Search our Database of Scientific Publications and Authors

I’m looking for a

    3024 results match your criteria BioSystems [Journal]

    1 OF 61

    Functional data analysis of single-trial auditory evoked potentials recorded in the awake rat.
    Biosystems 2017 Sep 15. Epub 2017 Sep 15.
    Auditory Research Laboratory, State University of New York, 107 Beaumont Hall, Plattsburgh, NY 12901, USA. Electronic address:
    Evoked potentials (EPs) reflect neural processing and are widely used to study sensory perception. However, methods of analyzing EP have been limited mostly to the conventional ensemble averaging of EP response trials to a repeated stimulus, and less so to single-trials analysis. Here we applied a new approach - functional data analysis (FDA) - to study auditory EP in the rat model of tinnitus, in which overdoses of salicylate (SS) are known to alter sound perception characteristically, as the same way as in humans. Read More

    Synchrony measure for a neuron driven by excitatory and inhibitory inputs and its adaptation to experimentally-recorded data.
    Biosystems 2017 Sep 15. Epub 2017 Sep 15.
    Department of Computer Science, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus. Electronic address:
    The aim of the current work is twofold: firstly to adapt an existing method measuring the input synchrony of a neuron driven only by excitatory inputs in such a way so as to account for inhibitory inputs as well and secondly to further appropriately adapt this measure so as to be correctly utilised on experimentally-recorded data. The existing method uses the normalized pre-spike slope (NPSS) of the membrane potential, resulting from observing the slope of depolarization of the membrane potential of a neuron prior to the moment of crossing the threshold within a short period of time, to identify the response-relevant input synchrony and through it to infer the operational mode of a neuron. The first adaptation of NPSS is made such that its upper bound calculation accommodates for the higher possible slope values caused by the lower average and minimum membrane potential values due to inhibitory inputs. Read More

    The optimal regulation mode of Bcl-2 apoptotic switch revealed by bistability analysis.
    Biosystems 2017 Sep 15. Epub 2017 Sep 15.
    Complex Systems Research Center, Shanxi University, Taiyuan, Shanxi 030006, PR China. Electronic address:
    In most cell types, apoptosis occurs by the mitochondrial outer membrane permeability (MOMP)-mediated pathway, which is controlled by Bcl-2 family proteins (often referred to as Bcl-2 apoptotic switch). These proteins, which display a range of bioactivities, can be divided into four types: effectors, inhibitors, activators and sensitizers. Although the complex interactions among Bcl-2 family members have been studied intensively, a unifying hypothesis for the mechanism they use to regulate MOMP remains elusive. Read More

    Mathematical Fundamentals for the Noise Immunity of the Genetic Code.
    Biosystems 2017 Sep 13. Epub 2017 Sep 13.
    Institute of Mathematical Biology, Faculty for Computer Sciences, Mannheim University of Applied Sciences, 68163 Mannheim, Germany. Electronic address:
    Symmetry is one of the essential and most visible patterns that can be seen in nature. Starting from the left-right symmetry of the human body, all types of symmetry can be found in crystals, plants, animals and nature as a whole. Similarly, principals of symmetry are also some of the fundamental and most useful tools in modern mathematical natural science that play a major role in theory and applications. Read More

    Dynamical properties of LFPs from mice with unilateral injection of TeNT.
    Biosystems 2017 Sep 13. Epub 2017 Sep 13.
    Institute of Biophysics, CNR-National Research Council, 56124 Pisa, Italy. Electronic address:
    Local field potential (LFP) recordings were performed from the visual cortex (V1) of a focal epilepsy mouse model. Epilepsy was induced by a unilateral injection of the synaptic blocker tetanus neurotoxin (TeNT). LFP signals were simultaneously recorded from V1 of both hemispheres of each animal under acute and chronic conditions (i. Read More

