Pedro Miramóntes

Universidad Nacional Autónoma de México

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G. Cocho

Universidad Nacional Autónoma de México

Wentian Li

Shanghai East Hospital

Ricardo Mansilla

Hospital Universitari Germans Trias i Pujol

Benjamín A. Itzá‐Ortiz

Universidad Autónoma del Estado de Hidalgo

Raúl Peralta

Universidad Autónoma del Estado de Morelos

ÓF

Óscar Fontanelli

Facultad Latinoamericana de Ciencias Sociales

Antonio Neme

Universidad Nacional Autónoma de México

Robert Cedergren

Université de Montréal

Cruz Vargas‐De‐León

Instituto Politécnico Nacional

Augusto Cabrera-Becerril

Universidad Nacional Autónoma de México

Cooperative Institutions

Universidad Nacional Autónoma de México

Universidad Autónoma del Estado de Morelos

Instituto Politécnico Nacional

Universidad Autónoma de la Ciudad de México

Instituto de Ecología

Center for Research and Advanced Studies of the National Polytechnic Institute

Universidad Autónoma del Estado de Hidalgo

Consejo Superior de Investigaciones Científicas

Université de Montréal

Centro Medico Nacional Siglo XXI

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Distribution of Hammerhead and Hammerhead-like RNA Motifs Through the GenBank

Genome Research (2000)

Gerardo Ferbeyre Véronique Bourdeau M. Pageau Pedro Miramóntes Robert Cedergren

Hammerhead ribozymes previously were found in satellite RNAs from plant viroids and in repetitive DNA from certain species of newts and schistosomes. To determine if this catalytic RNA motif has a wider distribution, we decided to scrutinize the GenBank database for RNAs that contain hammerhead or hammerhead-like motifs. The search shows a widespread distribution of this kind of RNA motif in different sequences suggesting that they might have a more general role in RNA biology. The frequency of the hammerhead motif is half of that expected from a random distribution, but this fact comes from the low CpG representation in vertebrate sequences and the bias of the GenBank for those sequences. Intriguing motifs include those found in several families of repetitive sequences, in the satellite RNA from the carrot red leaf luteovirus, in plant viruses like the spinach latent virus and the elm mottle virus, in animal viruses like the hepatitis E virus and the caprine encephalitis virus, and in mRNAs such as those coding for cytochrome P450 oxidoreductase in the rat and the hamster.

Hammerhead ribozyme

10.1101/gr.10.7.1011

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Citations (36)

On the Evolution of the Single-Subunit RNA Polymerases

Journal of Molecular Evolution (1997)

Nicolas Cermakian Tatsuya M. Ikeda Pedro Miramóntes B. Franz Lang Michael W. Gray

10.1007/pl00006271

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Citations (156)

Detecting lateral genetic material transfer

arXiv (Cornell University) (2012)

Claudia Irene Calderón Luis Delaye Víctor Mireles Pedro Miramóntes

The bioinformatical methods to detect lateral gene transfer events are mainly based on functional coding DNA characteristics. In this paper, we propose the use of DNA traits not depending on protein coding requirements. We introduce several semilocal variables that depend on DNA primary sequence and that reflect thermodynamic as well as physico-chemical magnitudes that are able to tell apart the genome of different organisms. After combining these variables in a neural classificator, we obtain results whose power of resolution go as far as to detect the exchange of genomic material between bacteria that are phylogenetically close.

Horizontal Gene Transfer

Coding region

10.48550/arxiv.1204.2601

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El color del ruido

Ciencias (México, D.F.) (1999)

Pedro Miramóntes

Source

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The Color of Noise and Weak Stationarity at the NREM to REM Sleep Transition in Mild Cognitive Impaired Subjects

Frontiers in Psychology (2018)

Alejandra Rosales-Lagarde Erika Elizabeth Rodríguez‐Torres Benjamín A. Itzá‐Ortiz Pedro Miramóntes Génesis Vázquez‐Tagle

In Older Adults (OAs), Electroencephalogram (EEG) slowing in frontal lobes and a diminished muscle atonia during Rapid Eye Movement sleep (REM) have each been effective tracers of Mild Cognitive Impairment (MCI), but this relationship remains to be explored by non-linear analysis. Likewise, data provided by EEG, EMG (Electromyogram) and EOG (Electrooculogram) —the three required sleep indicators— during the transition from REM to Non-REM (NREM) sleep have not been related jointly to MCI. Therefore, the main aim of the study was to explore, with results for Detrended Fluctuation Analysis (DFA) and multichannel DFA (mDFA), the Color of Noise (CN) at the NREM to REM transition in OAs with MCI versus subjects with good performances. The comparisons for the transition from NREM to REM were made for each group at each cerebral area, taking bilateral derivations to evaluate interhemispheric coupling and anteroposterior and posterior networks. In addition, stationarity analysis was carried out to explore if the three markers distinguished between the groups. Neuropsi and the Mini-Mental State Examination (MMSE) were administered, as well as other geriatric tests. One night polysomnography was applied to 6 OAs with MCI (68.1 ± 3) and to 7 subjects without it (CTRL) (64.5 ± 9), and pre-REM and REM epochs were analyzed for each subject. Lower scores for attention, memory and executive functions and a greater index of arousals was found for the MCI group. Results showed that EOGs constituted significant markers of MCI, increasing the CN for the MCI group in REM sleep. The CN of the EEG from pre-REM to REM showed an increase for the MCI group versus the opposite for the CTRL group at frontotemporal areas. Frontopolar interhemispheric scaling values also followed this trend as well as right anteroposterior networks. EMG values for both groups were lower than those for EEG and EOG. Stationarity analyses showed differences between stages in frontal areas and right and left EOGs for both groups. These results may demonstrate the breakdown of fractality in areas especially involved in executive functioning and the way weak stationarity analyses may help to distinguish between sleep stages in OAs.

