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Alejo, L., Atkinson, J., & Lackner, S. (2020). Looking deeper – exploring hidden patterns in reactor data of N-removal systems through clustering analysis. Water Sci. Technol., 81(8), 1569–1577.
Abstract: In this work, clustering analysis of two partial nitritation-anammox (PN-A) moving bed biofilm reactors (MBBR) containing different types of carrier material was explored for the identification of patterns and operational conditions that may benefit process performance. The systems ran for two years under fluctuations of temperature and organic matter. Ex situ batch activity tests were performed every other week during the operation of these reactors. These datasets and the parameters, which were monitored online and in the laboratory, were combined and analyzed applying clustering analysis to identify non-obvious information regarding the performance of the systems. The initial results were consistent with the literature and from an operational perspective, which allowed the parameters to be explored further. The new information revealed that the oxidation reduction potential (ORP) and the anaerobic ammonium oxidizing bacteria (AnAOB) activity correlated well. ORP also dropped when the reactors were exposed to real wastewater (presence of organic matter). Moreover, operating conditions during nitrite accumulation were identified through clustering, and also revealed inhibition of anammox bacteria already at low nitrite concentrations.
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Carrasco, M., Toledo, P., & Tischler, N. D. (2019). Macromolecule Particle Picking and Segmentation of a KLH Database by Unsupervised Cryo-EM Image Processing. Biomolecules, 9(12), 14 pp.
Abstract: Segmentation is one of the most important stages in the 3D reconstruction of macromolecule structures in cryo-electron microscopy. Due to the variability of macromolecules and the low signal-to-noise ratio of the structures present, there is no generally satisfactory solution to this process. This work proposes a new unsupervised particle picking and segmentation algorithm based on the composition of two well-known image filters: Anisotropic (Perona-Malik) diffusion and non-negative matrix factorization. This study focused on keyhole limpet hemocyanin (KLH) macromolecules which offer both a top view and a side view. Our proposal was able to detect both types of views and separate them automatically. In our experiments, we used 30 images from the KLH dataset of 680 positive classified regions. The true positive rate was 95.1% for top views and 77.8% for side views. The false negative rate was 14.3%. Although the false positive rate was high at 21.8%, it can be lowered with a supervised classification technique.
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Castaneda, P., & Reus, L. (2019). Suboptimal investment behavior and welfare costs: A simulation based approach. Financ. Res. Lett., 30, 170–180.
Abstract: We propose a representation of suboptimal investment behavior based on the stochastic discount factor (SDF) paradigm. Suboptimal investment behavior is rationalized as being the investor's optimal decision under a wrong SDF, while wealth trajectories and budget constraints are based on the true SDF. We develop a novel Monte Carlo simulation approach to compute the welfare costs for this suboptimal behavior. We study the suboptimal portfolio choice under CRRA preferences using two financial market models. The Monte Carlo simulation delivers comparable welfare losses to those computed in the original studies, which are based on partial differential equations (PDE) and – finite-difference schemes.
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Franchi, O., Alvarez, M. I., Pavissich, J. P., Belmonte, M., Pedrouso, A., del Rio, A. V., et al. (2024). Operational variables and microbial community dynamics affect granulation stability in continuous flow aerobic granular sludge reactors. J. Water Process Eng., 59, 104951.
Abstract: Retrofitting wastewater treatment plants with continuous aerobic granular sludge reactors is a promising alternative to enhance treatment capacities and reduce footprint. This study investigates the main variables influencing granulation and microbial dynamics in two reactor configurations (25 L): stirred tanks in series (R1) and a plug-flow-like system (R2). Granule formation was achieved by increasing the organic loading rate (OLR) from 0.7 to 4.1 kg COD/(m3 & sdot;d) and the up-flow velocity in the biomass selector from 1.4 to 6.9 m/h. However, irreversible granule destabilization occurred at day 68 for R1 and day 108 for R2. Principal component analysis and examination of food-to-microorganisms (F/M) ratio medians identified the F/M ratio as the primary variable associated with instability. Microbial analysis revealed that a high F/M ratio induced significant increases in the abundance of specific genera such as Arcobacter, Cloacibacterium, Rikenella, Aquaspirillum and Sphaerotillus, whose overgrowth may negatively impact granule stability. Based on these findings, maximum F/M ratio thresholds were obtained to establish operational conditions allowing the maintenance of stable aerobic granules on continuous flow reactor configurations.
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Girard, A., Muneer, T., & Caceres, G. (2014). A validated design simulation tool for passive solar space heating: Results from a monitored house in West Lothian, Scotland. Indoor Built Environ., 23(3), 353–372.
