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Arias-Garzón, D., Tabares-Soto, R., Bernal-Salcedo. J., & Ruz, G. A. (2023). Biases associated with database structure for COVID-19 detection in X-ray images. Sci. Rep., 13, 3477.
Abstract: Several artificial intelligence algorithms have been developed for COVID-19-related topics. One that has been common is the COVID-19 diagnosis using chest X-rays, where the eagerness to obtain early results has triggered the construction of a series of datasets where bias management has not been thorough from the point of view of patient information, capture conditions, class imbalance, and careless mixtures of multiple datasets. This paper analyses 19 datasets of COVID-19 chest X-ray images, identifying potential biases. Moreover, computational experiments were conducted using one of the most popular datasets in this domain, which obtains a 96.19% of classification accuracy on the complete dataset. Nevertheless, when evaluated with the ethical tool Aequitas, it fails on all the metrics. Ethical tools enhanced with some distribution and image quality considerations are the keys to developing or choosing a dataset with fewer bias issues. We aim to provide broad research on dataset problems, tools, and suggestions for future dataset developments and COVID-19 applications using chest X-ray images.
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Cabrera, M., Cordova-Lepe, F., Gutierrez-Jara, J. P. -, & Vogt-Geisse, K. (2021). An SIR-type epidemiological model that integrates social distancing as a dynamic law based on point prevalence and socio-behavioral factors. Sci. Rep., 11(1), 10170.
Abstract: Modeling human behavior within mathematical models of infectious diseases is a key component to understand and control disease spread. We present a mathematical compartmental model of Susceptible-Infectious-Removed to compare the infected curves given by four different functional forms describing the transmission rate. These depend on the distance that individuals keep on average to others in their daily lives. We assume that this distance varies according to the balance between two opposite thrives: the self-protecting reaction of individuals upon the presence of disease to increase social distancing and their necessity to return to a culturally dependent natural social distance that occurs in the absence of disease. We present simulations to compare results for different society types on point prevalence, the peak size of a first epidemic outbreak and the time of occurrence of that peak, for four different transmission rate functional forms and parameters of interest related to distancing behavior, such as: the reaction velocity of a society to change social distance during an epidemic. We observe the vulnerability to disease spread of close contact societies, and also show that certain social distancing behavior may provoke a small peak of a first epidemic outbreak, but at the expense of it occurring early after the epidemic onset, observing differences in this regard between society types. We also discuss the appearance of temporal oscillations of the four different transmission rates, their differences, and how this oscillatory behavior is impacted through social distancing; breaking the unimodality of the actives-curve produced by the classical SIR-model.
Keywords: EFFECTIVE REPRODUCTION NUMBER; INFECTIOUS-DISEASE; TRANSMISSION; COVID-19; BEHAVIOR; CHALLENGES; AWARENESS; IMPACT; RISK
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Gazitua, M. C., Morgante, V., Poupin, M. J., Ledger, T., Rodriguez-Valdecantos, G., Herrera, C., et al. (2021). The microbial community from the early-plant colonizer (Baccharis linearis) is required for plant establishment on copper mine tailings. Sci. Rep., 11(1), 10448.
Abstract: Plants must deal with harsh environmental conditions when colonizing abandoned copper mine tailings. We hypothesized that the presence of a native microbial community can improve the colonization of the pioneer plant, Baccharis linearis, in soils from copper mining tailings. Plant growth and microbial community compositions and dynamics were determined in cultivation pots containing material from two abandoned copper mining tailings (Huana and Tambillos) and compared with pots containing fresh tailings or surrounding agricultural soil. Controls without plants or using irradiated microbe-free substrates, were also performed. Results indicated that bacteria (Actinobacteria, Gammaproteobacteria, and Firmicutes groups) and fungi (Glomus genus) are associated with B. linearis and may support plant acclimation, since growth parameters decreased in both irradiated (transiently without microbial community) and fresh tailing substrates (with a significantly different microbial community). Consistently, the composition of the bacterial community from abandoned copper mining tailings was more impacted by plant establishment than by differences in the physicochemical properties of the substrates. Bacteria located at B. linearis rhizoplane were clearly the most distinct bacterial community compared with those of fresh tailings, surrounding soil and non-rhizosphere abandoned tailings substrates. Beta diversity analyses showed that the rhizoplane bacterial community changed mainly through species replacement (turnover) than species loss (nestedness). In contrast, location/geographical conditions were more relevant than interaction with the plants, to explain fungal community differences.