Electrooculography

Sleep Stages

K-complex

10.3389/fpsyg.2018.01205

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A theoretical framework for defining some concepts in evolution.

Rivista di biologia (2006)

Pablo Padilla Pedro Miramóntes

We present a theoretical framework for biological evolution with the intention of giving precise mathematical definitions of some concepts in evolutionary biology such as fitness, evolutionary pressure, specialization and natural selection. In this framework, such concepts are identified with well-known mathematical terms within the theory of dynamical systems. We also discuss some more general implications in evolution; for instance, the fact that our model naturally exhibits a frequency spectrum of the type 1/f for low frequencies of evolutionary events.

Evolutionary Dynamics

Evolutionary game theory

Evolutionary Theory

10.1400/56203

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Direct Simulation of the CoVid-19 epidemic

medRxiv (Cold Spring Harbor Laboratory) (2021)

Augusto Cabrera-Becerril Pedro Miramóntes Raúl Peralta

A bstract We introduce an agent-based model to simulate the epidemiological dynamics of COVID-19. Most computational models proposed to study this epidemic do no take into account human mobility. We present a direct simulation model where mobility plays a key role and propose as well four quarantine strategies. The results show that the no-quarantine strategy does lead to a high peak of contagions with no rebound. Quarantined strategies, for their part, show a re-emergence of the epidemic with smaller and softer peaks.

Epidemic model

2019-20 coronavirus outbreak

Pandemic

10.1101/2021.01.14.21249829

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A Visual Overview of Coprime Numbers

Springer eBooks (2020)

Benjamín A. Itzá‐Ortiz Roberto López-Hernández Pedro Miramóntes

Coprime integers

Cartesian product

10.1007/978-3-319-70658-0_139-1

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Beta rank function: A smooth double-Pareto-like distribution

Communication in Statistics- Theory and Methods (2020)

Óscar Fontanelli Pedro Miramóntes Ricardo Mansilla G. Cocho Wentian Li

The beta rank function (BRF), x(u)=A(1−u)b/ua, where u is the normalized and continuous rank of an observation x, has wide applications in fitting real-world data. The underlying probability density function (pdf) fX(x) is not expressible in terms of elementary functions except for specific parameter values. We show however that it is approximately a unimodal skewed two-sided power law, or double-Pareto, or log-Laplacian distribution. Analysis of the pdf is simplified when the independent variable is log-transformed; the pdf fZ= log X(z) is smooth at the peak; probability is partitioned by the peak with proportion b/a (left to right); decay on left and right tails is approximately exponential, ez− log (A)b/b and e−z− log (A)a/a respectively. On the other hand, fX(x) behaves like a power distribution x1/b−1 when x∼0 and decays like a Pareto 1/x1/a+1 when x≫0. We give closed-form expressions of both pdf's in terms of Fox-H functions and propose numerical algorithms to approximate them. We suggest a way to elucidate if a data set follows a one-sided power law, a lognormal, a two-sided power law or a BRF. Finally, we illustrate the usefulness of these distributions in data analysis through a few examples.

Log-normal distribution

Rank (graph theory)

Power function

BETA (programming language)

10.1080/03610926.2020.1800739

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Distribuciones de probabilidad en las ciencias de la complejidad: una perspectiva contemporánea

arXiv (Cornell University) (2020)

Óscar Fontanelli Pedro Miramóntes Ricardo Mansilla

Science in the 21st century seems to be governed by novel approaches involving interdisciplinary work, systemic perspectives and complexity theory concepts. These new paradigms force us to leave aside our elder mechanistic approaches and embrace new starting points based on stochasticity, chaoticity, statistics and probability. In this work we review the fundamental ideas of complexity theory and the classic probabilistic models to study complex systems, based on the law of large numbers, central limit theorems and stable distributions. We also talk about power laws as the most common model for phenomena showing long tail distributions and we explore the principal difficulties that arise in practice with this kind of models. We show a novel alternative for the descripition of this type of phenomena and lastly we show two examples that illustrate the applications of this new model.

10.48550/arxiv.2002.09263

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