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Augusto Gonzalez

Publications and source records attributed to Augusto Gonzalez.

At least 19 recordsLinked to original sources
arXiv2026

Face morphometric profiles of groups as early markers for certain diseases?

Background: Face morphometry has been shown to work as a diagnosis tool in a set of syndromes. Face similarities are usually indications of more complete genetic similarities. Purpose: To show preliminary results on the face morphometry profile of the Cuban population and to argue that it could be used to define early markers for diseases, like Alzheimer. Methods: A dataset composed of photos of 200000 men is processed. Facial landmarks are extracted by means of the DLIB library and distances between them are computed. By clustering samples with similar facial traits, groups are formed and their densities inside the population are computed. Results: The face morphometry profiles for two age cohorts are obtained, showing the population dynamics. Genes involved in facial development are shown to be related to Alzheimer's disease. Conclusions: Late multifactorial diseases develop against the genetic background of each individual, which is expressed by its face morphometry. The latter can be thus considered a risk marker.

q-bio.PE↗
arXiv2023

Average fold-change of genetic pathways in biological transitions

A biological transition from a state N to a state T is characterized by a rearrangement of the gene expression profile in the system, quantitatively measured through the differential expression of genes. In contrast, changes in genetic pathways are usually evaluated by means of hypothesis testing schemes. We introduce a quantitative measure in order to evaluate the average fold-change of genetic pathways in biological transitions and applied it to characterize in general grounds the transition from a normal tissue to a tumor. Additionally, we study the transformation from primary to metastatic melanoma. Gene expression data from the TCGA portal for 16 tumors and the Reactome compilation of pathways are used for this purpose.

q-bio.TO↗
arXiv2023

A new mean field approach to finite spin systems

It is shown that a spin system is equivalent to a set of constrained harmonic oscillators. For finite, but large, systems, a continuous approximation to the density of states can be used, and the oscillator frequencies can be exactly computed. In the phase transition, the effective frequency of the lowest mode passes through zero, that is, it becomes an inverted oscillator. In the small oscillations regime, the oscillators can be treated as independent and the thermodynamic magnitudes can be computed. We show explicit calculations in a disordered, frustrated, high coordination number Blume Capel model with 60,000 spins.

cond-mat.mtrl-sci↗
arXiv2020

Constraint on the stem cell numbers and division rates posed by the risk of cancer

Compiled data for the stem cell numbers, Ns, and division rates, ms, is reanalized in order to show that we can distinguish two groups of human tissues. In the first one, there is a relatively high fraction of maintenance (stem and transit) cells in the tissue, but the division rates are low. The second group, on the other hand, is characterized by very high transit cell division rates, of around one division per day. These groups do not have an embrionary origin. We argue that their properties arise from a combination of the needs of tissue homeostasis (in particular turnover rate) and a bound on cancer risk, which is roughly a linear function of the product Ns ms. The bound on cancer risk leads to a threshold at ms = 8/year, where the fraction of stem cells falls down two orders of magnitude.

q-bio.TO↗
arXiv2020

Estimating the number of available states for normal and tumor tissues in gene expression space

The topology of gene expression space for a set of 12 cancer types is studied by means of an entropy-like magnitude, which allows the characterization of the regions occupied by tumor and normal samples. The comparison indicates that the number of available states in gene expression space is much greater for tumors than for normal tissues, suggesting the irreversibility of the progression to the tumor phase. The entropy is nearly constant for tumors, whereas exhibits a higher variability in normal tissues, probably due to tissue differentiation. In addition, we show an interesting correlation between the fraction of available states and the overlapping between the tumor and normal sample clouds, interpreted as a way of reducing the decay rate to the tumor phase in more ordered or structured tissues.

q-bio.TO↗
arXiv2020

On the gene expression landscape of cancer

A principal component analysis of the TCGA data for 15 cancer localizations unveils the following qualitative facts about tumors: 1) The state of a tissue in gene expression space may be described by a few variables. In particular, there is a single variable describing the progression from a normal tissue to a tumor. 2) Each cancer localization is characterized by a gene expression profile, in which genes have specific weights in the definition of the cancer state. There are no less than 2500 differentially-expressed genes, which lead to power-like tails in the expression distribution functions. 3) Tumors in different localizations share hundreds or even thousands of differentially expressed genes. There are 6 genes common to the 15 studied tumor localizations. 4) The tumor region is a kind of attractor. Tumors in advanced stages converge to this region independently of patient age or genetic variability. 5) There is a landscape of cancer in gene expression space with an approximate border separating normal tissues from tumors.

q-bio.TO↗
arXiv2018

Modeling evolution in a Long Time Evolution Experiment with E. Coli

Taking into account an evolutionary model of mutations in term of Levy Fights that was previously constructed, we designed an algorithm to reproduce the evolutionary dynamics of the Long-Term Evolution Experiment (LTEE) with E. Coli bacteria. The algorithm enables us to simulate mutations under natural selection conditions. The results of simulations on competition of clones, mean fitness, etc., are compared with experimental data. We attained to reproduce the behavior of the mean fitness of the bacteria cultures, get our own interpretations and more tuned descriptions of some phenomena taking part within the experiment, such as fixation and drift processes, clonal interference and epistasis.

