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Bio Systems

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https://www.readbyqxmd.com/read/28923485/functional-data-analysis-of-single-trial-auditory-evoked-potentials-recorded-in-the-awake-rat
#1
Ondrej Pokora, Jan Kolaicek, Tzai-Wen Chiu, Wei Qiu
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...
September 15, 2017: Bio Systems
https://www.readbyqxmd.com/read/28923484/editorial
#2
EDITORIAL
Chris Christodoulou, Lubomir Kostal, Ansgar Büschges
No abstract text is available yet for this article.
September 15, 2017: Bio Systems
https://www.readbyqxmd.com/read/28923483/synchrony-measure-for-a-neuron-driven-by-excitatory-and-inhibitory-inputs-and-its-adaptation-to-experimentally-recorded-data
#3
Christina Zavou, Antria Kkoushi, Achilleas Koutsou, Chris Christodoulou
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...
September 15, 2017: Bio Systems
https://www.readbyqxmd.com/read/28923482/the-optimal-regulation-mode-of-bcl-2-apoptotic-switch-revealed-by-bistability-analysis
#4
Zhiyong Yin, Hong Qi, Lili Liu, Zhen Jin
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...
September 15, 2017: Bio Systems
https://www.readbyqxmd.com/read/28918301/mathematical-fundamentals-for-the-noise-immunity-of-the-genetic-code
#5
Elena Fimmel, Lutz Strüngmann
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. As a consequence, it is not surprising that the desire to understand the origin of life, based on the genetic code, forces us to involve symmetry as a mathematical concept...
September 13, 2017: Bio Systems
https://www.readbyqxmd.com/read/28918300/dynamical-properties-of-lfps-from-mice-with-unilateral-injection-of-tent
#6
Eleonora Vannini, Matteo Caleo, Santi Chillemi, Angelo Di Garbo
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.e. during and after the period of TeNT action). All data were analysed by using nonlinear time series methods. Suitable values of the lag time and embedding dimension for phase space reconstruction were estimated by employing well-known methods...
September 13, 2017: Bio Systems
https://www.readbyqxmd.com/read/28916462/causation-constructors-and-codes
#7
Jan-Hendrik S Hofmeyr
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...
September 12, 2017: Bio Systems
https://www.readbyqxmd.com/read/28903058/insuperable-problems-of-the-genetic-code-initially-emerging-in-an-rna-world
#8
Peter R Wills, Charles W Carter
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...
September 10, 2017: Bio Systems
https://www.readbyqxmd.com/read/28899791/toward-a-hierarchical-virtual-screening-and-toxicity-risk-analysis-for-identifying-novel-ca-xii-inhibitors
#9
Elmira Nazarshodeh, Sajjad Gharaghani
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. The pharmacophore model indicated the important features of inhibitors for the binding with the CA XII. The model was then utilized to screen the ZINC and CoCoCo databases for retrieving potential hit compounds of CA XII...
September 9, 2017: Bio Systems
https://www.readbyqxmd.com/read/28890344/a-new-parallel-dna-algorithm-to-solve-the-task-scheduling-problem-based-on-inspired-computational-model
#10
Zhaocai Wang, Zuwen Ji, Xiaoming Wang, Tunhua Wu
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...
September 7, 2017: Bio Systems
https://www.readbyqxmd.com/read/28887177/a-step-into-the-rna-world-conditional-analysis-of-hydrogel-formation-of-adenosine-5-monophosphate-induced-by-cyanuric-acid
#11
Takumi Yokosawa, Ryota Enomoto, Sho Uchino, Ito Hirasawa, Takuya Umehara, Koji Tamura
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. However, we observed that other canonical ribonucleotides did not gel under the same condition...
September 5, 2017: Bio Systems
https://www.readbyqxmd.com/read/28887176/ecoacoustic-codes-and-ecological-complexity
#12
Almo Farina
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...
September 5, 2017: Bio Systems
https://www.readbyqxmd.com/read/28882507/stochastic-noncooperative-and-cooperative-evolutionary-game-strategies-of-a-population-of-biological-networks-under-natural-selection
#13
REVIEW
Bor-Sen Chen, Chin-Hsun Yeh
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...
September 4, 2017: Bio Systems
https://www.readbyqxmd.com/read/28866047/mathematical-models-in-cancer-therapy
#14
Giuseppe Jordão, João Nuno Tavares
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...
August 30, 2017: Bio Systems
https://www.readbyqxmd.com/read/28860070/index-incremental-depth-extension-approach-for-protein-protein-interaction-networks-alignment
#15
Abolfazl Mir, Mahmoud Naghibzadeh, Nayyereh Saadati
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. This paper proposes a new algorithm named INDEX for the global alignment of protein-protein interaction networks...
August 28, 2017: Bio Systems
https://www.readbyqxmd.com/read/28860069/gernet-a-gene-regulatory-network-tool
#16
J S Dussaut, C A Gallo, F Cravero, M J Martínez, J A Carballido, I Ponzoni
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. A highly abstract model-free approach, called rule-based approach, offers several advantages performing data-driven analysis; such as the requirement of the least amount of data...
August 28, 2017: Bio Systems
https://www.readbyqxmd.com/read/28855098/the-bioelectric-code-an-ancient-computational-medium-for-dynamic-control-of-growth-and-form
#17
REVIEW
Michael Levin, Christopher J Martyniuk
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. Here, we describe an important mechanism by which cellular networks implement pattern regulation and plasticity: bioelectricity...
August 27, 2017: Bio Systems
https://www.readbyqxmd.com/read/28851657/computer-simulation-and-experimental-self-assembly-of-irradiated-glycine-amino-acid-under-magnetic-fields-its-possible-significance-in-prebiotic-chemistry
#18
Alejandro Heredia, María Colín-García, Teresa Pi I Puig, Leticia Alba-Aldave, Adriana Meléndez, Jorge A Cruz-Castañeda, Vladimir A Basiuk, Sergio Ramos-Bernal, Alicia Negrón Mendoza
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. γ-glycine polymorph formation increases in irradiated samples interacting with static magnetic fields...
August 26, 2017: Bio Systems
https://www.readbyqxmd.com/read/28847742/a-global-optimization-algorithm-inspired-in-the-behavior-of-selfish-herds
#19
Fernando Fausto, Erik Cuevas, Arturo Valdivia, Adrián González
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. Depending on their classification as either a prey or a predator, each individual is conducted by a set of unique evolutionary operators inspired by such prey-predator relationship...
August 25, 2017: Bio Systems
https://www.readbyqxmd.com/read/28838871/optimism-in-the-face-of-uncertainty-supported-by-a-statistically-designed-multi-armed-bandit-algorithm
#20
Moto Kamiura, Kohei Sano
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. The objective of the present paper is to redefine the value functions of Overtaking method and to unify the formulation of them. The unified Overtaking method is associated with upper bounds of confidence intervals of expected rewards on statistics...
August 22, 2017: Bio Systems
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