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Cordova-Lepe, F., & Vogt-Geisse, K. (2022). Adding a reaction-restoration type transmission rate dynamic-law to the basic SEIR COVID-19 model. PLos One, 17(6), e0269843.
Abstract: The classical SEIR model, being an autonomous system of differential equations, has important limitations when representing a pandemic situation. Particularly, the geometric unimodal shape of the epidemic curve is not what is generally observed. This work introduces the beta SEIR model, which adds to the classical SEIR model a differential law to model the variation in the transmission rate. It considers two opposite thrives generally found in a population: first, reaction to disease presence that may be linked to mitigation strategies, which tends to decrease transmission, and second, the urge to return to normal conditions that pulls to restore the initial value of the transmission rate. Our results open a wide spectrum of dynamic variabilities in the curve of new infected, which are justified by reaction and restoration thrives that affect disease transmission over time. Some of these dynamics have been observed in the existing COVID-19 disease data. In particular and to further exemplify the potential of the model proposed in this article, we show its capability of capturing the evolution of the number of new confirmed cases of Chile and Italy for several months after epidemic onset, while incorporating a reaction to disease presence with decreasing adherence to mitigation strategies, as well as a seasonal effect on the restoration of the initial transmissibility conditions.
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Demongeot, J., Goles, E., Morvan, M., Noual, M., & Sene, S. (2010). Attraction Basins as Gauges of Robustness against Boundary Conditions in Biological Complex Systems. PLoS One, 5(8), 18 pp.
Abstract: One fundamental concept in the context of biological systems on which researches have flourished in the past decade is that of the apparent robustness of these systems, i.e., their ability to resist to perturbations or constraints induced by external or boundary elements such as electromagnetic fields acting on neural networks, micro-RNAs acting on genetic networks and even hormone flows acting both on neural and genetic networks. Recent studies have shown the importance of addressing the question of the environmental robustness of biological networks such as neural and genetic networks. In some cases, external regulatory elements can be given a relevant formal representation by assimilating them to or modeling them by boundary conditions. This article presents a generic mathematical approach to understand the influence of boundary elements on the dynamics of regulation networks, considering their attraction basins as gauges of their robustness. The application of this method on a real genetic regulation network will point out a mathematical explanation of a biological phenomenon which has only been observed experimentally until now, namely the necessity of the presence of gibberellin for the flower of the plant Arabidopsis thaliana to develop normally.
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Gaitan-Espitia, J. D., Arias, M. B., Lardies, M. A., & Nespolo, R. F. (2013). Variation in Thermal Sensitivity and Thermal Tolerances in an Invasive Species across a Climatic Gradient: Lessons from the Land Snail Cornu aspersum. PLoS One, 8(8).
Abstract: The ability of organisms to perform at different temperatures could be described by a continuous nonlinear reaction norm (i.e., thermal performance curve, TPC), in which the phenotypic trait value varies as a function of temperature. Almost any shift in the parameters of this performance curve could highlight the direct effect of temperature on organism fitness, providing a powerful framework for testing thermal adaptation hypotheses. Inter-and intraspecific differences in this performance curve are also reflected in thermal tolerances limits (e. g., critical and lethal limits), influencing the biogeographic patterns of species' distribution. Within this context, here we investigated the intraspecific variation in thermal sensitivities and thermal tolerances in three populations of the invasive snail Cornu aspersum across a geographical gradient, characterized by different climatic conditions. Thus, we examined population differentiation in the TPCs, thermal-coma recovery times, expression of heat-shock proteins and standard metabolic rate (i.e., energetic costs of physiological differentiation). We tested two competing hypotheses regarding thermal adaptation (the “hotter is better” and the generalist-specialist trade-offs). Our results show that the differences in thermal sensitivity among populations of C. aspersum follow a latitudinal pattern, which is likely the result of a combination of thermodynamic constraints (“hotter is better”) and thermal adaptations to their local environments (generalist-specialist trade-offs). This finding is also consistent with some thermal tolerance indices such as the Heat-Shock Protein Response and the recovery time from chill-coma. However, mixed responses in the evaluated traits suggest that thermal adaptation in this species is not complete, as we were not able to detect any differences in neither energetic costs of physiological differentiation among populations, nor in the heat-coma recovery.
