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Other Quantitative Biology

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preprint2017arXiv

Traditional aging theories: which ones are useful?

Many theories have been proposed to answer two questions on aging: "Why do we age?" and "How do we age?" Among them, evolutionary theories are proposed to interpret the evolutionary advantage of aging, and "saving resources for group benefit" is thought to be the purpose of aging. However for saving resources, a more economic strategy should be to make a rapid death to the individuals who are over the reproduction age rather than to make them aging. Biological theories are proposed to identify the causes and the biological processes of aging. However, some theories including cell senescence/telomere theory, gene-controlling theory, and developmental theory, have unfortunately ignored the influence of damage on aging. Free-radical theory suggests that free radicals by causing intrinsic damage are the main cause of aging. However, even if intracellular free radicals cause injuries, they could be only associated with some but not all of the aging changes. Damage (fault)-accumulation theory predicts that faults as intrinsic damage can accumulate and lead to aging. However, in fact an unrepaired fault could not possibly remain in a living organism, since it can d

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preprint2016arXiv

Autoantibody recognition mechanisms of MUC1

The most cost-effective blood-based, noninvasive molecular cancer biomarkers are based on p53 epitopes and MUC1 tandem repeats. Here we use dimensionally compressed bioinformatic fractal scaling analysis to compare the two distinct and comparable probes, which examine different sections of the autoantibody population, achieving combined sensitivities of order 50%. We discover a promising MUC1 epitope in the SEA region outside the tandem repeats.

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preprint2016arXiv

Flux ratios and channel structures

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. Ussing's flux ratios generally depend on all physical parameters involved in ionic flows, particularly, on bulk conditions and channel structures. Certain setups of ion channel experiments result in flux ratios that are universal in the sense that their values depend on bulk conditions but not on channel structures; other setups lead to flux ratios that are specific in the sense that their values depend on channel structures too. Universal flux ratios could serve some purposes better than specific flux ratios in some circumstances and worse in other circumstances. We focus on two treatments of tracer flux measurements that serve as estimators of important properties of ion channels. The fir

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preprint2011arXiv

Mean Exit Time and Escape Probability for a Tumor Growth System under Non-Gaussian Noise

Effects of non-Gaussian $α-$stable Lévy noise on the Gompertz tumor growth model are quantified by considering the mean exit time and escape probability of the cancer cell density from inside a safe or benign domain. The mean exit time and escape probability problems are formulated in a differential-integral equation with a fractional Laplacian operator. Numerical simulations are conducted to evaluate how the mean exit time and escape probability vary or bifurcates when $α$ changes. Some bifurcation phenomena are observed and their impacts are discussed.

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preprint2016arXiv

The design of a proto-animal brain based upon spike timing

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. Together, these logic cells generate a pulse train that forms a recurrent fractal in the form of coherent square waves that consist of an equal number of set pulses and reset pulses. These pulses drive the actuators that pump water and food through its shell. Some of these individuals lose their permanent attachment to the sea floor, and evolve the ability to move around using the feeding motions. This creates the hazard of getting stuck against an object or moving away from its breeding community. They evolve a sensor system and logic cells that produce a restoring motion for each avoidance motion. This keeps the animal in the specific region of an object that it encounters (hefting), and maintains the zero sum (coherence) of the fractal, and connects the organism

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preprint2016arXiv

Interspecific allometric scaling of unicellular organisms as an evolutionary process of food chain creation

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. We argue that the cause of interspecific allometric scaling is the total effect of physiological and adaptation mechanisms inherent to organisms composing a food chain. Together, the workings of these mechanisms are united by a primary goal of any living creature - its successful reproduction. This primary necessity of each organism and of the entire food chain is that common denominator, to which all organisms adjust their metabolic rates. In this article, we consider unicellular organisms, while the second paper studies multicellular organisms and the entire concept in more detail. Here, using the proposed concepts and experimentally verified growth models of five different unicellular organisms, we obtain close to experimental findings values of allometric exponents of 0.757 for the end of growth and 0.853 for the beginning of growth. These results comply with experimental observations and prove ou

