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arXiv2015

Native American Flute Ergonomics

This study surveyed ergonomic issues in 308 Native American flute players. It also correlated the physical measurements of a subgroup of 33 participants with the largest flute they found comfortable. The data was used to derive a predictive formula for the largest comfortable flute based on physical measurements. The median age of players was 63 years with a mean of 6.9 years playing Native American flute. Females reported significantly less time playing the instrument (p = .004), but significantly faster self-reported progress rates (p = .001). Physical discomfort was experienced by 47-64% of players at least some of the time. Over 10% of players reported moderate discomfort on an average basis. Females report significantly higher maximum and average physical discomfort than males (p < .001 and p = .015, respectively). Height, arm span, hand span, and reported length of time playing and experience level all correlated with the largest flute that the player found comfortable. Multivariate coefficient analysis on those factors yielded a formula with a strong correlation to the largest comfortable flute (r = +.650). However, the formula does not have sufficient correlation to have value in predicting flute design. Customization of Native American flutes with the goal of improving ergonomics is proposed as a worthwhile goal.

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arXiv2015

Heart rate and its variability as an indicator of mental health in male prisoners

Heart rate (HR) and its variability (HRV) has been proposed as a marker for depressive symptoms and other aspects of mental health. However, the real correlation between them is presently uncertain, as previous studies have generally been conducted on the basis of small samples. In a sample of 113 adult male prisoners, we analyzed correlations between five measures of HR/HRV and five psychological measures of mental health aspects (depression, state and trait anxiety, and social relationships). We used Nadaraya-Watson non-parametric regression in both directions and age-stratified Spearman correlation to detect possible relations. Despite strong correlations among HR/HRV measures and among psychological measures, correlations between HR/HRV and psychological measures were low and non-significant for the overall sample. However, we found an age dependency, suggesting some correlations in younger people (HR with STAI-State, r = 0.39; with HADS-Anxiety, r = 0.52; both p < .005). Overall, the general utility of HR/HRV as a marker for mental health across populations remains unclear. Future research should address age and other potential confounders more consistently.

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arXiv2015

Comment on Activation of Visual Pigments by Light and Heat (Science 332, 1307-312, 2011)

It is known that the Arrhenius equation, based on the Boltzmann distribution, can model only a part (e.g. half of the activation energy) for retinal discrete dark noise observed for vertebrate rod and cone pigments. Luo et al (Science, 332, 1307-312, 2011) presented a new approach to explain this discrepancy by showing that applying the Hinshelwood distribution instead the Boltzmann distribution in the Arrhenius equation solves the problem successfully. However, a careful reanalysis of the methodology and results shows that the approach of Luo et al is questionable and the results found do not solve the problem completely.

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arXiv2015

Measurement in biological systems from the self-organisation point of view

Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological systems as dynamical systems far from not only their chemical equilibrium, but, in most cases, also of their Lyapunov stable states. Thus, in biological experiments, we do not observe states, but distinct trajectories followed by the examined organism. If one of the possible sequences is selected, a minute sub-section of the whole problem is obtained, sometimes in a seemingly highly reproducible manner. But the state of the organism is known only if a complete set of possible trajectories is known. And this is often practically impossible. Therefore, we propose a different framework for reporting and analysis of biological experiments, respecting the view of non-linear mathematics. This view should be used to avoid overoptimistic results, which have to be consequently retracted or largely complemented. An increase of specification of experimental procedures is the way for better understanding of the scope of paths, which the biological system may be evolving. And it is hidden in the evolution of experimental protocols.