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Goldstein-Daruech, N., Cope, E. K., Zhao, K. Q., Vukovic, K., Kofonow, J. M., Doghramji, L., et al. (2011). Tobacco Smoke Mediated Induction of Sinonasal Microbial Biofilms. PLoS One, 6(1), 7 pp.
Abstract: Cigarette smokers and those exposed to second hand smoke are more susceptible to life threatening infection than nonsmokers. While much is known about the devastating effect tobacco exposure has on the human body, less is known about the effect of tobacco smoke on the commensal and commonly found pathogenic bacteria of the human respiratory tract, or human respiratory tract microbiome. Chronic rhinosinusitis (CRS) is a common medical complaint, affecting 16% of the US population with an estimated aggregated cost of $6 billion annually. Epidemiologic studies demonstrate a correlation between tobacco smoke exposure and rhinosinusitis. Although a common cause of CRS has not been defined, bacterial presence within the nasal and paranasal sinuses is assumed to be contributory. Here we demonstrate that repetitive tobacco smoke exposure induces biofilm formation in a diverse set of bacteria isolated from the sinonasal cavities of patients with CRS. Additionally, bacteria isolated from patients with tobacco smoke exposure demonstrate robust in vitro biofilm formation when challenged with tobacco smoke compared to those isolated from smoke naive patients. Lastly, bacteria from smoke exposed patients can revert to a non-biofilm phenotype when grown in the absence of tobacco smoke. These observations support the hypothesis that tobacco exposure induces sinonasal biofilm formation, thereby contributing to the conversion of a transient and medically treatable infection to a persistent and therapeutically recalcitrant condition.
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Lykidis, A., Perez-Pantoja, D., Ledger, T., Mavromatis, K., Anderson, I. J., Ivanova, N. N., et al. (2010). The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader. PLoS One, 5(3), 13 pp.
Abstract: Background: Cupriavidus necator JMP134 is a Gram-negative beta-proteobacterium able to grow on a variety of aromatic and chloroaromatic compounds as its sole carbon and energy source. Methodology/ Principal Findings: Its genome consists of four replicons (two chromosomes and two plasmids) containing a total of 6631 protein coding genes. Comparative analysis identified 1910 core genes common to the four genomes compared (C. necator JMP134, C. necator H16, C. metallidurans CH34, R. solanacearum GMI1000). Although secondary chromosomes found in the Cupriavidus, Ralstonia, and Burkholderia lineages are all derived from plasmids, analyses of the plasmid partition proteins located on those chromosomes indicate that different plasmids gave rise to the secondary chromosomes in each lineage. The C. necator JMP134 genome contains 300 genes putatively involved in the catabolism of aromatic compounds and encodes most of the central ring-cleavage pathways. This strain also shows additional metabolic capabilities towards alicyclic compounds and the potential for catabolism of almost all proteinogenic amino acids. This remarkable catabolic potential seems to be sustained by a high degree of genetic redundancy, most probably enabling this catabolically versatile bacterium with different levels of metabolic responses and alternative regulation necessary to cope with a challenging environment. From the comparison of Cupriavidus genomes, it is possible to state that a broad metabolic capability is a general trait for Cupriavidus genus, however certain specialization towards a nutritional niche (xenobiotics degradation, chemolithoautotrophy or symbiotic nitrogen fixation) seems to be shaped mostly by the acquisition of “specialized” plasmids. Conclusions/Significance: The availability of the complete genome sequence for C. necator JMP134 provides the groundwork for further elucidation of the mechanisms and regulation of chloroaromatic compound biodegradation.
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Mondschein, S., Quinteros, M., & Yankovic, N. (2020). Gender bias in the Chilean public health system: Do we all wait the same? Plos One, 15(9), e0239445.