    Causation, Constructors and Codes.
    Biosystems 2017 Sep 12. Epub 2017 Sep 12.
    Centre for Complex Systems in Transition and Dept. of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa. Electronic address:
    Relational biology relies heavily on the enriched understanding of causal entailment that Robert Rosen's formalisation of Aristotle's four causes has made possible, although to date efficient causes and the rehabilitation of final cause have been its main focus. Formal cause has been paid rather scant attention, but, as this paper demonstrates, is crucial to our understanding of many types of processes, not necessarily biological. The graph-theoretic relational diagram of a mapping has played a key role in relational biology, and the first part of the paper is devoted to developing an explicit representation of formal cause in the diagram and how it acts in combination with efficient cause to form a mapping. Read More

    Insuperable problems of the genetic code initially emerging in an RNA World.
    Biosystems 2017 Sep 10. Epub 2017 Sep 10.
    Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, Unites States.
    Differential equations for error-prone information transfer (template replication, transcription or translation) are developed in order to consider, within the theory of autocatalysis, the advent of coded protein synthesis. Variations of these equations furnish a basis for comparing the plausibility of contrasting scenarios for the emergence of specific tRNA aminoacylation, ultimately by enzymes, and the relationship of this process with the origin of the universal system of molecular biological information processing embodied in the Central Dogma. The hypothetical RNA World does not furnish an adequate basis for explaining how this system came into being, but principles of self-organisation that transcend Darwinian natural selection furnish an unexpectedly robust basis for a rapid, concerted transition to genetic coding from a peptide•RNA world. Read More

    Toward a hierarchical virtual screening and toxicity risk analysis for identifying novel CA XII inhibitors.
    Biosystems 2017 Sep 9. Epub 2017 Sep 9.
    Laboratory of Bioinformatics and Drug Design (LBD), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. Electronic address:
    Carbonic anhydrase isoform XII (CA XII) is a potential target for cancer treatment. In this study, pharmacophore modeling, hierarchical virtual screening, and toxicity risk analysis were performed for identifying novel CA XII inhibitors. A pharmacophore model of two classes of CA XII inhibitors was generated. Read More

    A new parallel DNA algorithm to solve the task scheduling problem based on inspired computational model.
    Biosystems 2017 Sep 7. Epub 2017 Sep 7.
    School of Information and Engineering, Wenzhou Medical University, Wenzhou 325035, PR China. Electronic address:
    As a promising approach to solve the computationally intractable problem, the method based on DNA computing is an emerging research area including mathematics, computer science and molecular biology. The task scheduling problem, as a well-known NP-complete problem, arranges n jobs to m individuals and finds the minimum execution time of last finished individual. In this paper, we use a biologically inspired computational model and describe a new parallel algorithm to solve the task scheduling problem by basic DNA molecular operations. Read More

    A step into the RNA world: conditional analysis of hydrogel formation of adenosine 5'-monophosphate induced by cyanuric acid.
    Biosystems 2017 Sep 5. Epub 2017 Sep 5.
    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:
    Nucleotide polymerization occurs by the nucleophilic attack of 3'-oxygen of the 3'-terminal nucleotide on the α-phosphorus of the incoming nucleotide 5'-triphosphate. The π-stacking of mononucleotides is an important factor for prebiotic RNA polymerization in terms of attaining the proximity of two reacting moieties. Adenosine and adenosine 5'-monophosphate (AMP) are known to form hydrogel in the presence of cyanuric acid at neutral pH. Read More

    Ecoacoustic Codes and Ecological Complexity.
    Biosystems 2017 Sep 5. Epub 2017 Sep 5.
    Department of Pure and Applied Sciences, Urbino University, Urbino, Italy.
    Multi-layer communication and sensing network assures the exchange of relevant information between animals and their umwelten, imparting complexity to the ecological systems. Individual soniferous species, the acoustic community, and soundscape are the three main operational levels that comprise this multi-layer network. Acoustic adaptation and acoustic niche are two more important mechanisms that regulate the acoustic performances at the first level while the acoustic community model explains the complexity of the interspecific acoustic network at the second level. Read More

