Searcharxiv⌕ Search

SEARCH · Searcharxiv

Results for “q-bio.OT”

Search indexed arXiv papers on artificial intelligence, large language models, computer vision and robotics. Read source abstracts and follow links to arXiv.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 253 records · Page 14Linked to original sources
arXiv2014

Synthetic biology: From a word to a world

Synthetic biology is one of the battlefields where the main countries fight for the supremacy in science. The word synthetic biology hides a big world, ready to be explored by interdisciplinary research collaborations. The purpose of this investigation is to reveal the what, where, when of the current situation in this emerging field. A keyword search string for the field was constructed and applied in the Web of Science and in the Derwent Innovations Index. In particular, we calculated year based h-type indices for high-frequent keywords.

q-bio.OT↗
arXiv2015

A Set of Discrete Formulae for the Performance of a Tsetse Population During Aerial Spraying

A set of discrete formulae that calculates the hypothetical impact of aerial spraying on a tsetse population is derived and the work is thought to be novel. Both the original population and the subsequent generations which survive the aerial spraying, may ultimately be thought of as deriving from two, distinct sources. These origins are, however, neither distinct, nor relevant by the third generation. It is for this reason that the female population is considered to be composed of the following four categories for the purposes of derivation: Original flies which existed as such at the commencement of spraying; original pupae which existed as such at the commencement of spraying; the immediate descendants of both the aforementioned categories, during spraying; third and higher generation descendants. In theory, the latter category is a recurrence relation. In practice, the third generation's pupal stage has hardly come into existence, even by the end of a completed operation. Implicit in the formulae is the assumption of one, temperature-dependent mortality rate for the entire pupal stage, a second for the period between eclosion and ovulation and yet a third for the entire, adult life-span. Gravid female resistance to the insecticide is assumed to be inconsequential. A further assumption of the formulae is that at least one male is always available (degree of sterility variable).

q-bio.OT↗
arXiv2014

The genetic code invariance: when Euler and Fibonacci meet

The number of atoms in the four ribonucleotides uridine monophosphate, cytidine monophosphate, adenine monophosphate and guanine monophosphate is taken as a key parameter. A mathematical relation describing the condensation of the three basic subunits a nucleobase, a ribose and a phosphate group, to form a ribonucleotide, is first obtained from this parameter. Next, the use of the latter and Euler totient function is shown to lead to the atom number content of the 64 codons and also to Rakocevic pattern. Finally, selected finite sums of Fibonacci numbers are shown to lead to the nucleon number content of the amino acids in various degeneracy patterns, and also to the multiplet structure of the 20 amino acids as well as to the degeneracy.

q-bio.OT↗
arXiv2014

The model of circular and longitudinal smooth muscle motions in the motility of intestinal segment

Coordination in circular and longitudinal muscle motions are of crucial importance in the motor function of gastrointestinal (GI) tract. Intestinal wall motions depend on myogenic-active properties of smooth muscles layers of intestinal wall, which is the ability to create active contractile forces in response to distension. Considering the stress in the circular and longitudinal smooth muscles as a sum of passive, depending on muscle deformations, and active, depending on muscle tone, components, and also assuming that the change in the muscle tone depends on the current stress-strain condition, the system of four ordinary differential equations (ODE) is obtained, which describes filling-emptying cycle of intestinal segment as a process of coordinated activities of circular and longitudinal muscles of intestinal wall. A general approach in formulating the modelling conditions is based on the previously described model restricted to the circularly distensible reservoir of constant length. Obtained results illustrate the character of coordinated activities of two orthogonal muscle layers, which are alternating phases of reciprocally and uniformly changing modalities such as stretching of the wall and muscle tone. The results also contribute to the existing understanding of the roles of Auerbach's and Meisner's intermuscular and submucous neural plexuses in regulations of autonomous intestinal motility, as well as clarify functional mechanisms of the interstitial cells of Cajal (ICC) in triggering of smooth muscle contractions.

