attain a system level understanding and improve the predictive power of biological models is an important research field in systems biology. The task itself presents several challenges, since the problem is of combinatorial nature and highly depends on several biological constraints and also the intended application. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.10.008DOI Listing
December 2018
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On the significance of sodium ionic channels in analysis of the breast cancer metastaticity.

Biosystems 2019 Mar 9;177:34-38. Epub 2018 Oct 9.

Department of Physical Chemistry and Technology of Polymers, Section of Physics and Applied Mathematics, Silesian University of Technology, Ks. M. Strzody 9, 44-100 Gliwice, Poland. Electronic address:

Using the results from previous modeling of the ball and chain inactivation of the potassium channels we try to model the inactivation of the Na 1.5 sodium channels in adult and neonatal form. The (fast) inactivation of sodium channels differs from the inactivation of the potassium channels by the use of a inactivating hinge rather than a ball on a chain. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.10.007DOI Listing
March 2019
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Local and global dynamics in collective movements of embryonic cells.

Biosystems 2018 Nov 6;173:36-51. Epub 2018 Oct 6.

Laboratory of Developmental Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia. Electronic address:

Several important morphogenetic processes belong to the category of collective cell movements (CCM), by which we mean coordinated rearrangements of many neighboring cells. The causes of the dynamic order established during CCM are still unclear. We performed statistical studies of rates and angular orientations of cell rearrangements in two kinds of embryonic tissues, which we categorized as "committed" (in the sense of being capable of autonomous CCM) as opposed to "naïve" tissues, which are those that require external forces in order to exhibit full scale CCM. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.09.011DOI Listing
November 2018
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Electromechanics of polarized cell growth.

Biosystems 2018 Nov 6;173:114-132. Epub 2018 Oct 6.

Department of Plant Physiology and Biochemistry, St. Petersburg State University, 7/9 Universitetskaya nab., St. Petersburg, 199034, Russia. Electronic address:

One of the most challenging questions in cell and developmental biology is how molecular signals are translated into mechanical forces that ultimately drive cell growth and motility. Despite an impressive body of literature demonstrating the importance of cytoskeletal and motor proteins as well as osmotic stresses for cell developmental mechanics, a host of dissenting evidence strongly suggests that these factors per se cannot explain growth mechanics even at the level of a single tip-growing cell. The present study addresses this issue by exploring fundamental interrelations between electrical and mechanical fields operating in cells. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.10.004DOI Listing
November 2018
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Increasing complexity: Mechanical guidance and feedback loops as a basis for self-organization in morphogenesis.

Biosystems 2018 Nov 4;173:133-156. Epub 2018 Oct 4.

Laboratory of Developmental biophysics, Department of Embryology, Faculty of Biology, Moscow State University, Moscow, 119234, Russia. Electronic address:

The article is devoted to physical views on embryo development as a combination of structurally stable dynamics and symmetry-breaking events in the general process of self-organization. The first corresponds to the deterministic aspect of embryo development. The second type of processes is associated with sudden increase of variability in the periods of symmetry-breaking, which manifests unstable dynamics. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.10.001DOI Listing
November 2018
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A mathematical model of the biochemical network underlying left-right asymmetry establishment in mammals.

Biosystems 2018 Nov 4;173:281-297. Epub 2018 Oct 4.

Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada. Electronic address:

The expression of the TGF-β protein Nodal on the left side of vertebrate embryos is a determining event in the development of internal-organ asymmetry. We present a mathematical model for the control of the expression of Nodal and its antagonist Lefty consisting entirely of realistic elementary reactions. We analyze the model in the absence of Lefty and find a wide range of parameters over which bistability (two stable steady states) is observed, with one stable steady state a low-Nodal state corresponding to the right-hand developmental fate, and the other a high-Nodal state corresponding to the left. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.10.003DOI Listing
November 2018
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Evolution as a search for organizational equilibrium.

Biosystems 2018 Nov 3;173:174-180. Epub 2018 Oct 3.

Paleontological Institute, Russian Academy of Sciences, Moscow 117997, Russia. Electronic address:

Evolution of living systems is a succession of historical changes in their equilibrium states. In the individual life cycle, every such state is realized as an equilibrium of developmental system, i.e. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.10.002DOI Listing
November 2018
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Computational, theoretical, and experimental approaches to morphogenesis.

Biosystems 2018 Nov 29;173:1-3. Epub 2018 Sep 29.

Faculty of Biology, Lomonosov Moscow State University, 119899, Moscow, Russia. Electronic address:

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http://dx.doi.org/10.1016/j.biosystems.2018.09.018DOI Listing
November 2018
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Cell differentiation processes as spatial networks: Identifying four-dimensional structure in embryogenesis.

Biosystems 2018 Nov 29;173:235-246. Epub 2018 Sep 29.

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

One overarching principle of eukaroytic development is the generative spatial emergence and self-organization of cell populations. As cells divide and differentiate, they and their descendents form a spatiotemporal explicit and increasingly compartmentalized complex system. Yet despite this comparmentalization, there is selective functional overlap between these structural components. Read More

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http://dx.doi.org/10.1016/j.biosystems.2018.09.009DOI Listing
November 2018
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