Keywords: BACTERIAL COMMUNITIES; HEAVY-METALS; PHYTOSTABILIZATION; REVEGETATION; RHIZOSPHERE; REMEDIATION; IMPACT; GROWTH; NORTH
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Goles, E., Mascareno, A., Medina, P., & Rica, S. (2020). Migration-induced transition in social structures: a view through the Sakoda model of social interactions. Sci. Rep., 10(1), 18338.
Abstract: We study the dynamics of three populations evolving in a two-dimensional discrete grid according to rules of attraction, rejection, or indifference following the framework of the seminal model by Sakoda and we apply it to migration phenomena. An interesting feature of the Sakoda model is the existence of a Potts-like energy which, as a common principle, decreases as time passes by. Here we consider the evolution of two populations until stabilization, then, we perturb this attractor by the inclusion of a third arrival: the immigrants. We show the conditions under which this irruption does not alter significantly the previous attractor (a sociological morphostatic behaviour) or it is dramatically changed (morphogenetic behaviour). We observe empirically that for a morphostatic behaviour the energy decreases while for morphogenesis this energy increases, revealing an escalation of social tension.
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Gutierrez-Jara, J. P., Vogt-Geisse, K., Cabrera, M., Cordova-Lepe, F., & Munoz-Quezada, M. T. (2022). Effects of human mobility and behavior on disease transmission in a COVID-19 mathematical model. Sci. Rep., 12(1), 10840.
Abstract: Human interactions and perceptions about health risk are essential to understand the evolution over the course of a pandemic. We present a Susceptible-Exposed-Asymptomatic-Infectious-Recovered-Susceptible mathematical model with quarantine and social-distance-dependent transmission rates, to study COVID-19 dynamics. Human activities are split across different location settings: home, work, school, and elsewhere. Individuals move from home to the other locations at rates dependent on their epidemiological conditions and maintain a social distancing behavior, which varies with their location. We perform simulations and analyze how distinct social behaviors and restrictive measures affect the dynamic of the disease within a population. The model proposed in this study revealed that the main focus on the transmission of COVID-19 is attributed to the “home” location setting, which is understood as family gatherings including relatives and close friends. Limiting encounters at work, school and other locations will only be effective if COVID-19 restrictions occur simultaneously at all those locations and/or contact tracing or social distancing measures are effectively and strictly implemented, especially at the home setting.
Keywords: INFECTIOUS-DISEASE; EPIDEMIC MODEL; DYNAMICS; CHALLENGES; RESISTANCE; DISTANCES; AWARENESS
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Lagos, N. A., Benitez, S., Grenier, C., Rodriguez-Navarro, A. B., Garcia-Herrera, C., Abarca-Ortega, A., et al. (2021). Plasticity in organic composition maintains biomechanical performance in shells of juvenile scallops exposed to altered temperature and pH conditions. Sci. Rep., 11(1), 24201.