q-bio.OT↗
arXiv2014

Biological Electric Fields and Rate Equations for Biophotons

Ultraweak bioluminescence - the emission of biophotons - remains an experimentally well-established, but theoretically poorly understood phenomenon. This paper presents several related investigations into the physical process of both spontaneous biophoton emission and delayed luminescence. Since light intensities depend upon the modulus squared of their corresponding electric fields we first make some general estimates about the inherent electric fields within various biological systems. Since photon emission from living matter following an initial excitation ("delayed luminescence") typically does not follow a simple exponential decay law after excitation we discuss such non-exponential decays from a general theoretical perspective and argue that they are often to be expected and why. We then discuss the dynamics behind some nonlinear rate equations, connecting them both to biological growth rates and biophoton emission rates, noting a possible connection with cancer. We then return to non-exponential decay laws seen for delayed luminescence in an experimental context and again note a possible connection with cancer.

physics.gen-ph↗
arXiv2014

Information -sharing, adaptive epigenetics and human longevity

Emerging empirical and theoretical thinking about human aging places considerable value upon the role of the environment as a major factor which can promote prolonged healthy longevity. Our contemporary, information-rich environment is taken to mean not merely the actual physical surroundings of a person but it is also considered in a more abstract sense, to denote cultural, societal and technological influences. Our modern environment is far from being static or stable. In fact, it is continually changing in an exponential manner, necessitating constant adaptive responses on behalf of our developmental and evolutionary mechanisms. In this paper, I attempt to describe how a continual, balanced and meaningful exposure to a stimulating environment, including exposure to information-that-requires-action (but NOT trivial information), has direct or indirect repercussions on epigenetic mechanisms which may then act to prolong healthy longevity. Information gained from our environment acts as a hormetic stimulus which up-regulates biological responses and feedback loops, eventually leading to improved repair of age-related damage. The consequence of this biological information-processing mechanism may influence resource allocation and redress the imbalance between somatic cell versus germ-line cell repairs. This can eventually have evolutionary consequences resulting in the drastic reduction of age-related disease and degeneration.

q-bio.OT↗
arXiv2014

Accounting for the 'network' in the Natura 2000 network: A response to Hochkirch et al. 2013

Worldwide, we are experiencing an unprecedented, accelerated loss of biodiversity triggered by a bundle of anthropogenic threats such as habitat destruction, environmental pollution and climate change. Despite all efforts of the European biodiversity conservation policy, initiated 20 years ago by the Habitats Directive that provided the legal basis for establishing the Natura 2000 network, the goal to halt the decline of biodiversity in Europe by 2010 has been missed. Hochkirch et al. (2013, Conserv. Lett. 6: 462-467) identified four major shortcomings of the current implementation of the directive concerning prioritization of the annexes, conservation plans, survey systems and financial resources. However they did not account for the intended network character of the Natura 2000 sites, an aspect of highest relevance. This response letter deals with this shortcoming as it is the prerequisite, over any other strategies, ensuring a Natura 2020 network being worth its name.

q-bio.OT↗
arXiv2014

Two-component feedback loops and deformed mechanics

It is shown that a general two-component feedback loop can be viewed as a deformed Hamiltonian system. Some of the implications of using ideas from theoretical physics to study biological processes are discussed.

q-bio.OT↗
arXiv2014

Geometry of Morphogenesis

We introduce a formalism for the geometry of eukaryotic cells and organisms.Cells are taken to be star-convex with good biological reason. This allows for a convenient description of their extent in space as well as all manner of cell surface gradients. We assume that a spectrum of such cell surface markers determines an epigenetic code for organism shape. The union of cells in space at a moment in time is by definition the organism taken as a metric subspace of Euclidean space, which can be further equipped with an arbitrary measure. Each cell determines a point in space thus assigning a finite configuration of distinct points in space to an organism, and a bundle over this configuration space is introduced with fiber a Hilbert space recording specific epigenetic data. On this bundle, a Lagrangian formulation of morphogenetic dynamics is proposed based on Gromov-Hausdorff distance which at once describes both embryo development and regenerative growth.

