pwc-archive/papers-with-abstracts huggingface dataset:
CoHSI IV: Unifying Horizontal and Vertical Gene Transfer - is Mechanism Irrelevant ?
Authors: Les Hatton, Gregory Warr
Date: 2018-11-05 00:00:00

In previous papers we have described with strong experimental support, the organising role that CoHSI (Conservation of Hartley-Shannon Information) plays in determining important global properties of all known proteins, from defining the length distribution, to the natural emergence of very long proteins and their relationship to evolutionary time. Here we consider the insight that CoHSI might bring to a different problem, the distribution of identical proteins across species. Horizontal and Vertical Gene Transfer (HGT/VGT) both lead to the replication of protein sequences across species through a diversity of mechanisms some of which remain unknown. In contrast, CoHSI predicts from fundamental theory that such systems will demonstrate power law behavior independently of any mechanisms, and using the Uniprot database we show that the global pattern of protein re-use is emphatically linear on a log-log plot (adj. $R^{2} = 0.99, p < 2.2 \times 10^{-16}$ over 4 decades); i.e. it is extremely close to the predicted power law. Specifically we show that over 6.9 million proteins in TrEMBL 18-02 are re-used, i.e. their sequence appears identically in between 2 and 9,812 species, with re-used proteins varying in length from 7 to as long as 14,596 amino acids. Using (DL+V) to denote the three domains of life plus viruses, 21,676 proteins are shared between two (DL+V); 22 between three (DL+V) and 5 are shared in all four (DL+V). Although the majority of protein re-use occurs between bacterial species those proteins most frequently re-used occur disproportionately in viruses, which play a fundamental role in this distribution. These results suggest that diverse mechanisms of gene transfer (including traditional inheritance) are irrelevant in determining the global distribution of protein re-use.
Hominin evolution was caused by introgression from Gorilla
Authors: Johan Nygren
Date: 2018-10-02 00:00:00

The discovery of Paranthropus deyiremeda in 3.3-3.5 million year old fossil sites in Afar, together with 30% of the gorilla genome showing lineage sorting between humans and chimpanzees, and a NUMT ("nuclear mitochondrial DNA segment") on chromosome 5 that is shared by both gorillas, humans and chimpanzees, and shown to have diverged at the time of the Pan-Homo split rather than the Gorilla/Pan-Homo split, provides conclusive evidence that introgression from the gorilla lineage caused the Pan-Homo split, and the speciation of both the Australopithecus lineage and the Paranthropus lineage.
An Inductive Logic Programming Approach to Validate Hexose Binding Biochemical Knowledge
Authors: Houssam Nassif, Hassan Al-Ali, Sawsan Khuri, Walid Keirouz, David Page
Date: 2018-10-02 00:00:00
Tasks: Inductive logic programming

Hexoses are simple sugars that play a key role in many cellular pathways, and in the regulation of development and disease mechanisms. Current protein-sugar computational models are based, at least partially, on prior biochemical findings and knowledge. They incorporate different parts of these findings in predictive black-box models. We investigate the empirical support for biochemical findings by comparing Inductive Logic Programming (ILP) induced rules to actual biochemical results. We mine the Protein Data Bank for a representative data set of hexose binding sites, non-hexose binding sites and surface grooves. We build an ILP model of hexose-binding sites and evaluate our results against several baseline machine learning classifiers. Our method achieves an accuracy similar to that of other black-box classifiers while providing insight into the discriminating process. In addition, it confirms wet-lab findings and reveals a previously unreported Trp-Glu amino acids dependency.
Nutritionally recommended food for semi- to strict vegetarian diets based on large-scale nutrient composition data
Authors: Seunghyeon Kim, Michael F. Fenech, Pan-Jun Kim
Date: 2018-03-12 00:00:00

Diet design for vegetarian health is challenging due to the limited food repertoire of vegetarians. This challenge can be partially overcome by quantitative, data-driven approaches that utilise massive nutritional information collected for many different foods. Based on large-scale data of foods' nutrient compositions, the recent concept of nutritional fitness helps quantify a nutrient balance within each food with regard to satisfying daily nutritional requirements. Nutritional fitness offers prioritisation of recommended foods using the foods' occurrence in nutritionally adequate food combinations. Here, we systematically identify nutritionally recommendable foods for semi- to strict vegetarian diets through the computation of nutritional fitness. Along with commonly recommendable foods across different diets, our analysis reveals favourable foods specific to each diet, such as immature lima beans for a vegan diet as an amino acid and choline source, and mushrooms for ovo-lacto vegetarian and vegan diets as a vitamin D source. Furthermore, we find that selenium and other essential micronutrients can be subject to deficiency in plant-based diets, and suggest nutritionally-desirable dietary patterns. We extend our analysis to two hypothetical scenarios of highly personalised, plant-based methionine-restricted diets. Our nutrient-profiling approach may provide a useful guide for designing different types of personalised vegetarian diets.
True Epidemic Growth Construction Through Harmonic Analysis
Authors: Steven G. Krantz, Peter Polyakov, Arni S. R. Srinivasa Rao
Date: 2018-08-29 00:00:00

