Quantitative Biology - Other Publications (50)

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Quantitative Biology - Other Publications

2017May
Affiliations: 1Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark, 2Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark, 3Section for Diagnostics and Scientific Advice, National Veterinary Institute, Technical University of Denmark, Kongens Lyngby, Denmark, 4Research group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark, 5Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark, 6Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark, 7Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark

With the increasing occurrence of antimicrobial resistance, more attention has been directed towards surveillance of both human and veterinary antimicrobial use. Since the early 2000s, several research papers on Danish pig antimicrobial usage have been published, based on data from the Danish Veterinary Medicines Statistics Program (VetStat). VetStat was established in 2000, as a national database containing detailed information on purchases of veterinary medicine. Read More


$\textbf{Background:}$ High mutability of HIV is the driving force of antiretroviral drug resistance, which represents a medical care challenge. $\textbf{Method and Model Equation:}$ To detect the mutability of each gene in the HIV-1 genome; a mathematical analysis of HIV-1 genome is performed, depending on a linear relation wherein the probability of spontaneous mutations emergence is directly proportional to the ratio of the gene length to the whole genome length. \begin{equation*} {P_g}{S_i} =\frac{g}{G} \end{equation*} $\textbf{Results:}$ $\textbf{tat}$, $\textbf{vpr}$ and $\textbf{vpu}$ are the least mutant genes in HIV-1 genome. Read More


The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of detecting similarities between animals, dangerous pests in crops, and so on. Some of the algorithms and data structures that have been created to solve this problem are Needleman Wunsch algorithm, DeBruijn graphs and greedy algorithms working on overlaps graphs; these try to work out the problem from different approaches that give place to certain advantages and disadvantages to be discussed. In this article we first expose a summary of the research done on already created solutions for the DNA assembly problem, to present later an on-line solution to the same matter, which, despite not considering mutations, would have the capacity of using only the necessary amount of readings to assemble an user specified amount of genes. Read More


$p$-Adic mathematical physics is a branch of modern mathematical physics based on the application of $p$-adic mathematical methods in modeling physical and related phenomena. It emerged in 1987 as a result of efforts to find a non-Archimedean approach to the spacetime and string dynamics at the Planck scale, but then was extended to many other areas including biology. This paper contains a brief review of main achievements in some selected topics of $p$-adic mathematical physics and its applications, especially in the last decade. Read More


One thing that discriminates living things from inanimate matter is their ability to generate similarly complex or non-random architectures in a large abundance. From DNA sequences to folded protein structures, living cells, microbial communities and multicellular structures, the material configurations in biology can easily be distinguished from non-living material assemblies. This is also true of the products of complex organisms that can themselves construct complex tools, machines, and artefacts. Read More


This article provides answers to the questions posed in the title. Contrary to the most common views, we show that neither the entropy, nor the Second Law may be used for either living systems, or to life phenomenon. Read More


The theoretical biologist Robert Rosen developed a highly original approach for investigating the question "What is life?", the most fundamental problem of biology. Considering that Rosen made extensive use of mathematics it might seem surprising that his ideas have only rarely been implemented in mathematical models. On the one hand, Rosen propagates relational models that neglect underlying structural details of the components and focus on relationships between the elements of a biological system, according to the motto "throw away the physics, keep the organisation". Read More


In the present article we demonstrate a new hybrid model of tumor growth. Our model is stochastic by tumor population development and strongly deterministic in cell motility dynamics and spatial propagation. In addition, it has excellent extendibility property. Read More


Ultrametric approach to the genetic code and the genome is considered and developed. $p$-Adic degeneracy of the genetic code is pointed out. Ultrametric tree of the codon space is presented. Read More


The importance of the notion of symmetry in physics is well established: could it also be the case for the genetic code? In this spirit, a model for the Genetic Code based on continuous symmetries and entitled the "Crystal Basis Model" has been proposed a few years ago. The present paper is a review of the model, of some of its first applications as well as of its recent developments. Indeed, after a motivated presentation of our mathematical model, we illustrate its pertinence by applying it for the elaboration and verification of sum rules for codon usage probabilities, as well as for establishing relations and some predictions between physical-chemical properties of amino-acids. Read More