Abstract: The exposure to environmental variations in pH and temperature has proven impacts on benthic ectotherms calcifiers, as evidenced by tradeoffs between physiological processes. However, how these stressors affect structure and functionality of mollusk shells has received less attention. Episodic events of upwelling of deep cold and low pH waters are well documented in eastern boundary systems and may be stressful to mollusks, impairing both physiological and biomechanical performance. These events are projected to become more intense, and extensive in time with ongoing global warming. In this study, we evaluate the independent and interactive effects of temperature and pH on the biomineral and biomechanical properties of Argopecten purpuratus scallop shells. Total organic matter in the shell mineral increased under reduced pH (similar to 7.7) and control conditions (pH similar to 8.0). The periostracum layer coating the outer shell surface showed increased protein content under low pH conditions but decreasing sulfate and polysaccharides content. Reduced pH negatively impacts shell density and increases the disorder in the orientation of calcite crystals. At elevated temperatures (18 degrees C), shell microhardness increased. Other biomechanical properties were not affected by pH/temperature treatments. Thus, under a reduction of 0.3 pH units and low temperature, the response of A. purpuratus was a tradeoff among organic compounds (biopolymer plasticity), density, and crystal organization (mineral plasticity) to maintain shell biomechanical performance, while increased temperature ameliorated the impacts on shell hardness. Biopolymer plasticity was associated with ecophysiological performance, indicating that, under the influence of natural fluctuations in pH and temperature, energetic constraints might be critical in modulating the long-term sustainability of this compensatory mechanism.
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Mellado, P. (2022). Intrinsic topological magnons in arrays of magnetic dipoles. Sci. Rep., 12(1), 1420.
Abstract: We study a simple magnetic system composed of periodically modulated magnetic dipoles with an easy axis. Upon adjusting the geometric modulation amplitude alone, chains and two-dimensional stacked chains exhibit a rich magnon spectrum where frequency gaps and magnon speeds are easily manipulable. The blend of anisotropy due to dipolar interactions between magnets and geometrical modulation induces a magnetic phase with fractional Zak number in infinite chains and end states in open one-dimensional systems. In two dimensions it gives rise to topological modes at the edges of stripes. Tuning the amplitude in two-dimensional lattices causes a band touching, which triggers the exchange of the Chern numbers of the volume bands and switches the sign of the thermal conductivity.
Keywords: SPIN-WAVES; PHASES; CHAIN; MODES
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Uranga, R. M., Millan, C., Barahona, M. J., Recabal, A., Salgado, M., Martinez, F., et al. (2017). Adenovirus-mediated suppression of hypothalamic glucokinase affects feeding behavior. Sci Rep, 7, 13 pp.
Abstract: Glucokinase (GK), the hexokinase involved in glucosensing in pancreatic beta-cells, is also expressed in arcuate nucleus (AN) neurons and hypothalamic tanycytes, the cells that surround the basal third ventricle (3V). Several lines of evidence suggest that tanycytes may be involved in the regulation of energy homeostasis. Tanycytes have extended cell processes that contact the feeding-regulating neurons in the AN, particularly, agouti-related protein (AgRP), neuropeptide Y (NPY), cocaine-and amphetamine-regulated transcript (CART) and proopiomelanocortin (POMC) neurons. In this study, we developed an adenovirus expressing GK shRNA to inhibit GK expression in vivo. When injected into the 3V of rats, this adenovirus preferentially transduced tanycytes. qRT-PCR and Western blot assays confirmed GK mRNA and protein levels were lower in GK knockdown animals compared to the controls. In response to an intracerebroventricular glucose injection, the mRNA levels of anorexigenic POMC and CART and orexigenic AgRP and NPY neuropeptides were altered in GK knockdown animals. Similarly, food intake, meal duration, frequency of eating events and the cumulative eating time were increased, whereas the intervals between meals were decreased in GK knockdown rats, suggesting a decrease in satiety. Thus, GK expression in the ventricular cells appears to play an important role in feeding behavior.
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Van Hemelryck, M., Bernal, R., Ispolatov, Y., & Dumais, J. (2018). Lily Pollen Tubes Pulse According to a Simple Spatial Oscillator. Sci Rep, 8, 10 pp.