    Stochastic Noncooperative and Cooperative Evolutionary Game Strategies of a Population of Biological Networks under Natural Selection.
    Biosystems 2017 Sep 4. Epub 2017 Sep 4.
    Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan 30013. Electronic address:
    We review current static and dynamic evolutionary game strategies of biological networks and discuss the lack of random genetic variations and stochastic environmental disturbances in these models. To include these factors, a population of evolving biological networks is modeled as a nonlinear stochastic biological system with Poisson-driven genetic variations and random environmental fluctuations (stimuli). To gain insight into the evolutionary game theory of stochastic biological networks under natural selection, the phenotypic robustness and network evolvability of noncooperative and cooperative evolutionary game strategies are discussed from a stochastic Nash game perspective. Read More

    Mathematical models in cancer therapy.
    Biosystems 2017 Sep 1;162:12-23. Epub 2017 Sep 1.
    Centro de Matemática da Universidade do Porto (CMUP), Faculty of Sciences of University of Porto, Gabinete de Estatística, Modelação e Aplicações Computacionais (GEMAC), Portugal. Electronic address:
    In this article, deterministic mathematical models are derived from biochemical models within a human cell in two distinct cases, for comparison: healthy cell and cancerous cell. The former model is based in the cell cycle model by Novak and Tyson and its adaptation by Conradie, and makes use of the MAPK cascade pathway and the PI3K/AKT pathway for signalling transduction, to create a wider updated model for the regulation of a healthy cell. The latter model, for the cancer cell, is derived from the healthy cell model by altering specific pathways and interpreting the outcome in the light of literature in cancer. Read More

    INDEX: Incremental Depth Extension Approach for Protein-Protein Interaction Networks Alignment.
    Biosystems 2017 Aug 28. Epub 2017 Aug 28.
    Department of Internal Medicine, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran.
    High-throughput methods have provided us with a large amount of data pertaining to protein-protein interaction networks. The alignment of these networks enables us to better understand biological systems. Given the fact that the alignment of networks is computationally intractable, it is important to introduce a more efficient and accurate algorithm which finds as large as possible similar areas among networks. Read More

    GeRNet: a gene regulatory network tool.
    Biosystems 2017 Aug 30;162:1-11. Epub 2017 Aug 30.
    Instituto de Ciencias e Ingeniería de la Computación, Universidad Nacional del Sur, CONICET, Bahía Blanca, Argentina. Electronic address:
    Gene regulatory networks (GRNs) are crucial in every process of life since they govern the majority of the molecular processes. Therefore, the task of assembling these networks is highly important. In particular, the so called model-free approaches have an advantage modeling the complexities of dynamic molecular networks, since most of the gene networks are hard to be mapped with accuracy by any other mathematical model. Read More

    The bioelectric code: An ancient computational medium for dynamic control of growth and form.
    Biosystems 2017 Sep 2. Epub 2017 Sep 2.
    Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA.
    What determines large-scale anatomy? DNA does not directly specify geometrical arrangements of tissues and organs, and a process of encoding and decoding for morphogenesis is required. Moreover, many species can regenerate and remodel their structure despite drastic injury. The ability to obtain the correct target morphology from a diversity of initial conditions reveals that the morphogenetic code implements a rich system of pattern-homeostatic processes. Read More

    Computer Simulation and Experimental Self-assembly of Irradiated Glycine Amino Acid Under Magnetic Fields: Its Possible Significance in Prebiotic Chemistry.
    Biosystems 2017 Aug 26. Epub 2017 Aug 26.
    Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior S/N, Coyoacán, C.P. 04510 Ciudad de México, D.F, Mexico.
    Ionizing radiation may have played a relevant role in chemical reactions for prebiotic biomolecule formation on ancient Earth. Environmental conditions such as the presence of water and magnetic fields were possibly relevant in the formation of organic compounds such as amino acids. ATR-FTIR, Raman, EPR and X-ray spectroscopies provide valuable information about molecular organization of different glycine polymorphs under static magnetic fields. Read More