Two years study was carried out during 2006-07 and 2007-08 crop seasons to study the response of different genotypes of oilseeds Brassica to Lipaphis erysimi (Kaltenbach) infestation both under field and screen house conditions and to find out the relationship of various biochemical constituents to aphid infestation. Among the various genotypes, the population of L. erysimi was significantly high on Brassica rapa variety brown sarson cv. Read More


Near all-sky imaging photometry was performed from a boat on the Gulf of Aqaba to measure the night sky brightness in a coastal environment. The boat was not anchored, and therefore drifted and rocked. The camera was mounted on a tripod without any inertia/motion stabilization. Read More


A petition for more careful considerations towards the usage of a quantification approach for ASL which has been recommended by the ISMRM perfusion study group and the European consortium for ASL in dementia. Read More


Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact, because the conventional wisdom avoids the question, there is little agreement as to whether the symmetrical nature actually even exists. Read More


Mapping forest AGB (Above Ground Biomass) is of crucial importance to estimate the carbon emissions associated with tropical deforestation. This study proposes a method to overcome the saturation at high AGB values of existing AGB map (Vieilledent's AGB map) by using a map of correction factors generated from GLAS (Geoscience Laser Altimeter System) spaceborne LiDAR data. The Vieilledent's AGB map of Madagascar was established using optical images, with parameters calculated from the SRTM Digital Elevation Model, climatic variables, and field inventories. Read More


The "reproducibility crisis" has been a highly visible source of scientific controversy and dispute. Here, I propose and review several avenues for identifying and prioritizing research studies for the purpose of targeted validation. Of the various proposals discussed, I identify scientific data science as being a strategy that merits greater attention among those interested in reproducibility. Read More


Groundwater contamination by heavy metals is a critical environmental problem for which in situ remediation is frequently the only viable treatment option. For such interventions, a three-dimensional reactive transport model of relevant biogeochemical processes is invaluable. To this end, we developed a model, CHROTRAN, for in situ treatment, which includes full dynamics for five species: a heavy metal to be remediated, an electron donor, biomass, a nontoxic conservative bio-inhibitor, and a biocide. Read More


A mathematical algorithm to describe DNA or RNA sequences of $N$ nucleotides by a string of $2N$ integers numbers is presented in the framework of the so called crystal basis model of the genetic code. The description allows to define a not trivial distance between two sequences and to perform the Discrete Fourier Transform on a sequence. Using the definition of distance the sequence of $\beta$-globin for Homo, Gallus and Opossum are compared. Read More


Ubiquitin tags diseased proteins and initiates an enzyme conjugation cascade, which has three stages. The first-stage enzyme Uba1 (E1) has evolved only modestly from slime mold to humans, and is > 14 times larger than Ub. Here we use critical point thermodynamic scaling theory to connect Uba1 (E1) evolution from yeast and slime mold to fruit flies and humans to subtle changes in its amino acid sequences. Read More


In multicellular organisms, relations among parts and between parts and the whole are contextual and interdependent. These organisms and their cells are ontogenetically linked: an organism starts as a cell that divides producing non-identical cells, which organize in tri-dimensional patterns. These association patterns and cells types change as tissues and organs are formed. Read More


This note presents a minimal approach to the origin of life, following standard ideas. We pay special attention to the point of view of non-equilibrium statistical mechanics, and in particular to detailed balance. As a consequence we propose a characterization of pre-biological states. Read More


The purpose of this study was to do a dataset distribution analysis, a classification performance analysis, and a topical analysis concerning what people are tweeting about four disease characteristics: symptoms, transmission, prevention, and treatment. A combination of natural language processing and machine learning techniques were used to determine what people are tweeting about Zika. Specifically, a two-stage classifier system was built to find relevant tweets on Zika, and then categorize these into the four disease categories. Read More


We investigate Ussing's unidirectional fluxes and flux ratios of charged tracers motivated particularly by the insightful proposal of Hodgkin and Keynes on a relation between flux ratios and channel structure. Our study is based on analysis of quasi-one-dimensional Poisson-Nernst-Planck type models for ionic flows through membrane channels. This class of models includes the Poisson equation that determines the electrical potential from the charges present and is in that sense consistent. Read More


One of the major characteristics of living organisms is metabolic rate - the amount of energy produced per unit time. When the size of organisms increases, the metabolic rate increases slower than organisms' mass, which has important implications for the evolutionary and ontogenetic development. Here, we study the fundamental causes of this phenomenon on the basis of metabolic properties of unicellular organisms (Amoeba Proteus, fission yeast S. Read More


