Papers by Marcelino Ramírez
Cornell University - arXiv, Sep 13, 2020
Motivation: With the aim to amplify and make sense of interactions of virus-human proteins in the... more Motivation: With the aim to amplify and make sense of interactions of virus-human proteins in the case of SARS-CoV-2, we performed a structural analysis of the network of protein interactions obtained from the integration of three sources: 1) proteins of virus SARS-CoV-2, 2)physical interactions between SARS-CoV-2 and human proteins, 3) known interactions of these human proteins between them and the dossier of affections in which these proteins are implicated. Results: As a product of this research, we present two networks, one from the interactions virus-host, and the other restricted to host-host, the last one is not usually considered for network analysis. We identified the most important proteins in both networks, those that have the maximal value of calculated invariants, these proteins are considered as the most: affected, connected or those that best monitor the flow of information in the network, among them we find UBC, a human protein related with ubiquination, linked with different stages of coronavirus disease, and ORF7A a virus protein that induces apoptosis in infected cells, associated with virion tethering. Using the constructed networks, we establish the more significant diseases corresponding with human proteins and their connections with other proteins. It is relevant that the identified diseases coincide with comorbidities, particularly the subnetwork of diabetes involves a great quantity of virus and human proteins (56%) and interactions (60%), this could explain the effect of this condition as an important cause of disease complications. Availability: Network data and programs in Python are included as additional material.
Journal of Tropical Ecology
Predator-prey interactions are one of the central themes in ecology due to their importance as a ... more Predator-prey interactions are one of the central themes in ecology due to their importance as a key mechanism in structuring biotic communities. In the predator-prey systems, the behaviours of persecution and avoidance impact on the ecosystem dynamics as much as the trophic interactions. We aimed to analyse the spatiotemporal co-occurrences between prey and predators in a community of medium- and large-sized mammals in southern Mexico. We predict prey will avoid sites where a predator previously passed. Contrarily, we expect a search behaviour by predators and a synchronization in activity patterns among them. We found prey does not occur either in time or space where predators have passed, suggesting an avoidance behaviour. Contrary to our expectations, we did not find significant search behaviours from predators to prey. Synchronization in the daily temporal overlap between predators was higher (Δ = 0.77–0.82) than with their prey (Δ = 0.43 – 0.81). The results suggest prey perce...
Tropical Conservation Science, 2022
Background and Research Aims Forest loss and fragmentation have a negative impact on large-sized ... more Background and Research Aims Forest loss and fragmentation have a negative impact on large-sized predators and prey, whose populations are reduced or extirpated locally. We explored the spatiotemporal coexistence of the mesopredators (< 15 kg) coyote, ocelot, and white-nosed coati, with their potential prey (< 15 kg) Mexican agouti, lowland paca, and collared peccary in a defaunated rainforest. Methods We used two-species occupancy-detection models between mesopredators and their potential prey, overlap index of circular models, and latency time measurements to evaluate temporal and spatial segregation and habitat use of species. Results Presence of ocelot and coyote was influenced by an increase in the detectability and occupancy of the Mexican agouti. Among most mesopredator–prey species pairs, the correlation for both the capture rates at camera-trap stations and the 1-hr intervals were mainly moderate or low. Some mesopredator–prey species pairs showed low or inverse corre...
Predator-prey interactions are one of the central themes in ecology due to their importance as a ... more Predator-prey interactions are one of the central themes in ecology due to their importance as a key mechanism in structuring biotic communities. In the predator-prey systems, the no-trophic interactions, such as persecution and avoidance, have more impact on ecosystems than the trophic ones. We analyze the spatiotemporal relations between prey and predators of a community of medium and large-size mammals in a tropical region. We analyzed time data series of camera-trap data. The observed data of time lags among occurrences of pairs of species were compared with random data using the Bootstrap method. We generate a network of co-occurrences to describe the significant spatiotemporal patterns between predators and prey and used the kernel density estimator to analyze the overlap of daily activity patterns themy. We found 26 predator-prey interactions (p<0.05), which involved 14 species. The results suggest that prey perceives the risk of predation and display avoidance behavior bo...
AKCE International Journal of Graphs and Combinatorics, 2019
The connection between the matching polynomial and the chromatic polynomial for triangle-free gra... more The connection between the matching polynomial and the chromatic polynomial for triangle-free graphs was revealed in the work of Farrell and Whitehead. We extend this result to all graph by mirroring the corresponding result of Godsil and Gutman for the acyclic polynomial and the characteristic polynomial. We also reintroduce the clique polynomial of Farrell as an evaluation of the U-polynomial of Noble and Welsh, which also happens to contain the matching and chromatic polynomials. c
Linear Algebra and its Applications, 2019
In this note we prove that the vertex energy of a graph, as defined in [2], can be calculated in ... more In this note we prove that the vertex energy of a graph, as defined in [2], can be calculated in terms of a Coulson integral formula. We present examples of how this formula can be used, and we show some applications to bipartite graphs.