    A global optimization algorithm inspired in the behavior of selfish herds.
    Biosystems 2017 Oct 25;160:39-55. Epub 2017 Aug 25.
    Departamento de Electrónica, Universidad de Guadalajara, CUCEI, Av. Revolución 1500, Guadalajara, Jal, Mexico.
    In this paper, a novel swarm optimization algorithm called the Selfish Herd Optimizer (SHO) is proposed for solving global optimization problems. SHO is based on the simulation of the widely observed selfish herd behavior manifested by individuals within a herd of animals subjected to some form of predation risk. In SHO, individuals emulate the predatory interactions between groups of prey and predators by two types of search agents: the members of a selfish herd (the prey) and a pack of hungry predators. Read More

    Optimism in the face of uncertainty supported by a statistically-designed multi-armed bandit algorithm.
    Biosystems 2017 Oct 22;160:25-32. Epub 2017 Aug 22.
    Graduate School of Science and Engineering, Tokyo Denki University, Japan.
    The principle of optimism in the face of uncertainty is known as a heuristic in sequential decision-making problems. Overtaking method based on this principle is an effective algorithm to solve multi-armed bandit problems. It was defined by a set of some heuristic patterns of the formulation in the previous study. Read More

    Sustainable cooperation based on reputation and habituation in the public goods game.
    Biosystems 2017 Oct 18;160:33-38. Epub 2017 Aug 18.
    College of Management and Economics, Tianjin University, Tianjin 300072, PR China.
    Reputation can promote cooperation in public goods game and player's cooperative behavior is not pure economical rationality, but habituation would influence their behaviors as well. One's habituation can be formed by repeated behaviors in daily life and be affected by habitual preference. We aim to investigate the sustainable cooperation based on reputation and habit formation. Read More

    Reviewing evidence for systematic transcriptional deletions, nucleotide exchanges, and expanded codons, and peptide clusters in human mitochondria.
    Biosystems 2017 Oct 12;160:10-24. Epub 2017 Aug 12.
    Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, 13385, France. Electronic address:
    Polymerization sometimes transforms sequences by (a) systematic deletions of mono-, dinucleotides after trinucleotides, or (b) 23 systematic nucleotide exchanges (9 symmetric, X<>Y, e.g. G<>T, 14 asymmetric, X > Y > Z > X, e. Read More

    Linked Gauss-Diffusion processes for modeling a finite-size neuronal network.
    Biosystems 2017 Aug 2. Epub 2017 Aug 2.
    Dipartimento di Matematica e Applicazioni, Università degli Studi di Napoli "Federico II", Complesso di Monte S. Angelo via Cintia, 80126 Napoli, Italy. Electronic address:
    A Leaky Integrate-and-Fire (LIF) model with stochastic current-based linkages is considered to describe the firing activity of neurons interacting in a (2×2)-size feed-forward network. In the subthreshold regime and under the assumption that no more than one spike is exchanged between coupled neurons, the stochastic evolution of the neuronal membrane voltage is subject to random jumps due to interactions in the network. Linked Gauss-Diffusion processes are proposed to describe this dynamics and to provide estimates of the firing probability density of each neuron. Read More

    Information reduction in a reverberatory neuronal network through convergence to complex oscillatory firing patterns.
    Biosystems 2017 Jul 27. Epub 2017 Jul 27.
    Taras Shevchenko National University of Kyiv, Volodymyrska Str., 60, Kyiv 01033, Ukraine. Electronic address:
    Dynamics of a reverberating neural net is studied by means of computer simulation. The net, which is composed of 9 leaky integrate-and-fire (LIF) neurons arranged in a square lattice, is fully connected with interneuronal communication delay proportional to the corresponding distance. The network is initially stimulated with different stimuli and then goes freely. Read More

    A single spike deteriorates synaptic conductance estimation.
    Biosystems 2017 Jul 27. Epub 2017 Jul 27.
    Institute of Physiology, The Czech Academy of Sciences, 142 20 Prague 4, Czech Republic.
    We investigated the estimation accuracy of synaptic conductances by analyzing simulated voltage traces generated by a Hodgkin-Huxley type model. We show that even a single spike substantially deteriorates the estimation. We also demonstrate that two approaches, namely, negative current injection and spike removal, can ameliorate this deterioration. Read More