A basal animal model is described as an organism similar to a Limpet that is attached to the sea floor living in a reproductive community. Its brain model uses logic cells (gates) to create a high frequency spike generator. Addition logic cells create a timing framework based upon Pulse Width Modulation (PWM), and create multi-cell, spike driven muscle actuators and bi-directional shift registers that serve as memories. Read More


The crisis in the reproducibility of experiments invites a re-evaluation of methods of inquiry and validation procedures. The text challenges current assumptions of knowledge acquisition and introduces G-complexity for defining decidable vs. non-decidable knowledge domains. Read More


Metabolic rate of organisms (amount of energy produced per unit time) increases slower than organisms' mass. This phenomenon, when considered across different taxa, is called interspecific allometric scaling. Its fundamental causes remain unknown. Read More


The organism is a fundamental concept in biology. However there is no universally accepted, formal, and yet broadly applicable definition of what an organism is. Here we introduce a candidate definition. Read More


Metabolism of living organisms is a foundation of life. The metabolic rate (energy production per unit time) increases slower than organisms' mass. When this phenomenon is considered across different species, it is called interspecific allometric scaling, whose causes are unknown. Read More


The crisis in the reproducibility of experiments invites a re-evaluation of methods of inquiry and validation procedures. The text challenges current assumptions of knowledge acquisition and introduces G-complexity for defining decidable vs. non-decidable knowledge domains. Read More


In this paper, we have identified and analyzed the emergence, structure and dynamics of the paradigmatic research fronts that established the fundamentals of the biomedical knowledge on HIV/AIDS. A search of papers with the identifiers "HIV/AIDS", "Human Immunodeficiency Virus" and "Acquired Immunodeficiency Syndrome" in the Web of Science (Thomson Reuters), was carried out. A citation network of those papers was constructed. Read More


Premise of the Study: Impatiens is a commonly seen garden flower, renowned for its strong adaptability and long history of cultivation. However, seldom has any research touched on its physiological resistance mechanism. In this experiment, the impatiens is selected from those which experienced aerospace mutation and thereafter 12 years of cultivation and breeding. Read More


Ubiquitin, discovered less than 50 years ago, tags thousands of diseased proteins for destruction. It is small (only 76 amino acids), and is found unchanged in mammals, birds, fish and even worms. Key features of its functionality are identified here using critical point thermodynamic scaling theory. Read More


This article reports on simulations that show how, starting with a form of neural lattice structure, it is possible to reversibly generate many alternative isomers with a lower structural symmetry, which results from twisting two hexagons around a central bond. Read More


An abdominal aortic aneurysm (AAA) is an enlargement of the abdominal aorta which, if left untreated, can progressively widen and may rupture with fatal consequences. In this paper, we determine an optimal treatment policy using Markov decision process modeling. The policy is optimal with respect to the number of quality adjusted life-years (QALYs) that are expected to be accumulated during the remaining life of a patient. Read More


Twelve single chambered, air-cathode Tubular Microbial Fuel Cells (TMFCs) have been filled up with fruit and vegetable residues. The anodes were realized by means of a carbon fiber brush, while the cathodes were realized through a graphite-based porous ceramic disk with Nafion membranes (117 Dupont). The performances in terms of polarization curves and power production were assessed according to different operating conditions: percentage of solid substrate water dilution, adoption of freshwater and a 35mg/L NaCl water solution and, finally, the effect of an initial potentiostatic growth. Read More


To find the possible equilibrium states of forest ecosystems one are suggested to use the theory of differential games. At within the 4-tier model of mosaic forest communities it established the existence of the Nash equilibrium states in such ecosystems Read More


The epidemiology of lumbar degenerative spondylolisthesis (DS) remains controversial. We performed a systemic review with the aim to have a better understanding of DS's prevalence in general population. The results showed the prevalence of DS is very gender specific and age specific. Read More


Objective: The purpose of this study was to assess and compare the seed germination response of six Acacia species under different NaCl concentrations in order to explore opportunities for selection and breeding salt tolerant genotypes. Methodology: Germination of seeds was evaluated under salt stresses using 5 treatment levels: 0, 100, 200, 300 and 400 mM of NaCl. Corrected germination rate (GC), germination rate index (GRI) and mean germination time (MGT) were recorded during 10 days. Read More