In this paper, we have proposed a two phase procedure (combining discrete graphs and wavelets) for constructing a true epidemic growth. In the first phase graph theory based approach was developed to update partial data available and in the second phase we used this partial data to generate a plausible complete data through wavelets. This procedure although novel and implementable, still leave some questions unanswered.
Reproducible research using biomodels
Authors: Pedro Mendes
Date: 2018-06-04 00:00:00

Like other types of computational research, modeling and simulation of biological processes (biomodels) is still largely communicated without sufficient detail to allow independent reproduction of results. But reproducibility in this area of research could easily be achieved by making use of existing resources, such as supplying models in standard formats and depositing code, models, and results in public repositories.
Physical mechanisms influencing life origin and development. Physical-biochemical paradigm of Life
Authors: Yuri K. Shestopaloff
Date: 2016-09-29 00:00:00

The present view of biological phenomena is based on a biochemical paradigm that development of living organisms is defined by information stored in a molecular form as some genetic code. However, new discoveries indicate that biological phenomena cannot be confined to a biochemical realm alone, but are also influenced by physical mechanisms. These mechanisms work at cellular, organ and whole organism spatial levels. They impose uniquely defined constraints on distribution of nutrients between biomass synthesis and maintenance of existing biomass, thus influencing the composition of biochemical reactions, their successive change and irreversibility during the organismal life cycle. Mathematically, such a growth mechanism is represented by a growth equation. Using this equation, we introduce growth models, show their adequacy to experimental data, and discover two types of division mechanisms, examining growth of unicellular organisms Amoeba, S. pombe, E. coli, B. subtilis, Staphylococcus. Also, on the basis of the growth equation, we find different metabolic characteristics of these organisms. For instance, it was shown that in logarithmic coordinates the values of their metabolic allometric exponents are located on a straight line. This fact has important implications with regard to evolutionary process of organisms within a food chain, considered as a single system. High adequateness of obtained results to experimental data, from different perspectives, as well as excellent compliance with previously proven more particular knowledge, and with general criteria for validation of scientific truths, proves validity of the introduced general growth mechanism and the growth equation. Taken together, the obtained results set solid grounds for introduction of a more comprehensive physical-biochemical paradigm of Life origin, development and evolution.
A Dynamical Systems Perspective on Chimeric Antigen Receptor T-Cell Dosing
Authors: Amir A. Toor, Alden Chesney, Jamal Zweit, Jason Reed, Shahrukh Hashmi
Date: 2018-05-08 00:00:00

Chimeric antigen receptor T cells (CAR T cells) are dosed similarly to donor lymphocyte infusions following hematopoietic cell transplantation. In this perspective paper a mathematical basis for personalized dosing of CAR T cells is introduced.
Activit{é} motrice des truies en groupes dans les diff{é}rents syst{è}mes de logement
Authors: Yannick Ramonet, Anaïs Tertre
Date: 2018-05-02 00:00:00

Assessment of the motor activity of group-housed sows in commercial farms. The objective of this study was to specify the level of motor activity of pregnant sows housed in groups in different housing systems. Eleven commercial farms were selected for this study. Four housing systems were represented: small groups of five to seven sows (SG), free access stalls (FS) with exercise area, electronic sow feeder with a stable group (ESFsta) or a dynamic group (ESFdyn). Ten sows in mid-gestation were observed in each farm. The observations of motor activity were made for 6 hours at the first meal or at the start of the feeding sequence, two consecutive days and at regular intervals of 4 minutes. The results show that the motor activity of group-housed sows depends on the housing system. The activity is higher with the ESFdyn system (standing: 55.7%), sows are less active in the SG system (standing: 26.5%), and FS system is intermediate. The distance traveled by sows in ESF system is linked to a larger area available. Thus, sows travel an average of 362 m $\pm$ 167 m in the ESFdyn system with an average available surface of 446 m${}^2$ whereas sows in small groups travel 50 m $\pm$ 15 m for 15 m${}^2$ available.
Non-hermitian operator modelling of basic cancer cell dynamics
Authors: F. Bagarello, F. Gargano
Date: 2018-04-09 00:00:00