    The lamin code.
    Biosystems 2017 Jul 19. Epub 2017 Jul 19.
    National Research Council of Italy, Institute of Molecular Genetics, IGM-CNR-IOR, Bologna, Italy. Electronic address:
    Unicellular eukaryotes and metazoa present a nuclear envelope (NE) and metazoa express in it one or more lamins that give rise to the nuclear lamina. The expression of different types of lamins is related to the complexity of the organism and the expression of type-A lamins is related to the initial steps of tissue-specific cell differentiation. Several posttranslational modifications characterize the expression of lamin A in the course of cell differentiation, and the alteration of this expression pattern leads to impressive phenotypic diseases that are collectively referred to as laminopathies. Read More

    Language: A fresh concept to integrate syntactic and semantic information in life sciences.
    Biosystems 2017 Oct 20;160:1-9. Epub 2017 Jul 20.
    CNRS, UMIFRE IFP, 605001, Pondicherry, India; AMAP, INRA, CNRS, IRD, Université Montpellier, Montpellier, France. Electronic address:
    Several fields in biology tend to view the concept of information from one or the other of two extreme positions. Exclusionists base their stance of total rejection on gene-centrism and gene-determinism, typified by the recently-established endo-Darwinist school of life sciences. At the other end of the spectrum, there is total acceptance, as in the newly developed information-centred paradigms that populate biosemiotics. Read More

    DNA based random key generation and management for OTP encryption.
    Biosystems 2017 Sep 18;159:51-63. Epub 2017 Jul 18.
    Institute of Computer Science and Technology, National University of Defense Technology, Changsha 410073, China.
    One-time pad (OTP) is a principle of key generation applied to the stream ciphering method which offers total privacy. The OTP encryption scheme has proved to be unbreakable in theory, but difficult to realize in practical applications. Because OTP encryption specially requires the absolute randomness of the key, its development has suffered from dense constraints. Read More

    To swim or not to swim: A population-level model of Xenopus tadpole decision making and locomotor behaviour.
    Biosystems 2017 Jul 15. Epub 2017 Jul 15.
    School of Psychology & Neuroscience, Westburn Lane, University of St Andrews, St Andrews KY16 9JP, UK.
    We present a detailed computational model of interacting neuronal populations that mimic the hatchling Xenopus tadpole nervous system. The model includes four sensory pathways, integrators of sensory information, and a central pattern generator (CPG) network. Sensory pathways of different modalities receive inputs from an "environment"; these inputs are then processed and integrated to select the most appropriate locomotor action. Read More

    The sugar code: Why glycans are so important.
    Biosystems 2017 Jul 11. Epub 2017 Jul 11.
    Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstraße 13, 80539 Munich, Germany. Electronic address:
    The cell surface is the platform for presentation of biochemical signals that are required for intercellular communication. Their profile necessarily needs to be responsive to internal and external factors in a highly dynamic manner. The structural features of the signals must meet the criterion of high-density information coding in a minimum of space. Read More

    Effect of diseases on symbiotic systems.
    Biosystems 2017 Sep 12;159:36-50. Epub 2017 Jul 12.
    Agricultural and Ecological Research Unit, Indian Statistical Institute, Kolkata, West Bengal 700108, India. Electronic address:
    There are many species living in symbiotic communities. In this study, we analyzed models in which populations are in the mutualism symbiotic relations subject to a disease spreading among one of the species. The main goal is the characterization of symbiotic relations of coexisting species through their mutual influences on their respective carrying capacities, taking into account that this influence can be quite strong. Read More

    Carrying pieces of information in organocatalytic bytes: Semiopoiesis-A new theory of life and its origins.
    Biosystems 2017 Jul 8. Epub 2017 Jul 8.
    State University of Maringa, Department of Biochemistry, Av. Colombo, 5790, Zona 7, Bloco I-89, Room 15, Maringa, Parana, Brazil. Electronic address:
    Living beings have been classically described as autopoietic machines: chemical systems, which maintain a reproducible steady state by producing their components and boundaries. On the other hand, very simple autopoietic micelles have been produced in laboratory. They consist in micelles able to catalyse the production of their own surfactants. Read More