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arXiv2015

Spices form the basis of food pairing in Indian cuisine

Culinary practices are influenced by climate, culture, history and geography. Molecular composition of recipes in a cuisine reveals patterns in food preferences. Indian cuisine encompasses a number of diverse sub-cuisines separated by geographies, climates and cultures. Its culinary system has a long history of health-centric dietary practices focused on disease prevention and promotion of health. We study food pairing in recipes of Indian cuisine to show that, in contrast to positive food pairing reported in some Western cuisines, Indian cuisine has a strong signature of negative food pairing; more the extent of flavor sharing between any two ingredients, lesser their co-occurrence. This feature is independent of recipe size and is not explained by ingredient category-based recipe constitution alone. Ingredient frequency emerged as the dominant factor specifying the characteristic flavor sharing pattern of the cuisine. Spices, individually and as a category, form the basis of ingredient composition in Indian cuisine. We also present a culinary evolution model which reproduces ingredient use distribution as well as negative food pairing of the cuisine. Our study provides a basis for designing novel signature recipes, healthy recipe alterations and recipe recommender systems.

physics.soc-ph↗

arXiv2015

Complexity and self-organization in Turing

We comment on Alan Turing's celebrated paper "The Chemical Basis of Morphogenesis" published in 1952 in the "Philosophical Transactions of the Royal Society of London". It is a typical example of a pioneering and inspired work in the domain of mathematical modelling.

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arXiv2015

Mass Action and Conservation of Current

The law of mass action is used widely. The law of mass action does not automatically conserve current, as is clear from mathematics of a simple case, chosen to illustrate the issues. The law of mass action does not force a series of chemical reactions to have the same current flow everywhere. Interruption of far-away current does not stop current everywhere in a series of chemical reactions, and so does not obey Maxwell equations. An additional constraint and equation is needed to enforce the global continuity of current flow. The additional constraint is introduced in this paper in the special case that the chemical reaction describes spatial movement through narrow channels. In that case, a fully consistent treatment is possible using a variety of models of charge movement. The general case must be dealt with by variational methods that enforce consistency of all the physical laws involved. Variational methods have only recently been developed to ensure that charge flow is conserved globally, along with mass, in dissipative systems like ions in solution or proteins. The Energy Variational Approach EnVarA should allow the development of more robust models of chemical, biochemical, and biological systems, making practical devices more easy to design and build. These difficulties arise away from equilibrium, when current flows, and the law of mass action is applied to a non-equilibrium situation, different from the systems considered when the law was originally derived. Non-equilibrium systems are important. Almost all of biology occurs away from equilibrium. Almost all devices of our technology function away from equilibrium. I believe robust models and device designs in the chemical world will not be possible until continuity of current is embedded in a generalization of the law of mass action using a consistent variational model of energy and dissipation.

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arXiv2015

Genomic Imaging Based on Codongrams and a^2grams

This paper introduces new tools for genomic signal processing, which can assist for genomic attribute extracting or describing biologically meaningful features embedded in a DNA. The codongrams and a2grams are offered as an alternative to spectrograms and scalograms. Twenty different a^2grams are defined for a genome, one for each amino acid (valgram is an a^2gram for valine; alagram is an a^2gram for alanine and so on). They provide information about the distribution and occurrence of the investigated amino acid. In particular, the metgram can be used to find out potential start position of genes within a genome. This approach can help implementing a new diagnosis test for genetic diseases by providing a type of DNA-medical imaging.

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arXiv2015

Music therapy for improving mental health in offenders: protocol for a systematic review and meta-analysis

This is a protocol for a systematic review of the effects of music therapy on offenders. Based on randomised controlled trials, the review aims to assess the effectiveness of music therapy on adolescent and adult offenders in custodial institutions including forensic psychiatric hospitals, and offenders or probationers in the community. The outcomes to be evaluated include alleviated symptoms of mental illness, psychosocial competencies and reduced recidivism.

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arXiv2017

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 destroy the integrity of tissue structure and cause rapid failure of the organism. These traditional theories are all incomplete on interpreting aging phenomena. Nevertheless, developmental theory and damage (fault)-accumulation theory are more useful, because they have recognized the importance of damage and development process in aging. Some physical theories are useful, because they point out the common characteristics of aging changes, including loss of complexity, consequence of increase of entropy, and failure of information-transmission. An advanced theory, which can include all of these useful ideas in traditional theories, is needed.