European Journal of Combinatorics, 2012
We prove that the Tutte polynomial of a coloopless paving matroid is convex along the portions of... more We prove that the Tutte polynomial of a coloopless paving matroid is convex along the portions of the line segments x + y = p lying in the positive quadrant. Every coloopless paving matroid is in the class of matroids which contain two disjoint bases or whose ground set is the union of two bases. For this latter class we give a proof that TM (a, a) ≤ max{TM (2a, 0), TM (0, 2a)} for a ≥ 2. We conjecture that TM (1, 1) ≤ max{TM (2, 0), TM (0, 2)} for the same class of matroids. We also prove this conjecture for some families of graphs and matroids.
This research presents a comparative study and an indoor thermal comfort analysis of self-constru... more This research presents a comparative study and an indoor thermal comfort analysis of self-constructed dwellings with different roofing in the Lower Papaloapan River Basin in Mexico. These include c...
We prove that if a matroid M contains two disjoint bases (or, dually, if its ground set is the un... more We prove that if a matroid M contains two disjoint bases (or, dually, if its ground set is the union of two bases), then T M (a, a) ≤ max{T M (2a, 0), T M (0, 2a)} for a ≥ 2. This resembles the conjecture that appears in C. Merino and D.J.A. Welsh, Forests, colourings and acyclic orientations of the square lattice, Annals of Combinatorics 3 (1999) pp. 417-429: If G is a 2-connected graph with no loops, then T G (1, 1) ≤ max{T G (2, 0), T (0, 2)}. We conjecture that T M (1, 1) ≤ max{T M (2, 0), T M (0, 2)} for matroids which contains two disjoint bases or its ground set is the union of two bases. We also prove the latter for some families of graphs and matroids.
The Tutte polynomial of a graph or a matroid, named after W. T. Tutte, has the important universa... more The Tutte polynomial of a graph or a matroid, named after W. T. Tutte, has the important universal property that essentially any mul-tiplicative graph or network invariant with a deletion and contraction reduction must be an evaluation of it. The deletion and contraction operations are natural reductions for many network models arising from a wide range of problems at the heart of computer science, engi-neering, optimization, physics, and biology. Even though the invariant is #P-hard to compute in general, there are many occasions when we face the task of computing the Tutte polynomial for some families of graphs or matroids. In this work we compile known formulas for the Tutte polynomial of some families of graphs and matroids. Also, we give brief explanations of the techniques that were use to find the for-mulas. Hopefully, this will be useful for researchers in Combinatorics and elsewhere.
Database
We present RegulomePA, a database that contains biological information on regulatory interactions... more We present RegulomePA, a database that contains biological information on regulatory interactions between transcription factors (TFs), sigma factor (SFs) and target genes in Pseudomonas aeruginosa PAO1. RegulomePA consists of 4827 regulatory interactions between 2831 nodes, which represent the interactions of TFs and SFs with their target genes, from the total of predicted RegulomePA including 27.27% of the TFs, 54.16% of SFs and 50.8% of the total genes. Each entry in the database corresponds to one node in the network and provides comprehensive details about the gene and its regulatory interactions such as gene description, nucleotide sequence, genome-strand position and links to other databases as well as the type of regulation it exerts or to which it is being subject (repression or activation), the associated experimental evidence and references, and topological information. Additionally, RegulomePA provides a way to recover information on the regulatory circuits of the network...
European Journal of Combinatorics, 2011
We prove that the Tutte polynomial of a coloopless paving matroid is convex along the portions of... more We prove that the Tutte polynomial of a coloopless paving matroid is convex along the portions of the line segments x + y = p lying in the positive quadrant. Every coloopless paving matroids is in the class of matroids which contain two disjoint bases or whose ground set is the union of two bases of M * . For this latter class we give a proof that TM (a, a) ≤ max{TM (2a, 0), TM (0, 2a)} for a ≥ 2. We conjecture that TM (1, 1) ≤ max{TM (2, 0), TM (0, 2)} for the same class of matroids. We also prove this conjecture for some families of graphs and matroids.
We give two proofs that the $h$-vector of any paving matroid is a pure O-sequence, thus answering... more We give two proofs that the $h$-vector of any paving matroid is a pure O-sequence, thus answering in the affirmative a conjecture made by R. Stanley, for this particular class of matroids. We also investigate the problem of obtaining good lower bounds for the number of bases of a paving matroid given its rank and number of elements.
Books by Marcelino Ramírez
En este libro se reúnen 16 contribuciones derivadas de avances y resultados de proyectos de 26 in... more En este libro se reúnen 16 contribuciones derivadas de avances y resultados de proyectos de 26 investigación, relacionados con áreas temáticas de Educación (5 capítulos), Educación y TIC (4 capítulos), Derecho y Educación en Salud (4 capítulos) y Emprendurismo (3 capítulos), producto del trabajo de docentes, profesores-investigadores y tesistas de la Región del Papaloapan, Oaxaca y estados vecinos.
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Papers by Marcelino Ramírez
Books by Marcelino Ramírez