Thermodynamic scaling theory, previously applied mainly to small proteins, here analyzes quantitative evolution of the titled functional network giant hub enzymes. The broad domain structure identified homologically is confirmed hydropathically using amino acid sequences only. The most surprising results concern the evolution of the tyrosine kinase globular surface roughness from avian to mammals, which is first order, compared to the evolution within mammals from rodents to humans, which is second order. Read More


Here we review the development of protein scaling theory, starting from backgrounds in mathematics and statistical mechanics, and leading to biomedical applications. Evolution has organized each protein family in different ways, but scaling theory is both simple and effective in providing readily transferable dynamical insights complementary for many proteins represented in the 90 thousand static structures contained in the online Protein Data Base (PDB). Scaling theory is a simplifying magic wand that enables one to search the hundreds of millions of protein articles in the Web of Science, and identify those proteins that present new cost-effective methods for early detection and/or treatment of disease through individual protein sequences (personalized medicine). Read More


This work gives a mathematical study of tissue dynamics. We combine within-cell genome dynamics and diffusion between cells, where the synthesis of the two gives rise to the emergence of function. We introduce a concept of monotonicity and prove that monotonicity together with hardwiring, defined as all cells of the same tissue having the same genome dynamics, is sufficient for the global convergence of the tissue dynamics. Read More


Emergent patterns in complex systems are related to many intriguing phenomena in modern science and philosophy. Several conceptions such as weak, strong and robust emergence have been proposed to emphasize different epistemological and ontological aspects of the problem. One of the most important concerns is whether emergence is an intrinsic property of the reality we observe, or it is rather a consequence of epistemological limitations. Read More


We consider a general growth mechanism, which acts at cellular level and above (organs, systems and whole organisms). Using its mathematical representation, the growth equation, we study the growth and division mechanisms of amoeba and fission yeast Schizosaccharomyces pombe. We show how this mechanism, together with biomolecular machinery, governs growth and reproduction of cells, and these organisms in particular. Read More


From the basic impact of nutrient intake on health maintenance to the psychosocial benefits of mealtime, great advancements in nutritional sciences for support of human space travel have occurred over the past 60 years. Nutrition in space has many areas of impact, including provision of required nutrients and maintenance of endocrine, immune, and musculoskeletal systems. It is affected by environmental conditions such as radiation, temperature, and atmospheric pressures, and these are reviewed. Read More


Modellers of large scale genome rearrangement events, in which segments of DNA are inverted, moved, swapped, or even inserted or deleted, have found a natural syntax in the language of permutations. Despite this, there has been a wide range of modelling choices, assumptions and interpretations that make navigating the literature a significant challenge. Indeed, even authors of papers that use permutations to model genome rearrangement can struggle to interpret each others' work, because of subtle differences in basic assumptions that are often deeply ingrained (and consequently sometimes not even mentioned). Read More


There are evidences that organic life cannot be reduced to a single biomolecular realm, but, similar to other natural phenomena, rather involves different mechanisms acting at different scale levels, which together define evolvement of the living world. Here we show that a certain biophysical mechanism of general nature, acting at a cellular scale level and above, is also an influential factor in life phenomena. In inherent unity with biomolecular mechanisms, it governs growth and reproduction of cells, organs and whole organisms, and secures irreversibility of the life cycle progression. Read More


Conservation of current and conservation of charge are nearly the same thing: when enough is known about charge movement, conservation of current can be derived from conservation of charge, in ideal dielectrics, for example. Conservation of current is enforced implicitly in ideal dielectrics by theories that conserve charge. But charge movement in real materials like semiconductors or ionic solutions is never ideal. Read More


We apply the renormalization group theory to the dynamical systems with the simplest example of basic biological motifs. This includes the interpretation of complex networks as the perturbation to simple network. This is the first step to build our original framework to infer the properties of biological networks, and the basis work to see its effectiveness to actual complex systems. Read More


We study the build up of complexity on the example of 1 kg matter in different forms. We start on the simplest example of ideal gases, and then continue with more complex chemical, biological, life and social and technical structures. We assess the complexity of these systems quantitatively, based on their entropy. Read More