We propose a dynamical system of tumor cells proliferation based on operatorial methods. The approach we propose is quantum-like: we use ladder and number operators to describe healthy and tumor cells birth and death, and the evolution is ruled by a non-hermitian Hamiltonian which includes, in a non reversible way, the basic biological mechanisms we consider for the system. We show that this approach is rather efficient in describing some processes of the cells. We further add some medical treatment, described by adding a suitable term in the Hamiltonian, which controls and limits the growth of tumor cells, and we propose an optimal approach to stop, and reverse, this growth.
Some preliminary results on relation between triplet composition and tissue source in larch total transcriptome
Authors: Michael Sadovsky, Tatiana Guseva, Vladislav Birukov, Tatiana Shpagina, Victoria Fedotovskaya
Date: 2018-03-09 00:00:00
Tasks: Relation, Triplet

We studied the structuredness ensemble of transcriptome of Siberian larch. The clusters in 64-dimensional space were identified with $K$-means technique, where the objects to be clusterized are the different fragments of the genome. A tetrahedron like structure in distribution of these fragments was found. Chargaff's discrepancy measure was determined for each class, as well as that latter between the classes. It reveals a relative similitude of the classes. The results have been compared to those obtained for specific transcriptome of each tissue. Also, a surrogate transcriptome has been developed comprising the contigs assembled for specific tissues; that latter has been compared with the real total transcriptome, and significant difference has been observed.
An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems
Authors: Hector Zenil, Narsis A. Kiani, Francesco Marabita, Yue Deng, Szabolcs Elias, Angelika Schmidt, Gordon Ball, Jesper Tegnér
Date: 2017-09-15 00:00:00
Tasks: Causal Discovery, Dimensionality Reduction, feature selection

We demonstrate that the algorithmic information content of a system is deeply connected to its potential dynamics, thus affording an avenue for moving systems in the information-theoretic space and controlling them in the phase space. To this end we performed experiments and validated the results on (1) a very large set of small graphs, (2) a number of larger networks with different topologies, and (3) biological networks from a widely studied and validated genetic network (e.coli) as well as on a significant number of differentiating (Th17) and differentiated human cells from high quality databases (Harvard's CellNet) with results conforming to experimentally validated biological data. Based on these results we introduce a conceptual framework, a model-based interventional calculus and a reprogrammability measure with which to steer, manipulate, and reconstruct the dynamics of non- linear dynamical systems from partial and disordered observations. The method consists in finding and applying a series of controlled interventions to a dynamical system to estimate how its algorithmic information content is affected when every one of its elements are perturbed. The approach represents an alternative to numerical simulation and statistical approaches for inferring causal mechanistic/generative models and finding first principles. We demonstrate the framework's capabilities by reconstructing the phase space of some discrete dynamical systems (cellular automata) as case study and reconstructing their generating rules. We thus advance tools for reprogramming artificial and living systems without full knowledge or access to the system's actual kinetic equations or probability distributions yielding a suite of universal and parameter-free algorithms of wide applicability ranging from causation, dimension reduction, feature selection and model generation.
Telling apart <I>Felidae</I> and <I>Ursidae</I> from the distribution of nucleotides in mitochondrial DNA
Authors: Andrij Rovenchak
Date: 2018-02-07 00:00:00

Rank--frequency distributions of nucleotide sequences in mitochondrial DNA are defined in a way analogous to the linguistic approach, with the highest-frequent nucleobase serving as a whitespace. For such sequences, entropy and mean length are calculated. These parameters are shown to discriminate the species of the <I>Felidae</I> (cats) and <I>Ursidae</I> (bears) families. From purely numerical values we are able to see in particular that giant pandas are bears while koalas are not. The observed linear relation between the parameters is explained using a simple probabilistic model. The approach based on the nonadditive generalization of the Bose-distribution is used to analyze the frequency spectra of the nucleotide sequences. In this case, the separation of families is not very sharp. Nevertheless, the distributions for <I>Felidae</I> have on average longer tails comparing to <I>Ursidae</I>.
Reactive species involved in higher seeds germination and shoots vigor through direct plasma exposure and plasma-activated liquids
Authors: T. Dufour, S. Zhang, S. Simon, A. Rousseau
Date: 2018-02-06 00:00:00

Cold atmospheric plasma treatments have been applied on lenses seeds and shoots to improve their germination and vigor rates. Two approaches have been considered: direct plasma exposure and plasma activation of liquids (tap water, demineralized water and liquid fertilizer). A special focus has been drawn on reactive oxygen species generated in the plasma phase but also in plasma activated media to understand their impact on germination process as well as on plants growth.
Development of aging changes: self-accelerating and inhomogeneous
Authors: Jicun Wang-Michelitsch, Thomas Michelitsch
Date: 2015-03-26 00:00:00
Tasks: Sensitivity

