Quantitative Biology - Other Publications (50)

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Quantitative Biology - Other Publications

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, in which each of the four mRNA nucleotide bases is assigned a unique 2-bit identifier. These designations have a physiological meaning derived from the molecular structures of, and relationships between, the bases. In this scheme, the 64 possible triplet codons are each indexed by a 6-bit label. 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


Kinetics Monte Carlo simulation has been done for solving Master equation about dynamics of intracellular viral reaction kinetics. Scaling relationship between equilibrium time and initial population of template has been founded as power low, , where N , are the number of initial population of template species , equilibrium time, a = 274.2, b = - 0. Read More


The objective of this short report is to reconsider the subject of bioinformatics as just being a tool of experimental biological science. To do that, we introduce three examples to show how bioinformatics could be considered as an experimental science. These examples show how the development of theoretical biological models generates experimentally verifiable computer hypotheses, which necessarily must be validated by experiments in vitro or in vivo. Read More


We present a general computational theory of stem cell networks and their developmental dynamics. Stem cell networks are special cases of developmental control networks. Our theory generates a natural classification of all possible stem cell networks based on their network architecture. Read More


Cooperative breeding is an excellent example of altruistic cooperation in social groups. Domestic dogs have evolved from cooperatively hunting and breeding ancestors, but have adapted to a facultatively social scavenging lifestyle on streets, and solitary living in human homes. Pets typically breed and reproduce under human supervision, but free-ranging dogs can provide insights into the natural breeding biology of dogs. Read More


Mammalian offspring require parental care, at least in the form of suckling during their early development. While mothers need to invest considerable time and energy in ensuring the survival of their current offspring, they also need to optimize their investment in one batch of offspring in order to ensure future reproduction and hence lifetime reproductive success. Free-ranging dogs live in small social groups, mate promiscuously, and lack the cooperative breeding biology of other group living canids. Read More


Parent-offspring conflict theory predicts the emergence of weaning conflict between a mother and her offspring arising from skewed relatedness benefits. Empirical observations of weaning conflict has not been carried out in canids. In a field-based study on free-ranging dogs we observed that suckling bout durations reduce, proportion of mother-initiated suckling bouts reduce and mother-initiated suckling terminations increase, with pup age. Read More


Sea shells are found to be a very rich natural resource for calcium carbonate. Sea shells are made up of CaCO3 mainly in the aragonite form, which are columnar or fibrous or microsphere structured crystals. The bioactivity of nanoparticles of sea shell has been studied in this work. Read More


Chalmer's famously identified pinpointing an explanation for our subjective experience as the "hard problem of consciousness". He argued that subjective experience constitutes a "hard problem" in the sense that its explanation will ultimately require new physical laws or principles. Here, we propose a corresponding "hard problem of life" as the problem of how `information' can affect the world. Read More


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. Read More


This thesis broadly concerns the origins of life problem, pursuing a joint approach that combines general philosophical/conceptual reflection on the problem along with more detailed and formal scientific modelling work oriented in the conceptual perspective developed. The central subject matter addressed is the emergence and maintenance of compartmentalised chemistries as precursors of more complex systems with a proper cellular organization. Whereas an evolutionary conception of life dominates prebiotic chemistry research and overflows into the protocells field, this thesis defends that the 'autonomous systems perspective' of living phenomena is a suitable - arguably the most suitable - conceptual framework to serve as a backdrop for protocell research. Read More


Aims: To document and preserve folkloric beliefs and art inspired by velvet worms (Onychophora), rare invertebrates that are considered "living fossils", have full placental organs and capture prey with a rough "net" built in a fraction of a second. Study Design: This study is a combination of field interviews, online surveys and automatic database search. Methods: We asked open-ended questions to farmers who know the worms, consulted experts and searched the Internet to document folkloric and artistic instances using all the names that these animals receive in English, Spanish and Portuguese (languages of the countries where they occur) as well as other languages, and automatic image search, in Web of Science, CrossRef, Google Scholar and Google. Read More


Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. Read More


This study develops an equation for describing three-dimensional membrane transformation through proliferation of its component cells regulated by morphogen density distributions on the membrane. The equation is developed in a two-dimensional coordinate system mapped on the membrane, referred to as the membrane coordinates. When the membrane expands, the membrane coordinates expand in the same manner so that the membrane is invariant in the coordinates. Read More


Advances in biology have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. Theoretical biology used to primarily provide a basis to rationally examine the frameworks within which biological experiments were carried out and to shed light on overlooked gaps in understanding. Today, however, theoretical biology has generally become synonymous with computational and mathematical biology. Read More