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arXiv2018

Development of aging changes: self-accelerating and inhomogeneous

Aging changes including age spots and atherosclerotic plaques develop in an inhomogeneous and accelerated manner. For understanding this phenomenon, some aging changes are analyzed by Misrepair mechanism, a mechanism proposed in Misrepair-accumulation theory. I. Misrepair is a strategy of repair for survival of an organism in situations of severe injuries; however a Misrepair alters the structure of a tissue, a cell or a molecule, which are the sub-structures of an organism. II. Misrepair of a sub-structure also alters the spatial relationship of this sub-structure with its neighbor sub-structures. Thus a Misrepair leads to increased damage-sensitivity and reduced repair-efficiency of these sub-structures. As a result, Misrepairs have a tendency to occur to the sub-structure and its neighbor sub-structures where an old Misrepair has taken place. In return, new Misrepairs will increase again the damage-sensitivity of these sub-structures and the surrounding sub-structures. By such a vicious circle, the frequency of Misrepairs to these sub-structures is increased and the range of affected sub-structures is enlarged after each time of Misrepair. Thus, accumulation of Misrepairs is focalized and self-accelerating. III. Focalized accumulation of Misrepairs leads to formation and growing of a "spot" or "plaque" in a tissue. Growing of a spot is self-accelerating, and old spots grow faster than new ones. New spots tend to develop close to old ones, resulting in an inhomogeneous distribution of spots. In conclusion, the inhomogeneous development of aging changes is a result of self-accelerated and focalized accumulation of Misrepairs; and the process of aging is self-accelerating.

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arXiv2016

Taylor's power law: before and after 50 years of scientific scrutiny

Taylor's power law is one of the mostly widely known empirical patterns in ecology discovered in the 20th century. It states that the variance of species population density scales as a power-law function of the mean population density. Taylor's power law was named after the British ecologist Lionel Roy Taylor. During the past half-century, Taylor's power law was confirmed for thousands of biological species and even for non-biological quantities. Numerous theories and models have been proposed to explain the mechanisms of Taylor's power law. However an understanding of the historical origin of this ubiquitous scaling pattern is lacking. This work reviews two research aspects that are fundamental to the discovery of Taylor's power law and provides an outlook of its future studies.

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arXiv2015

Quaternionic representation of the genetic code

A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick on the origin and evolution of the code as well as with the chronological order of appearence of the amino acids along the evolution as inferred from work that mixtures known experimental results with theoretical speculations. Suggested by the diagram we propose a Hamilton quaternions based mathematical representation of the code as it stands now-a-days. The central object in the description is a codon function that assigns to each amino acid an integer quaternion in such a way that the observed code degeneration is preserved. We emphasize the advantages of a quaternionic representation of amino acids taking as an example the folding of proteins. With this aim we propose an algorithm to go from the quaternions sequence to the protein three dimensional structure which can be compared with the corresponding experimental one stored at the Protein Data Bank. In our criterion the mathematical representation of the genetic code in terms of quaternions merits to be taken into account because it describes not only most of the known properties of the genetic code but also opens new perspectives that are mainly derived from the close relationship between quaternions and rotations.

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arXiv2015

TOPO: Improving remote homologue recognition via identifying common protein structure framework

Protein structure prediction remains a challenge in the field of computational biology. Traditional protein structure prediction approaches include template-based modelling (say, homology modelling, and threading), and ab initio. A threading algorithm takes a query protein sequence as input, recognizes the most likely fold, and finally reports the alignments of the query sequence to structure-known templates as output. The existing threading approaches mainly utilizes the information of protein sequence profile, solvent accessibility, contact probability, etc., and correctly recognize folds for some proteins. However, the existing threading approaches show poorly performance for remote homology proteins. How to improve the fold recognition for remote homology proteins remains to be a difficult task for protein structure prediction.