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.
Thermodynamic Mechanism of Life and Aging
Authors: Marko Popovic
Date: 2018-01-09 00:00:00

Life is a complex biological phenomenon represented by numerous chemical, physical and biological processes performed by a biothermodynamic system/cell/organism. Both living organisms and inanimate objects are subject to aging, a biological and physicochemical process characterized by changes in biological and thermodynamic state. Thus, the same physical laws govern processes in both animate and inanimate matter. All life processes lead to change of an organism's state. The change of biological and thermodynamic state of an organism in time underlies all of three kinds of aging (chronological, biological and thermodynamic). Life and aging of an organism both start at the moment of fertilization and continue through entire lifespan. Fertilization represents formation of a new organism. The new organism represents a new thermodynamic system. From the very beginning, it changes its state by changing thermodynamic parameters. The change of thermodynamic parameters is observed as aging and can be related to change in entropy. Entropy is thus the parameter that is related to all others and describes aging in the best manner. In the beginning, entropy change appears as a consequence of accumulation of matter (growth). Later, decomposition and configurational changes dominate, as a consequence of various chemical reactions (free radical, decomposition, fragmentation, accumulation of lipofuscin-like substances...).
Outward Sodium Current, Fine-structure Constant and Ferroelectric Hysteresis Regimes in the Giant Squid Axon Propagating Action Potential: a Phase Space Approach
Authors: Nikola K. Jurisic, Fred Cooper
Date: 2017-11-09 00:00:00

We derive a charge-conserving phase space cable equation for the propagating action potential, expressing ionic, membrane, and capacitive currents as functions of membrane potential. Analysis of the ionic current during the recovery phase reveals an outward sodium current, unobserved in voltage-clamp experiments, arising from the axoplasmic modulated Ohmic current creating a positive charge gradient opposing the sodium concentration gradient. Using a single assumption, that the fraction of open channels follows a time-dependent modified Avrami (mAvrami) equation that incorporates the ionic time rate yielding the fine-structure constant as a dimensionless scaling factor, we fit experimental ionic currents across different ions and biological temperatures. These results accurately predict several established observations, including the delayed onset of sodium inactivation, the magnitude of gating charges, and the fact that the fraction of open sodium channels is about 1/5 when most of the gating charges have moved. These alignments with already established facts logically increase confidence that the remaining predictions/hypotheses will be confirmed by future experiments. Notably, the mAvrami kinetics predictions include a universal role for the fine-structure constant in ion traversing ionic channels, and temperature-independent ionic activation energies are suggestive of quantum tunneling. Further predictions reveal continuous phase transitions in sodium channels at both initiation and peak of the action potential, implying symmetry changes in sodium channel states and pointing to a potential mechanism for memory encoding and storage. Also, the calculated optimal sodium channel density closely matches observed values. We also show that the action potential follows a heat-releasing ferroelectric hysteresis loop.
Application of Fractional Derivatives in Characterization of ECG graphs of Right Ventricular Hypertrophy Patients
Authors: Srijan Sengupta, Uttam Ghosh, Susmita Sarkar, Shantanu Das
Date: 2017-11-07 00:00:00

There are many functions which are continuous everywhere but non-differentiable at some or all points such functions are termed as unreachable functions. Graphs representing such unreachable functions are called unreachable graphs. For example, ECG is such an unreachable graph. Classical calculus fails in their characterization as derivatives do not exist at the unreachable points. Such unreachable functions can be characterized by fractional calculus as fractional derivatives exist at those unreachable points where classical derivatives do not exist. Definition of fractional derivatives has been proposed by several mathematicians like Grunwald-Letinikov, Riemann-Liouville, Caputo, and Jumarie to develop the theory of fractional calculus. In this paper, we have used Jumarie type fractional derivative and consequently the phase transition (P.T.) which is the difference between left fractional derivative and right fractional derivatives to characterize those points. A comparative study has been done between normal ECG sample and problematic ECG sample (Right Ventricular Hypertrophy) by the help of the above mentioned mathematical tool.
Mathematics at the eve of a historic transition in biology
Authors: Guo-Wei Wei
Date: 2017-11-06 00:00:00
Tasks: Descriptive

A century ago physicists and mathematicians worked in tandem and established quantum mechanism. Indeed, algebras, partial differential equations, group theory, and functional analysis underpin the foundation of quantum mechanism. Currently, biology is undergoing a historic transition from qualitative, phenomenological and descriptive to quantitative, analytical and predictive. Mathematics, again, becomes a driving force behind this new transition in biology.