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At least 325 records · Page 18Linked to original sources

arXiv2016

Minimal Immunogenic Epitopes Have Nine Amino Acids

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.

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arXiv2016

Semi-phenomenological classification models of the genetic code(s) using q-deformed numbers

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. Finally, a minimal number of amino acids, which could fit the small number of them which are thought to have been involved, at the origin of life on Earth, is found. All together, these results constitute our final semi-phenomenological model.

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arXiv2016

Why are we not able to see beyond three dimensions?

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.

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arXiv2016

Hypothesis: Homologous recombination depends on parallel search

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.

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arXiv2016

Correlations in Usage Frequencies and Shannon Entropy for Codons

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. It is remarked that the computed Shannon entropy for quartets is weakly dependent on the biological species. The observed correlations well fit in the mathematical scheme of the crystal basis model of the genetic code.

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arXiv2016

Renormalization Group Transformation for Hamiltonian Dynamical Systems in Biological Networks

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.

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arXiv2016

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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arXiv2016

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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arXiv2016

Space nutrition: the key role of nutrition in human space flight

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. Nutrition with respect to space flight is closely interconnected with other life sciences research disciplines including the study of hematology, immunology, as well as neurosensory, cardiovascular, gastrointestinal, circadian rhythms, and musculoskeletal physiology. Psychosocial aspects of nutrition are also important for more productive missions and crew morale. Research conducted to determine the impact of spaceflight on human physiology and subsequent nutritional requirements will also have direct and indirect applications in Earth-based nutrition research. Cumulative nutritional research over the past five decades has resulted in the current nutritional requirements for astronauts. Realization of the full role of nutrition during spaceflight is critical for the success of extended-duration missions. Long-duration missions will require quantitation of nutrient requirements for maintenance of health and protection against the effects of microgravity. Keywords: Space nutrition, space flight, effects of microgravity, astronauts, space food

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arXiv2016

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 development of such scheme. Interestingly, we observe that our framework is unable to identify global constraints, clearly linking the epistemological limits of the framework with an ontological feature of the system. This allows us to propose a definition of emergence strength which we make compatible with the scientific method through the active intervention of the observer on the system. We think that this definition reconciles previous attempts to classify emergent processes, at least for the specific kind we discuss here. The paper finishes discussing the relevance of global constraints in biological systems, understood as a downward causal influence exerted by natural selection.

physics.soc-ph↗

arXiv2016

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 effective scales involve either hydropathic globular sculpting interactions averaged over length scales centered on membrane dimensions, or exposed beta strand propensities associated with aggregative (strong) protein-protein interactions.

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arXiv2016

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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arXiv2016

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 (Chinese, Japanese, and Korean) and European and American Caucasians, being around 2:1 in elderly population. The existing data also suggest that menopause may be a contributing factor for the accelerated DS development in post-menopausal

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arXiv2016

The Nash equilibrium of forest ecosystems

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

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arXiv2016

Towards the neural code endowed in cortical microcolumns

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.

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arXiv2016

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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arXiv2016

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 differences between gene SoS2 and gene RD29b in the drought lower reaches, it is verified that the mutagenized impatiens has more advantages than the normal impatiens, and it Can further cultivate become drought resistance varieties impatiens. Conclusions: In this experiment,which is a positive mutation, the mutagenized impatiens improves drought resistance through radiative mutation. The so obtained impatiens is more pleasing in sight in terms of color and shape and has higher application value in garden virescence.

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arXiv2016

No crisis should go to waste

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. A "second Cartesian revolution" should result in scientific methods that transcend determinism and reductionism.

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