Quantitative Biology - Other Publications (50)


Quantitative Biology - Other Publications

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

The usage frequencies for codons belonging to quartets are analized, over the whole exonic region, for 92 biological species. Correlation is put into evidence, between the usage frequencies of synonymous codons with third nucleotide A and C and between the usage frequencies of non synonymous codons, belonging to suitable subsets of the quartets, with the same third nucleotide. A correlation is pointed out between amino acids belonging to subsets of the set encoded by quartets of codons. Read More

The discovery of past spikes in atmospheric radiocarbon activity, caused by major solar energetic particle events, has opened up new possibilities for high-precision chronometry. The two spikes, or Miyake Events, have now been widely identified in tree-rings that grew in the years 775 and 994 CE. Furthermore, all other plant material that grew in these years would also have incorporated the anomalously high concentrations of radiocarbon. Read More

It is not known how a cell manages to find a specific DNA sequence sufficiently fast to repair a broken chromosome through homologous recombination. I propose that the solution is based on a parallelized search implemented by freely diffusing molecules programmed with sequences corresponding to those flanking the break site. Read More

We address the need for expanding the presence of the Lisp family of programming languages in bioinformatics and computational biology research. Languages of this family, like Common Lisp, Scheme, or Clojure, facilitate the creation of powerful and flexible software models that are required for complex and rapidly evolving domains like biology. We will point out several important key features that distinguish languages of the Lisp family from other programming languages and we will explain how these features can aid researchers in becoming more productive and creating better code. Read More

This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA bases is assigned a unique 2-bit identifier, so that the 64 triplet codons are each indexed by a 6-bit label. The ordering of the bits reflects the hierarchical organization manifested by the DNA replication/repair and tRNA translation systems. Read More

The mathematical concept of q-deformations, in particular the one of qnumbers, is used to study the genetic code(s). After considering two kinds of q-numbers, for comparison, a phenomenological classification scheme of the genetic code together with its numerous minor variants is, first, established. Next, numbers describing the presence of additional amino acids, such as Selenocysteine or/and Pyrrolysine, are also produced. Read More

This is perhaps a philosophical question rather than a mathematical one, we do not expect to give a full answer, even though we hope to clarify some ideas. In addition, we would like to provide a new perspective on the subject. We will find curious analogies with the way we perceive color and make some imaginary experiments showing that, even living imprisoned in three dimensions it could be different. Read More

To be cost-effective, biomedical proteins must be optimized with regard to many factors. Road maps are customary for large-scale projects, and here descriptive methods based on bioinformatic fractal thermodynamic scales are tested against an important example, HPV vaccine. Older scales from before 2000 are found to yield inconclusive results, but modern bioinformatic scales are amazingly accurate, with a high level of internal consistency, and little ambiguity. Read More