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preprint2016arXiv

A quantitative definition of organismality and its application to lichen

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. We adopt the view that the "organism" is a functional concept, used by scientists to address particular questions concerning the future state of a biological system, rather than something wholly defined by that system. In this approach organisms are a coarse-graining of a fine-grained dynamical model of a biological system. Crucially, the coarse-graining of the system into organisms is chosen so that their dynamics can be used by scientists to make accurate predictions of those features of the biological system that interests them, and do so with minimal computational burden. To illustrate our framework we apply it to a dynamic model of lichen symbiosis---a system where either the lichen or its constituent fungi and algae could reasonably be considered "organisms." We find that the best choice for what organisms are in this scenario are complex mixtures of many entities that do not resemble standard notions of organisms. When we restrict our allowed coarse-grainings

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preprint2016arXiv

Configuration Interaction of Hydropathic Waves Enables Ubiquitin Functionality

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. These include Fano interference between first- and second-order elements of globular surface shape transitions. Comparison with its closest relative, 76 amino acid Nedd8, shows that the latter lacks these features. A cracked elastic network model is proposed for the common target shared by many diseased proteins.

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preprint2016arXiv

The Drought-Stress Response of a Drought Resistant Impatiens Processed in PEG-6000 Solution in a Simulation Test

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. Therefore, it is superior to the non-mutagenized impatiens in terms of drought resistance and demonstrates tremendous differences from the normal impatiens in physiology, which intrigues scholars to search for the underlying reasons . Methods: By reference to Impatiens balsamina L,this experiment uses mutagenized impatiens seeds, processed by PEG-6000 in different solution concentration, to measure the germination rate of impatiens, its relative enzymatic activity and expression differences between gene SoS2 and gene RD29b in the drought lower reaches. Key results: Under simulated drought stress, there is no distinct difference between the mutagenized impatiens and the normal impatiens in terms of germination rate. But by measuring the root tillers and the length, the relative enzymatic activity, MDA, and the expression d

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preprint2016arXiv

Low pH, high salinity: too much for Microbial Fuel Cells?

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. All TMFCs operated at low pH (pH$=3.0 \pm 0.5$), as no pH amendment was carried out. Despite the harsh environmental conditions, our TMFCs showed a Power Density (PD) ranging from 20 to 55~mW/m$^2 \cdot$kg$_{\text{waste}}$ and a maximum CD of 20~mA/m$^2 \cdot$kg$_{\text{waste}}$, referred to the cathodic surface. COD removal after a $28-$day period was about $45 \%$. The remarkably low pH values as well as the fouling of Nafion membrane very likely limited TMFC performances. However, a scale-up estimation of our reactors provides interesting values in terms of power production, compared to actual a

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preprint2016arXiv

A Markov Decision Process Model to Guide Treatment of Abdominal Aortic Aneurysms

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. The new policy takes into account factors that are ignored by the current clinical policy (e.g. the life-expectancy and the age-dependent surgical mortality). The resulting optimal policy is structurally different from the current policy. In particular, the policy suggests that young patients with small aneurysms should undergo surgery. The robustness of the policy structure is demonstrated using simulations. A gain in the number of expected QALYs is shown, which indicates a possibility of improved care for patients with AAAs.

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preprint2016arXiv

Comparative Salt Tolerance Study of Some Acacia Species at Seed Germination Stage

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. Results: The results indicated that germination was significantly reduced in all species with the increase in NaCl concentrations. However, significant interspecific variation for salt tolerance was observed. The greatest variability in tolerance was observed at moderate salt stress (200 mM of NaCl) and the decrease in germination appeared to be more accentuated in A. cyanophylla and A. cyclops. Although, A. raddiana, remains the most interesting, it preserved the highest percentage (GC = 80%) and velocity of germination in all species studied in this study, even in the high salt levels. This species exhibited a particular adaptability to salt environment, at least at this stage in the life cycle an

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preprint2016arXiv

Conservation of Charge and Conservation of Current

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. We present an apparently universal derivation of conservation of current and advocate using that conservation law explicitly as a distinct part of theories and calculations of charge movement in complex fluids and environments. Classical models using ordinary differential equations rarely satisfy conservation of current, including the chemical kinetic models implementing the law of mass action and Markov models. These models must be amended if they are to conserve current. Strict enforcement of conservation of current is likely to aid numerical analysis by preventing artifactual accumulation of charge.