Abstract: Polar growth is a fundamental mode of cell morphogenesis observed in nearly all major groups of organisms. Among polarly growing cells, the angiosperm pollen tubes have emerged as powerful experimental systems in large part because of their oscillatory growth, which provides a window into the network of interactions regulating morphogenesis. Empirical studies of oscillatory pollen tubes have sought to uncover the temporal sequence of cellular and molecular events that constitutes an oscillatory cycle. Here we show that in lily pollen tubes the distance or wavelength (lambda = 6.3 +/- 1.7 μm) over which an oscillatory cycle unfolds is more robust than the period of oscillation (tau = 39.1 +/- 17.6 s) (n = 159 cells). Moreover, the oscillatory cycle is divided into slow and fast phases, with each phase unfolding over precisely one half of the wavelength. Using these observations, we show that a simple spatial bi-oscillator predicts the most common modes of oscillation observed in pollen tubes. These results call into question the traditional view of pollen tube morphogenesis as a temporal succession of cellular events. Space, not time, may be the most natural metric to inteprete the morphogenetic dynamics of these cells.
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Verdugo, I., Cruz, J. J., Alvarez, E., Reszka, P., da Silva, L. F. F., & Fuentes, A. (2020). Candle flame soot sizing by planar time-resolved laser-induced incandescence. Sci Rep, 10(1), 12 pp.
Abstract: Soot emissions from flaming combustion are relevant as a significant source of atmospheric pollution and as a source of nanomaterials. Candles are interesting targets for soot characterization studies since they burn complex fuels with a large number of carbon atoms, and yield stable and repeatable flames. We characterized the soot particle size distributions in a candle flame using the planar two-color time-resolved laser induced incandescence (2D-2C TiRe-LII) technique, which has been successfully applied to different combustion applications, but never before on a candle flame. Soot particles are heated with a planar laser sheet to temperatures above the normal flame temperatures. The incandescent soot particles emit thermal radiation, which decays over time when the particles cool down to the flame temperature. By analyzing the temporal decay of the incandescence signal, soot particle size distributions within the flame are obtained. Our results are consistent with previous works, and show that the outer edges of the flame are characterized by larger particles (approximate to 60 nm), whereas smaller particles (approximate to 25 nm) are found in the central regions. We also show that our effective temperature estimates have a maximum error of 100 K at early times, which decreases as the particles cool.
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Wijnhoven, I. B., Vallejos, R., Santibanez, J. F., Millan, C., & Vivanco, J. F. (2020). Analysis of cell-biomaterial interaction through cellular bridge formation in the interface between hGMSCs and CaP bioceramics. Sci Rep, 10(1), 14 pp.
Abstract: The combination of biomaterials and stem cells for clinical applications constitute a great challenge in bone tissue engineering. Hence, cellular networks derived from cells-biomaterials crosstalk have a profound influence on cell behaviour and communication, preceding proliferation and differentiation. The purpose of this study was to investigate in vitro cellular networks derived from human gingival mesenchymal stem cells (hGMSCs) and calcium phosphate (CaP) bioceramic interaction. Biological performance of CaP bioceramic and hGMSCs interaction was evaluated through cell adhesion and distribution, cellular proliferation, and potential osteogenic differentiation, at three different times: 5 h, 1 week and 4 weeks. Results confirmed that hGMSCs met the required MSCs criteria while displaying osteogenic differentiaton capacities. We found a significant increase of cellular numbers and proliferation levels. Also, protein and mRNA OPN expression were upregulated in cells cultured with CaP bioceramic by day 21, suggesting an osteoinductible effect of the CaP bioceramic on hGMSCs. Remarkably, CaP bioceramic aggregations were obtained through hGMSCs bridges, suggesting the in vitro potential of macrostructures formation. We conclude that hGMSCs and CaP bioceramics with micro and macropores support hGMSC adhesion, proliferation and osteogenic differentiation. Our results suggest that investigations focused on the interface cells-biomaterials are essential for bone tissue regenerative therapies.
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