q-bio.OT↗
arXiv2014

Selectivity filter gate versus voltage-sensitive gate: A study of quantum probabilities in the Hodgkin-Huxley equation

The Hodgkin-Huxley (HH) model is a powerful model to explain different aspects of spike generation in excitable cells. However, the HH model was proposed in 1952 when the real structure of the ion channel was unknown. It is now common knowledge that in many ion-channel proteins the flow of ions through the pore is governed by a gate, comprising a so-called selectivity filter inside the ion channel, which can be controlled by electrical interactions. The selectivity filter is believed to be responsible for the selection and fast conduction of particular ions across the membrane of an excitable cell. Other (generally larger) parts of the molecule such as the pore-domain gate control the access of ions to the channel protein. In fact, two types of gates are considered here for ion channels: the external gate, which is the voltage sensitive gate, and the internal gate which is the selectivity filter gate (SFG). Some quantum effects are to expected in the SFG due to its small dimensions, which may play an important role in the operation of an ion channel. Here, we examine parameters in a generalized model of HH to see whether any parameter affects the spike generation. Our results indicate that the previously suggested semi-quantum-classical equation proposed by Bernroider and Summhammer (BS) agrees strongly with the HH equation under different conditions and may even provide a better explanation in some cases. We conclude that the BS model can refine the classical HH model substantially.

q-bio.OT↗
arXiv2014

The role of Junk DNA

Many efforts have been done in order to explain the role of junk DNA, but its function remain to be elucidated. In addition the GC-content variations among species still represent an enigma. Both these two misteries can have a common explanation: we hypothesize that the role of junk DNA is to preserve the mutations probability that is intrinsically reduced in GC-poorest genomes.

q-bio.OT↗
arXiv2014

Experimental Investigation of Distant Cellular Interaction among Adipose Derived Stem-Cells

In addition to chemical and mechanical interactions between cells electromagnetic field produced by cells has been considered as another form of signaling for cell-cell communication. The aim of this study is evaluation of electromagnetic effects on viability of Adipose-derived stem cells (ADSCs) without co-culturing. In this study, stem cells were isolated from human adipose tissue enzymatically and proliferated in monolayer culture. Then, 5.(10^4) adipose-derived stem cells were cultured in each well of the test plate. In the first row (4 wells), ADSCs as inducer cells were cultured in DMEM1 with 10 ng/ml Fibroblast growth factor (FGF). In adjacent and the last rows, ADSCs were cultured without FGF (as detector cells). After the three and five days the viability of cells were evaluated. Moreover, ADSCs were cultured in the same conditions but the inducer cells were placed once in the UV-filter tube and once in the quartz tube to see whether there is electromagnetic interaction among cells. Inducer cells caused significant cell proliferation in adjacent row cells (p- value<0.01) in the fifth day. However, using the UV-filter tube and quartz tube both reduced the effect of inducer cells on adjacent cells significantly. As a conclusion, we could detect distant cellular interaction (DCI) among adipose derived stem cells (ADSCs), but it was not electromagnetic signaling. Our results show that ADSCs affect each other via volatile signaling as a chemical distant cellular interaction (CDCI).

q-bio.OT↗
arXiv2014

Is there any measurable benefit in publishing preprints in the arXiv section Quantitative Biology?

A public preprint server such as arXiv allows authors to publish their manuscripts before submitting them to journals for peer review. It offers the chance to establish priority by making the results available upon completion. This article presents the arXiv section Quantitative Biology and investigates the advantages of preprint publications in terms of reception, which can be measured by means of citations. This paper focuses on the publication and citation delay, citation counts and the authors publishing their e-prints on arXiv. Moreover, the paper discusses the benefit for scientists as well as publishers. The results that are based on 12 selected journals show that submitting preprints to arXiv has become more common in the past few years, but the number of papers submitted to Quantitative Biology is still small and represents only a fraction of the total research output in biology. An immense advantage of arXiv is to overcome the long publication delay resulting from peer review. Although preprints are visible prior to the officially published articles, a significant citation advantage was only found for the Journal of Theoretical Biology.