q-bio.PE↗
arXiv2017

Gene expression rearrangements denoting changes in the biological state

In many situations, the gene expression signature is a unique marker of the biological state. We study the modification of the gene expression distribution function when the biological state of a system experiences a change. This change may be the result of a selective pressure, as in the Long Term Evolution Experiment with E. Coli populations, or the progression to Alzheimer disease in aged brains, or the progression from a normal tissue to the cancer state. The first two cases seem to belong to a class of transitions, where the initial and final states are relatively close to each other, and the distribution function for the differential expressions is short ranged, with a tail of only a few dozens of strongly varying genes. In the latter case, cancer, the initial and final states are far apart and separated by a low-fitness barrier. The distribution function shows a very heavy tail, with thousands of silenced and over-expressed genes. We characterize the biological states by means of their principal component representations, and the expression distribution functions by their maximal and minimal differential expression values and the exponents of the Pareto laws describing the tails.

q-bio.QM↗
arXiv2016

Mathematical control theory, the immune system, and cancer

Simple ideas, endowed from the mathematical theory of control, are used in order to analyze in general grounds the human immune system. The general principles are minimization of the pathogen load and economy of resources. They should constrain the parameters describing the immune system. In the simplest linear model, for example, where the response is proportional to the load, the annihilation rate of pathogens in any tissue should be greater than the pathogen's average rate of growth. When nonlinearities are added, a reference value for the number of pathogens is set, and a stability condition emerges, which relates strength of regular threats, barrier height and annihilation rate. The stability condition allows a qualitative comparison between tissues. On the other hand, in cancer immunity, the linear model leads to an expression for the lifetime risk, which accounts for both the effects of carcinogens (endogenous or external) and the immune response.

q-bio.TO↗
arXiv2016

Mutations as Levy flights

Data from a long time evolution experiment with Escherichia Coli and from a large study on copy number variations in subjects with european ancestry are analyzed in order to argue that mutations can be described as Levy flights in the mutation space. These Levy flights have at least two components: random single-base substitutions and large DNA rearrangements. From the data, we get estimations for the time rates of both events and the size distribution function of large rearrangements.

q-bio.PE↗
arXiv2016

Estimating the number of tissue resident macrophages

I provide a simple estimation for the number of macrophages in a tissue, arising from the hypothesis that they should keep infections below a certain threshold, above which neutrophils are recruited from blood circulation. The estimation reads Nm=a Ncel^α/Nmax, where a is a numerical coefficient, the exponent α is near 2/3, and Nmax is the maximal number of pathogens a macrophage may engulf in the time interval, tr, between pathogen replications.

q-bio.TO↗
arXiv2015

Levy model of cancer

A small portion of a tissue defines a microstate in gene expression space. Mutations, epigenetic events or external factors cause microstate displacements which are modeled by combining small independent gene expression variations and large Levy jumps, resulting from the collective variations of a set of genes. The risk of cancer in a tissue is estimated as the microstate probability to transit from the normal to the tumor region in gene expression space. The formula coming from the contribution of large Levy jumps seems to provide a qualitatively correct description of the lifetime risk of cancer, and reveals an interesting connection between the risk and the way the tissue is protected against infections.

q-bio.PE↗
arXiv2015

The NIST compilation of ionization potentials revisited (I): From He-like to Xe-like ions

The National Institute of Standards and Technology (NIST) database on ionization potentials for neutral atoms and ions is examined. For each isoelectronic sequence, we construct a regularized perturbative series that exactly matches the large-$Z$ and $Z\approx N-1$ regions. Comparison of the NIST data with this series allows the identification of problematic values in the reported data.

physics.atom-ph↗
arXiv2014

Mutagenesis and Background Neutron Radiation

We suggest a possible correlation between the ionization events caused by the background neutron radiation and the experimental data on mutations with damage in the DNA repair mechanism, coming from the Long Term Evolution Experiment in E. Coli populations.

q-bio.PE↗
arXiv2013

Atoms in the anionic domain, Z < N

We study atoms with N electrons, and nuclear charge Z. It is well known that the cationic regime, Z > N is qualitatively described by Thomas-Fermi theory. The anionic regime, Z < N, on the other hand, is characterized by an instability threshold at Z_c <~ N-1, below which the atom spontaneously emits an electron. We compute the slope of the energy curve at Z=N-1 by means of a simple model that depends on the electron affinity and the covalent radius of the neutral atom with N-1 electrons. This slope is used in order to estimate Z_c, which is compared with previous numerical results. Extrapolation of the linear behaviour in the opposite direction, up to Z=N, allows us to estimate the ionization potential of the atom with N electrons. The fact that the obtained ionization potentials are qualitatively correct is an indication that, with regard to certain properties, neutral atoms are closer to the anionic instability threshold than they are to the Thomas-Fermi, large Z, regime. A regularized series is written for the ionization potential that fits both, the large Z and Z\to Z_c regimes.

physics.atom-ph↗
arXiv2012

Terahertz absorption by excitonic polaritons

We use linear response theory in order to compute the light absorption spectrum, in the terahertz band, of a polariton system composed by excitons in a quantum dot very strongly coupled to the lowest photon mode of a thin micropillar. In a thermalized (Bose condensed) system at low temperatures, the spectral function shows a peak (GDR) associated to a 1s - 2p exciton transition, enhanced by polariton effects. On the other hand, in a non-equilibrium system absorption is peaked at low energies. Thus, a measurement of terahertz absorption could give an indication of the degree of thermalization in the polariton system.

cond-mat.mes-hall↗
arXiv2012

Perturbative calculation of the Sternheimer anti-shielding factor with Hartree-Fock atomic orbitals

We report a calculation of the Sternheimer anti-shielding factor, γ, by means of first order perturbation theory. In quality of basis functions, we use Hartree-Fock electronic orbitals, expanded on hydrogenic atomic states. The computed γ(r) for Fe^{3+} and Cu^{1+} inner electronic cores are reported and compared with literature values, obtained from alternative methodologies.

cond-mat.mtrl-sci↗