    Adaptive evolution of body size subject to indirect effect in trophic cascade system.
    Biosystems 2017 Sep 3;159:23-35. Epub 2017 Jul 3.
    School of Basic Science, Changchun University of Technology, 2055 Yanan Street, Changchun, Jilin 130012, PR China.
    Trophic cascades represent a classic example of indirect effect and are wide-spread in nature. Their ecological impact are well established, but the evolutionary consequences have received even less theoretical attention. We theoretically and numerically investigate the trait (i. Read More

    Efficiency of rate and latency coding with respect to metabolic cost and time.
    Biosystems 2017 Jul 3. Epub 2017 Jul 3.
    Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14220 Prague 4, Czech Republic. Electronic address:
    Recent studies on the theoretical performance of latency and rate code in single neurons have revealed that the ultimate accuracy is affected in a nontrivial way by aspects such as the level of spontaneous activity of presynaptic neurons, amount of neuronal noise or the duration of the time window used to determine the firing rate. This study explores how the optimal decoding performance and the corresponding conditions change when the energy expenditure of a neuron in order to spike and maintain the resting membrane potential is accounted for. It is shown that a nonzero amount of spontaneous activity remains essential for both the latency and the rate coding. Read More

    Elucidation of the molecular mechanism of heat shock proteins and its correlation with K722Q mutations in Lon protease.
    Biosystems 2017 Sep 1;159:12-22. Epub 2017 Jul 1.
    Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia, India. Electronic address:
    Cells withstand the effects of temperature change with the help of small heat shock proteins IbpA and IbpB. The IbpAB protein complex interacts with Lon protease in their free form and gets degraded at physiological temperature when there is no temperature stress. However, the proteolytic degradation of IbpAB is diminished when Lon is mutated. Read More

    Equalizing the information amounts of protein and mRNA by information theory.
    Biosystems 2017 Sep 15;159:1-11. Epub 2017 Jun 15.
    Biophysics Department, School of Medicine, Istanbul Kemerburgaz University, Istanbul, Turkey. Electronic address:
    Based on the Shannon's information communication theory, information amount of the entire length of a polymeric macromolecule can be calculated in bits through adding the entropies of each building block. Proteins, DNA and RNA are such macromolecules. When only the building blocks' variation is considered as the source of entropy, there is seemingly lower information in case of the protein if this approach is applied directly on a protein of specific size and the coding sequence size of the mRNA corresponding to the particular length of the protein. Read More

    Energy conservation and maximal entropy production in enzyme reactions.
    Biosystems 2017 Aug 7;158:47-56. Epub 2017 Jun 7.
    University of Maribor, Faculty of Natural Sciences and Mathematics, Koroška cesta 160, 2000 Maribor, Slovenia; University of Maribor, Faculty of Health Sciences, Žitna ulica 15, 2000 Maribor, Slovenia.
    A procedure for maximization of the density of entropy production in a single stationary two-step enzyme reaction is developed. Under the constraints of mass conservation, fixed equilibrium constant of a reaction and fixed products of forward and backward enzyme rate constants the existence of maximum in the density of entropy production is demonstrated. In the state with maximal density of entropy production the optimal enzyme rate constants, the stationary concentrations of the substrate and the product, the stationary product yield as well as the stationary reaction flux are calculated. Read More

    HOKF: High Order Kalman Filter for Epilepsy Forecasting Modeling.
    Biosystems 2017 Aug 30;158:57-67. Epub 2017 May 30.
    Department of Brain and Cognitive Engineering, Korea University, Seoul 136-713, South Korea. Electronic address:
    Epilepsy forecasting has been extensively studied using high-order time series obtained from scalp-recorded electroencephalography (EEG). An accurate seizure prediction system would not only help significantly improve patients' quality of life, but would also facilitate new therapeutic strategies to manage epilepsy. This paper thus proposes an improved Kalman Filter (KF) algorithm to mine seizure forecasts from neural activity by modeling three properties in the high-order EEG time series: noise, temporal smoothness, and tensor structure. Read More