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arXiv2015

Molecular geometry of alkaloids present in seeds of mexican prickly poppy

The work is a study of the geometry of the molecules via molecular mechanics of the main alkaloids found in the seeds of Argemone Mexicana Linn, a prickly poppy, which is considered one of the most important species of plants in traditional Mexican and Indian medicine system. The seeds have toxic properties as well as bactericide, hallucinogenic, fungicide, insecticide, in isoquinolines and sanguinarine alkaloids such as berberine. A computational study of the molecular geometry of the molecules through molecular mechanics of the main alkaloids compounds present in plant seeds is described in a computer simulation. The plant has active ingredients compounds: allocryptopine, berberine, chelerythrine, copsitine, dihydrosanguinarine, protopine and sanguinarine. The studied alkaloids form two groups having similar charge distribution among themselves, which have dipole moments of these two times higher than in the other group.

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arXiv2015

A stochastic model of ant trail following with two pheromones

Colonies of ants are systems of interacting living organisms in which interactions between individuals and their environment can produce a reliable performance of a complex tasks without the need for centralised control. Particularly remarkable is the process of formation of refined paths between the nest and food sources that is essential for successful foraging. We have designed a simple stochastic off-lattice model of ant foraging in the absence of direct communication. The motion of ants is governed by two components - a random change in direction of motion that improves ability to explore the environment (facilitating food discovery), and a non-random global indirect interaction component based on pheromone signalling. Using numerical simulations we have studied the model behaviour in different parameter regimes and tested the ability of our model ants to adapt to changes in the external environment. The simulated behaviour of ants in the model recapitulated the experimentally observed behaviours of real ants. Furthermore we observe interesting synchronization in ant movement patterns which vary with the diffusion properties of the pheromones.

physics.bio-ph↗

arXiv2015

A common origin for 3/4- and 2/3-power rules in metabolic scaling

A central debate in biology has been the allometric scaling of metabolic rate. Kleiber's observation that animals' basal metabolic rate scales to the 3/4-power of body mass (Kleiber's rule) has been the prevailing hypothesis in the last eight decades. Increasingly, more evidences are supporting the alternative 2/3-power scaling rule, especially for smaller animals. The 2/3-rule dates back to before Kleiber's time and was thought to originate from the surface to volume relationship in Euclidean geometry. In this study, we show that both the 3/4- and 2/3-scaling rules have in fact one common origin. They are governed by animals' nutrient supply networks-their vascular systems that obey Murray's law. Murray's law describes the branching pattern of energy optimized vascular network under laminar flow. It is generally regarded as being closely followed by blood vessels. Our analysis agrees with experimental observations and recent numerical analyses that showed a curvature in metabolic scaling. When applied to metabolic data, our model accurately produces the observed 2/3-scaling rule for small animals of ~10 kg or less and the 3/4-rule for all animals excluding the smallest ones (~15 g). The model has broad implications to the ongoing debate. It proves that both the 3/4- and 2/3-exponents are phenomenological approximations of the same scaling rule within their applicable mass ranges, and that the 2/3-rule does not originate from the classical surface law.

physics.bio-ph↗

arXiv2015

A Mathematical Model for the Genetic Code(s) Based on Fibonacci Numbers and their q-Analogues

This work aims at showing the relevance and the applications possibilities of the Fibonacci sequence, and also its q-deformed or quantum extension, in the study of the genetic code(s). First, after the presentation of a new formula, an indexed double Fibonacci sequence, comprising the first six Fibonacci numbers, is shown to describe the 20 amino acids multiplets and their degeneracy as well as a characteristic pattern for the 61 meaningful codons. Next, the twenty amino acids, classified according to their increasing atom-number (carbon, nitrogen, oxygen and sulfur), exhibit several Fibonacci sequence patterns. Several mathematical relations are given, describing various atom-number patterns. Finally, a q-Fibonacci simple phenomenological model, with q a real deformation parameter, is used to describe, in a unified way, not only the standard genetic code, when q=1, but also all known slight variations of this latter, when q~1, as well as the case of the 21st amino acid (Selenocysteine) and the 22nd one (Pyrrolysine), also when q~1. As a by-product of this elementary model, we also show that, in the limit q=0, the number of amino acids reaches the value 6, in good agreement with old and still persistent claims stating that life, in its early development, could have used only a small number of amino acids.

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