Abstract: Background
In 2002, Chile introduced a major health reform, designed to level out inequities in healthcare coverage, access and opportunities. In particular, the opportunity guarantees ensure a maximum time to receive the appropriate diagnosis and treatment, and thus, gender bias should not be observed. Objective To explore the existence of differences in the timeliness of treatment between women and men under the Chilean public health insurance system. We controlled by other observable variables, including age, insurance holder status, provider complexity and health district. Methods We used an individual level database that includes all interactions for the diseases covered under the national plan from 2014 to 2019. We excluded from the analysis the diseases affecting only men, women, and infants. To study the waiting time differences between women and men, we first perform a Welch two sample t-test. Then, we used a multilevel hierarchical regression model to further explore the impact of gender in waiting time. At the individual level, we included gender, insurance holder status, age, and the interaction between gender and age. For the aggregate levels, we used the specific opportunity guarantee, the type of provider, and health district. Results From the Welch two sample t-test, we found significant differences in waiting times between women and men, in seven opportunity guarantees. From the multilevel regression, the individual variables: holder status, ages between 35 and 49, and the interaction between gender and age for ages between 40 and 54 were statistically significant at 95% level. We remark that the major differences in waiting times between women and men were observed for individuals between ages from 40 to 54, with women waiting significantly longer. Conclusion Results show the existence of bias in the timeliness of treatment, proving that universal guarantees are not enough to reduce gender inequalities in health care. Keywords: Sex
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Morales-Bader, D., Castillo, R. D., Cox, R. F. A., & Ascencio-Garrido, C. (2023). Parliamentary roll-call voting as a complex dynamical system: The case of Chile. PLoS One, 18(4).
Abstract: A method is proposed to study the temporal variability of legislative roll-call votes in a parliament from the perspective of complex dynamical systems. We studied the Chilean Chamber of Deputies' by analyzing the agreement ratio and the voting outcome of each vote over the last 19 years with a Recurrence Quantification Analysis and an entropy analysis (Sample Entropy). Two significant changes in the temporal variability were found: one in 2014, where the voting outcome became more recurrent and with less entropy, and another in 2018, where the agreement ratio became less recurrent and with higher entropy. These changes may be directly related to major changes in the Chilean electoral system and the composition of the Chamber of Deputies, given that these changes occurred just after the first parliamentary elections with non-compulsory voting (2013 elections) and the first elections with a proportional system in conjunction with an increase in the number of deputies (2017 elections) were held.
Keywords: RECURRENCE QUANTIFICATION ANALYSIS; TIME; NETWORK; WORLD
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Poupin, M. J., Timmermann, T., Vega, A., Zuniga, A., & Gonzalez, B. (2013). Effects of the Plant Growth-Promoting Bacterium Burkholderia phytofirmans PsJN throughout the Life Cycle of Arabidopsis thaliana. PLoS One, 8(7), 15 pp.
Abstract: Plant growth-promoting rhizobacteria (PGPR) induce positive effects in plants, such as increased growth or reduced stress susceptibility. The mechanisms behind PGPR/plant interaction are poorly understood, as most studies have described short-term responses on plants and only a few studies have analyzed plant molecular responses under PGPR colonization. Here, we studied the effects of the PGPR bacterial model Burkholderia phytofirmans PsJN on the whole life cycle of Arabidopsis thaliana plants. We reported that at different plant developmental points, strain PsJN can be found in the rhizosphere and also colonizing their internal tissues. In early ontogeny, strain PsJN increased several growth parameters and accelerated growth rate of the plants. Also, an Arabidopsis transcriptome analysis revealed that 408 genes showed differential expression in PsJN-inoculated plants; some of these genes are involved in stress response and hormone pathways. Specifically, genes implicated in auxin and gibberellin pathways were induced. Quantitative transcriptional analyses of selected genes in different developmental stages revealed that the beginning of these changes could be evidenced early in development, especially among the down-regulated genes. The inoculation with heat-killed bacteria provoked a more severe transcriptional response in plants, but was not able to induce plant growth-promotion. Later in ontogeny, the growth rates of inoculated plants decreased with respect to the non-inoculated group and, interestingly, the inoculation accelerated the flowering time and the appearance of senescence signs in plants; these modifications correlate with the early up-regulation of flowering control genes. Then, we show that a single inoculation with a PGPR could affect the whole life cycle of a plant, accelerating its growth rate and shortening its vegetative period, both effects relevant for most crops. Thus, these findings provide novel and interesting aspects of these relevant biological interactions.