cs.DL↗
arXiv2014

A Model on Genome Evolution

A model of genome evolution is proposed. Based on three assumptions the evolutionary theory of a genome is formulated. The general law on the direction of genome evolution is given. Both the deterministic classical equation and the stochastic quantum equation are proposed. It is proved that the classical equation can be put in a form of the least action principle and the latter can be used for obtaining the quantum generalization of the evolutionary law. The wave equation and uncertainty relation for the quantum evolution are deduced logically. It is shown that the classical trajectory is a limiting case of the general quantum evolution depicted in the coarse-grained time. The observed smooth/sudden evolution is interpreted by the alternating occurrence of the classical and quantum phases. The speciation event is explained by the quantum transition in quantum phase. Fundamental constants of time dimension, the quantization constant and the evolutionary inertia, are introduced for characterizing the genome evolution. The size of minimum genome is deduced from the quantum uncertainty lower bound. The present work shows the quantum law may be more general than thought, since it plays key roles not only in atomic physics, but also in genome evolution.

q-bio.OT↗
arXiv2014

Beta sheet propensity and the genetic code

So far mutations analysis was performed in terms of transitions and trasversions, so on the basis of the molecule, or in terms of GC-content and isochors, through the quantification of GC->AT mutations over AT->GC mutations. We tried a different approach hypothesizing that probably we are partially protected (by the genetic code) from amyloid fibrils formation.

q-bio.OT↗
arXiv2014

Biological effects of pulsating magnetic fields: role of solitons

In this paper, we analyze biological effects produced by magnetic fields in order to elucidate the physical mechanisms, which can produce them. We show that there is a chierarchy of such mechanisms and that the mutual interplay between them can result in the synergetic outcome. In particular, we analyze the biological effects of magnetic fields on soliton mediated charge transport in the redox processes in living organisms. Such solitons are described by nonlinear systems of equations and represent electrons that are self-trapped in alpha-helical polypeptides due to the moderately strong electron-lattice interaction. They represent a particular type of disssipativeless large polarons in low-dimensional systems. We show that the effective mass of solitons in the is different from the mass of free electrons, and that there is a resonant effect of the magnetic fields on the dynamics of solitons, and, hence, on charge transport that accompanies photosynthesis and respiration. These effects can result in non-thermal resonant effects of magnetic fields on redox processes in particular, and on the metabolism of the organism in general. This can explain physical mechanisms of therapies based on applying magnetic fields.

physics.bio-ph↗
arXiv2015

A Simulation for Neurophotonic Quantum Computation in Visual Pathways

One of the answers to the measurement problem in quantum theory is given by the Copenhagen-Interpretation of quantum theory (i.e. orthodox quantum theory) in which the wave function collapse happens in (by) the mind of observer. In fact, at first, great scientists like Von Neumann, London, Bauer and Wigner (initially) believed that the wave function collapse occurs in the brain or is caused by the consciousness of observer. However, this issue has been stayed yet very controversial. In fact, there are many challenging discussions about the survival of quantum effects in microscopic structures of the human brain, which is mainly because of quick decoherence of quantum states due to hot, wet and noisy environment of the brain that forbids long life coherence for brain processing. Nevertheless, there are also several arguments and evidences that emergence of large coherent states is feasible in the brain. In this paper, our approach is based on the latter in which macroscopic quantum states are probable in the human brain. Here, we simulate the delayed luminescence of photons in neurons with a Brassard-like teleportation circuit, i.e. equivalent to the transfer of quantum states of photons through the visual pathways from retina to the visual cortex. Indeed, our simulation considers both classical and quantum mechanical aspects of processing in neurons. As a result and based on our simulation, it is possible for our brain to receive the exact quantum states of photons in the visual cortex to be collapsed by our consciousness, which supports the Copenhagen-Interpretation of measurement problem in quantum theory.

q-bio.OT↗