    Genetic coding and united-hypercomplex systems in the models of algebraic biology.
    Biosystems 2017 Aug 20;158:31-46. Epub 2017 May 20.
    Mechanical Engineering Research Institute of the Russian Academy of Sciences, 101990, Moscow, Russia. Electronic address:
    Structured alphabets of DNA and RNA in their matrix form of representations are connected with Walsh functions and a new type of systems of multidimensional numbers. This type generalizes systems of complex numbers and hypercomplex numbers, which serve as the basis of mathematical natural sciences and many technologies. The new systems of multi-dimensional numbers have interesting mathematical properties and are called in a general case as "systems of united-hypercomplex numbers" (or briefly "U-hypercomplex numbers"). Read More

    How tumor growth can be influenced by delayed interactions between cancer cells and the microenvironment?
    Biosystems 2017 Aug 12;158:17-30. Epub 2017 May 12.
    Normandie University - CORIA, Avenue de l'Université, F-76800 Saint-Etienne du Rouvray, France.
    Although recent advances in oncology emphasized the role of microenvironment in tumor growth, the role of delays for modeling tumor growth is still uncertain. In this paper, we considered a model, describing the interactions of tumor cells with their microenvironment made of immune cells and host cells, in which we inserted, as suggested by the clinicians, two time delays, one in the interactions between tumor cells and immune cells and, one in the action of immune cells on tumor cells. We showed analytically that the singular point associated with the co-existence of the three cell populations loses its stability via a Hopf bifurcation. Read More

    The living organism: Strengthening the basis.
    Biosystems 2017 Aug 7;158:10-16. Epub 2017 May 7.
    Department of Electronics and Informatics, Vrije Universiteit Brussel (VUB), Belgium. Electronic address:
    In spite of the considerable amount of literature dedicated to the living organism, it retains its mysteries. One of the most discussed aspects nowadays is whether the term "cognition" can be attributed to all classes of organisms, or whether it only refers to a metaphoric use of one human reality. Our approach consists of retaining the term "cognition" and making it a technical term, in order to propose a generic model. Read More

    Boredom begets creativity: a solution to the exploitation-exploration trade-off in predictive coding.
    Biosystems 2017 May 4. Epub 2017 May 4.
    Koelliker Hospital, Department of Psychology, University of Turin, Via Verdi, 10, 10124 Turin, Italy.
    Here we investigate whether systems that minimize prediction error e.g. predictive coding, can also show creativity, or on the contrary, prediction error minimization unqualifies for the design of systems that respond in creative ways to non recurrent problems. Read More

    In vitro molecular machine learning algorithm via symmetric internal loops of DNA.
    Biosystems 2017 Aug 29;158:1-9. Epub 2017 Apr 29.
    Graduate Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea; Graduate Program in Brain Science, Seoul National University, Seoul, Republic of Korea; School of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea; Graduate Program in Cognitive Science, Seoul National University, Seoul, Republic of Korea. Electronic address:
    Programmable biomolecules, such as DNA strands, deoxyribozymes, and restriction enzymes, have been used to solve computational problems, construct large-scale logic circuits, and program simple molecular games. Although studies have shown the potential of molecular computing, the capability of computational learning with DNA molecules, i.e. Read More

    Modeling Chagas disease in Chile: From vector to congenital transmission.
    Biosystems 2017 Jun - Jul;156-157:63-71. Epub 2017 Apr 20.
    Departamento de Ciencias Biológicas Animales, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Chile.
    Chagaś disease is a human health problem in Latin America. It is highly prevalent in northern Chile between the Arica-Parinacota and Coquimbo regions, with reported incidence of 3-11/100000 inhabitants and mortality of 0.3-0. Read More