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Rengifo, F., Ruz, G. A., & Mascareno, A. (2018). Managing the 1920s' Chilean educational crisis: A historical view combined with machine learning. PLoS One, 13(5), 23 pp.
Abstract: In the first decades of the 20 th century, political actors diagnosed the incubation of a crisis in the Chilean schooling process. Low rates of enrollment, literacy, and attendance, inefficiency in the use of resources, poverty, and a reduced number of schools were the main factors explaining the crisis. As a response, the Law on Compulsory Primary Education, considering mandatory for children between 6 and 14 years old to attend any school for at least four years, was passed in 1920. Using data from Censuses of the Republic of Chile from 1920 and 1930, reports of the Ministry of Justice, the Ministry of Education, and the Statistical Yearbooks between 1895 and 1930, we apply machine learning techniques (clustering and decision trees) to assess the impact of this law on the Chilean schooling process between 1920 and 1930. We conclude that the law had a positive impact on the schooling indicators in this period. Even though it did not overcome the differences between urban and rural zones, it brought about a general improvement of the schooling process and a more efficient use of resources and infrastructure in both big urban centers and small-urban and rural zones, thereby managing the so-called crisis of the Republic.
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Timmermann, T., Poupin, M. J., Vega, A., Urrutia, C., Ruz, G. A., & Gonzalez, B. (2019). Gene networks underlying the early regulation of Paraburkholderia phytofirmans PsJN induced systemic resistance in Arabidopsis. PLoS One, 14(8), 24 pp.
Abstract: Plant defense responses to biotic stresses are complex biological processes, all governed by sophisticated molecular regulations. Induced systemic resistance (ISR) is one of these defense mechanisms where beneficial bacteria or fungi prime plants to resist pathogens or pest attacks. In ISR, the defense arsenal in plants remains dormant and it is only triggered by an infection, allowing a better allocation of plant resources. Our group recently described that the well-known beneficial bacterium Paraburkholderia phytofirmans PsJN is able to induce Arabidopsis thaliana resistance to Pseudomonas syringae pv. tomato (Pst) DC3000 through ISR, and that ethylene, jasmonate and salicylic acid are involved in this protection. Nevertheless, the molecular networks governing this beneficial interaction remain unknown. To tackle this issue, we analyzed the temporal changes in the transcriptome of PsJN-inoculated plants before and after being infected with Pst DC3000. These data were used to perform a gene network analysis to identify highly connected transcription factors. Before the pathogen challenge, the strain PsJN regulated 405 genes (corresponding to 1.8% of the analyzed genome). PsJN-inoculated plants presented a faster and stronger transcriptional response at 1-hour post infection (hpi) compared with the non-inoculated plants, which presented the highest transcriptional changes at 24 hpi. A principal component analysis showed that PsJN-induced plant responses to the pathogen could be differentiated from those induced by the pathogen itself. Forty-eight transcription factors were regulated by PsJN at 1 hpi, and a system biology analysis revealed a network with four clusters. Within these clusters LHY, WRKY28, MYB31 and RRTF1 are highly connected transcription factors, which could act as hub regulators in this interaction. Concordantly with our previous results, these clusters are related to jasmonate, ethylene, salicylic, acid and ROS pathways. These results indicate that a rapid and specific response of PsJN-inoculated plants to the virulent DC3000 strain could be the pivotal element in the protection mechanism.
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