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preprint2016arXiv

Lumbar degenerative spondylolisthesis epidemiology: a systemic review with a focus on gender-specific and age-specific prevalence

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. Both women and men have few DS before 50 years old, after 50 years old both women and men start to develop DS, with women having a faster developing rate than men. For elderly Chinese (>=65 yrs, mean age: 72.5 yrs), large population based studies (MsOS(Hong Kong) and MrOS (Hong Kong), females n=2000 and males n=2000) showed DS prevalence was for 25.0% for women and 19.1% for men, and the prevalence F:M (women:men) ratio was 1.3:1. The published data (MsOS(USA) and MrOS(USA) studies) seem to show elderly Caucasian American has a higher DS prevalence, being approximately 60-70% higher than elderly Chinese; however the prevalence F:M ratio was similar to elderly Chinese population. Patient data showed female patients more often received treatment than men; and preliminary data show the ratio of numbers of female patients received treatment compared with men did not differ between Northeast Asians (Chi

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preprint2016arXiv

Emergence of Function

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.

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preprint2016arXiv

Quantitative Molecular Scaling Theory of Protein Amino Acid Sequences, Structure, and Functionality

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). Critical point theory is general, and recently it has proved to be the most effective way of describing protein networks that have evolved towards nearly perfect functionality in given environments (self-organized criticality). Evolutionary patterns are governed by common scaling principles, which can be quantified using scales that have been developed bioinformatically by studying thousands of PDB structures. The most e

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preprint2016arXiv

A topological approach to the problem of emergence in complex systems

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. To elucidate this question, we propose a novel approximation through constructive topology, a framework that allow us to map the space of observed objects (ontology) with the knowledge subject conceptual apparatus (epistemology). Focusing in a particular type of emergent processes, namely those accessible through experiments and from which we have still no clue on the mechanistic processes yielding its formation, we analyse how a knowledge subject would build a conceptual explanatory framework. Working on these systems, we identify concept disjunction as a critical logical operation needed to identify the constraints of the system. Next, focusing on a three-bits synthetic system, we show how the number and scope of the constraints hinder the develo

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preprint2016arXiv

Position and content paradigms in genome rearrangements: the wild and crazy world of permutations in genomics

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). In this paper, we describe the different ways in which permutations have been used to model genomes and genome rearrangement events, presenting some features and limitations of each approach, and show how the various models are related. This paper will help researchers navigate the landscape of genome rearrangement models, and make it easier for authors to present clear and consistent models.

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preprint2016arXiv

Multivariate information measures: a unification using Möbius operators on subset lattices

Information related measures are useful tools for multi variable data analysis, as measures of dependence among variables, and as descriptions of order in biological and physical systems. Information related measures, like marginal entropies, mutual / interaction / multi-information, have been used in a number of fields including descriptions of systems complexity and biological data analysis. The mathematical relationships among these measures are therefore of significant interest. Relations between common information measures include the duality relations based on Möbius inversion on lattices. These are the direct consequence of the symmetries of the lattices of the sets of variables (subsets ordered by inclusion). While the mathematical properties and relationships among these information-related measures are of significant interest, there has been, to our knowledge, no systematic examination of the full range of relationships and no unification of this diverse range of functions into a single formalism as we do here. In this paper we define operators on functions on these lattices based on the Möbius inversion idea that map the functions into one another (Möbius operators.) We

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preprint2016arXiv

Biological Systems as Systems of Increasing Entropy: Language and Genetics

In this paper we will try to provide a formalization of some characteristics of the development of biological systems aiming at the highest level of adequacy: justificative adequacy, that is, not only what we observe (descriptive adequacy) and how we think it occurs (explanatory adequacy) but also what architectural properties (in terms of matter configuration, for example) license the occurrence of certain phenomena. In the case of a biological instantiation of a physical system, justificative adequacy is to be found in the genotype-phenotype dynamics. Moreover, we will claim that such dynamics should be analyzed from a mathematical point of view, since the genotype is hypersensitive to initial conditions: a small change in a certain state of the system may have drastic effects on the output. Regarding methodology, we will use chaos theory applied to biology and also physical genetics in order to frame our research and give it theoretical weight.

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