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  1. Effects of the transmissibility and virulence of pathogens on intraguild predation in fragmented landscapes.

    Biosystems 129:44 (2015) PMID 25659991

    We here explore the effect of pathogenic infection on the spatial dynamics of species that also engage in intraguild predation (IGP) in a fragmented landscape. First, the shared pathogen by the predator and prey can enhance species coexistence in the IGP system, consistent with results for non-spati...
  2. Global warming description using Daisyworld model with greenhouse gases.

    Biosystems 125:1 (2014) PMID 25236841

    Daisyworld is an archetypal model of the earth that is able to describe the global regulation that can emerge from the interaction between life and environment. This article proposes a model based on the original Daisyworld considering greenhouse gases emission and absorption, allowing the descripti...
  3. Periodic coupling strength-dependent multiple coherence resonance by time delay in Newman-Watts neuronal networks.

    Biosystems 114(3):186 (2013) PMID 24060612

    We study how the temporal coherence of spiking behavior and coherence resonance by time delay change when the frequency of periodic coupling strength is varied. It is found that delay induced coherence resonance is dependent on periodic coupling strength and increases when the frequency of periodic...
  4. Chlorophyll fluorescence in the leaves of Tradescantia species of different ecological groups: induction events at different intensities of ...

    Biosystems 114(2):85 (2013) PMID 23948518

    We describe results of our study of the effects of actinic light intensity on photosynthetic performance in Tradescantia species of different ecological groups. Using the chlorophyll fluorescence as a probe of photosynthetic activity, we have found that the shade-tolerant species Tradescantia flumin...
  5. Sequence classification with side effect machines evolved via ring optimization.

    Biosystems 113(1):9 (2013) PMID 23603215

    The explosion of available sequence data necessitates the development of sophisticated machine learning tools with which to analyze them. This study introduces a sequence-learning technology called side effect machines. It also applies a model of evolution which simulates the evolution of a ring spe...
  6. Symmetrizing object and meta levels organizes thinking.

    Biosystems 107(2):95 (2012) PMID 22100872

    We present a single non-cellular finite automaton model first shown to exhibit self-organizing behavior with intermittency and criticality, through a self-referential process. We propose a method to make self-referential contradiction a dynamic process of interaction with the selves in first person...
  7. Nucleotide correlation based measure for identifying origin of replication in genomic sequences.

    Biosystems 107(1):52 (2012) PMID 21945744

    We propose a correlation measure and show that it is correctly able to predict the origin of replication in most of the bacterial genomes. When applied to Methanocaldococcus jannaschii, Plasmodium falciparum apicoplast and Nicotiana tabacum plastid, this correlation based method is able to correctly...
  8. A mathematical consideration of the word-composition vector method in comparison of biological sequences.

    Biosystems 106(2-3):67 (2011) PMID 21745534

    We count the appearance frequencies of all the K-tuple words throughout each of two given sequences. Then, the two given sequences are transformed into their respective word-composition vectors. Next, the distance metrics, for example the angle between the two vectors, are calculated. A significant...
  9. Monte Carlo simulation from proton slip to "coupled" proton flow in ATP synthase based on the bi-site mechanism.

    Biosystems 105(3):233 (2011) PMID 21664229

    We simulated the proton conduction from proton slip to "coupled" proton flow in ATP synthase using the Monte Carlo method. Good agreement is obtained between the simulated and available experimental results. Our model provides deeper insight into the nucleotide dependence of ATP catalysis, and the k...
  10. Comparison of metabolite profiles in U87 glioma cells and mesenchymal stem cells.

    Biosystems 105(2):130 (2011) PMID 21605622

    Gas chromatography-mass spectrometry (GC-MS) profiles were generated from U87 glioma cells and human mesenchymal stem cells (hMSC). 37 metabolites representing glycolysis intermediates, TCA cycle metabolites, amino acids and lipids were selected for a detailed analysis. The concentrations of these m...