    On plant roots logical gates.
    Biosystems 2017 Jun - Jul;156-157:40-45. Epub 2017 Apr 17.
    International Laboratory of Plant Neurobiology, University of Florence, Italy.
    Theoretical constructs of logical gates implemented with plant roots are morphological computing asynchronous devices. Values of Boolean variables are represented by plant roots. A presence of a plant root at a given site symbolises the logical True, an absence the logical False. Read More

    Cellular non-linear network model of microbial fuel cell.
    Biosystems 2017 Jun - Jul;156-157:53-62. Epub 2017 Apr 17.
    Bristol BioEnergy Centre, University of the West of England, Bristol BS16 1QY, UK.
    A cellular non-linear network (CNN) is a uniform regular array of locally connected continuous-state machines, or nodes, which update their states simultaneously in discrete time. A microbial fuel cell (MFC) is an electro-chemical reactor using the metabolism of bacteria to drive an electrical current. In a CNN model of the MFC, each node takes a vector of states which represent geometrical characteristics of the cell, like the electrodes or impermeable borders, and quantify measurable properties like bacterial population, charges produced and hydrogen ion concentrations. Read More

    Particle sorting by Paramecium cilia arrays.
    Biosystems 2017 Jun - Jul;156-157:46-52. Epub 2017 Apr 12.
    Unconventional Computing Laboratory, University of the West of England, Bristol, United Kingdom; Bristol Robotics Laboratory, University of the West of England, Bristol, United Kingdom.
    Motile cilia are cell-surface organelles whose purposes, in ciliated protists and certain ciliated metazoan epithelia, include generating fluid flow, sensing and substance uptake. Certain properties of cilia arrays, such as beating synchronisation and manipulation of external proximate particulate matter, are considered emergent, but remain incompletely characterised despite these phenomena having being the subject of extensive modelling. This study constitutes a laboratory experimental characterisation of one of the emergent properties of motile cilia: manipulation of adjacent particulates. Read More

    Computational complexity of algorithms for sequence comparison, short-read assembly and genome alignment.
    Biosystems 2017 Jun - Jul;156-157:72-85. Epub 2017 Apr 6.
    Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica 57001, Greece. Electronic address:
    A multitude of algorithms for sequence comparison, short-read assembly and whole-genome alignment have been developed in the general context of molecular biology, to support technology development for high-throughput sequencing, numerous applications in genome biology and fundamental research on comparative genomics. The computational complexity of these algorithms has been previously reported in original research papers, yet this often neglected property has not been reviewed previously in a systematic manner and for a wider audience. We provide a review of space and time complexity of key sequence analysis algorithms and highlight their properties in a comprehensive manner, in order to identify potential opportunities for further research in algorithm or data structure optimization. Read More

    Optimal control problems of mosquito-borne disease subject to changes in feeding behavior of Aedes mosquitoes.
    Biosystems 2017 Jun - Jul;156-157:23-39. Epub 2017 Apr 3.
    Department of Mathematics, Kyungpook National University, South Korea. Electronic address:
    Dengue viruses (DENV) are transmitted to humans by the bite of Aedes mosquitoes. It is known that dengue virus infection in Aedes aegypti female mosquitoes makes a change in the feeding behavior of the infected mosquitoes. In this study, using the forces of infection, we incorporated the effect of changes in the feeding behavior of mosquitoes into the standard vector-borne SIR-SI model. Read More

    A biophysical approach to cancer dynamics: Quantum chaos and energy turbulence.
    Biosystems 2017 Jun - Jul;156-157:1-22. Epub 2017 Apr 2.
    Cancer Research, McGill University, Montreal, Canada. Electronic address:
    Cancer is a term used to define a collective set of rapidly evolving cells with immortalized replication, altered epimetabolomes and patterns of longevity. Identifying a common signaling cascade to target all cancers has been a major obstacle in medicine. A quantum dynamic framework has been established to explain mutation theory, biological energy landscapes, cell communication patterns and the cancer interactome under the influence of quantum chaos. Read More

    1 OF 61