Abstract: Determining the availability of renewable sources on a particular site would result in increasing the efficiency of buildings through appropriate design. The overall aim of the project is to develop a pioneering software tool allowing the assessment of possible energy sources for any building design project. The package would allow the user to simulate the efficiency of the Passive Solar Space Heating referred in the Low and Zero Carbon Energy Sources (LZCES) Strategic Guide stated by the Office of the Deputy Prime Minister (2006) and the Building Regulations. This research paper presents the tool for modelling the passive solar sources availability in relation to low-carbon building. A 3-month experimental set up monitoring a solar house in West Lothian, Scotland, was also undertaken to validate the simulation tool. Experimental and simulation results were found in good agreement following a one-to-one relationship demonstrating the ability of the newly developed tool to assess potential solar gain available for buildings. This modelling tool is highly valuable in consideration of the part L of the Building Regulations (updated in 2010).
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Goles, E., Slapnicar, I., & Lardies, M. A. (2021). Universal Evolutionary Model for Periodical Species. Complexity, 2021, 2976351.
Abstract: Real-world examples of periodical species range from cicadas, whose life cycles are large prime numbers, like 13 or 17, to bamboos, whose periods are large multiples of small primes, like 40 or even 120. The periodicity is caused by interaction of species, be it a predator-prey relationship, symbiosis, commensalism, or competition exclusion principle. We propose a simple mathematical model, which explains and models all those principles, including listed extremal cases. This rather universal, qualitative model is based on the concept of a local fitness function, where a randomly chosen new period is selected if the value of the global fitness function of the species increases. Arithmetically speaking, the different interactions are related to only four principles: given a couple of integer periods either (1) their greatest common divisor is one, (2) one of the periods is prime, (3) both periods are equal, or (4) one period is an integer multiple of the other.
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Leiva, V., Tejo, M., Guiraud, P., Schmachtenberg, O., Orio, P., & Marmolejo-Ramos, F. (2015). Modeling neural activity with cumulative damage distributions. Biol. Cybern., 109(4-5), 421–433.
Abstract: Neurons transmit information as action potentials or spikes. Due to the inherent randomness of the inter-spike intervals (ISIs), probabilistic models are often used for their description. Cumulative damage (CD) distributions are a family of probabilistic models that has been widely considered for describing time-related cumulative processes. This family allows us to consider certain deterministic principles for modeling ISIs from a probabilistic viewpoint and to link its parameters to values with biological interpretation. The CD family includes the Birnbaum-Saunders and inverse Gaussian distributions, which possess distinctive properties and theoretical arguments useful for ISI description. We expand the use of CD distributions to the modeling of neural spiking behavior, mainly by testing the suitability of the Birnbaum-Saunders distribution, which has not been studied in the setting of neural activity. We validate this expansion with original experimental and simulated electrophysiological data.
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McGruder, C. D., Lopez-Morales, M., Brahm, R., & Jordan, A. (2023). The Similar Seven: A Set of Very Alike Exoplanets to Test Correlations between System Parameters and Atmospheric Properties. Astrophys. J. Lett., 944(2), L56.
Abstract: Studies of exoplanetary atmospheres have found no definite correlations between observed high-altitude aerosols and other system parameters. This could be, in part, because of the lack of homogeneous exoplanet samples for which specific parameters can be isolated and inspected. Here, we present a set of seven exoplanets with very similar system parameters. We analyze existing photometric time series, Gaia parallax, and high-resolution spectroscopic data to produce a new set of homogeneous stellar, planetary, and orbital parameters for these systems. With this, we confirm that most measured parameters for all systems are very similar, except for the host stars' metallicities and possibly high-energy irradiation levels, which require UV and X-ray observations to constrain. From the sample, WASP-6b, WASP-96b, and WASP-110b have observed transmission spectra that we use to estimate their aerosol coverage levels using the Na i doublet 5892.9 angstrom. We find a tentative correlation between the metallicity of the host stars and the planetary aerosol levels. The trend we find with stellar metallicity can be tested by observing transmission spectra of the remaining planets in the sample. Based on our prediction, WASP-25b and WASP-55b should have higher levels of aerosols than WASP-124b and HATS-29b. Finally, we highlight how targeted surveys of alike planets similar to the ones presented here might prove key for identifying driving factors for atmospheric properties of exoplanets in the future and could be used as a sample selection criterion for future observations with, e.g., JWST, ARIEL, and the next generation of ground-based telescopes.
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McGruder, C. D., Lopez-Morales, M., Kirk, J., Rackham, B. V., May, E., Ahrer, E. M., et al. (2023). ACCESS, LRG-BEASTS, and MOPSS: Featureless Optical Transmission Spectra of WASP-25b and WASP-124b. Astron. J., 166(3), 120.
Abstract: We present new optical transmission spectra for two hot Jupiters: WASP-25b (M = 0.56 M ( J ); R = 1.23 R ( J ); P = 3.76 days) and WASP-124b (M = 0.58 M ( J ); R = 1.34 R ( J ); P = 3.37 days), with wavelength coverages of 4200-9100 & ANGS; and 4570-9940 & ANGS;, respectively. These spectra are from the ESO Faint Object Spectrograph and Camera (v.2) mounted on the New Technology Telescope and Inamori-Magellan Areal Camera & Spectrograph on Magellan Baade. No strong spectral features were found in either spectra, with the data probing 4 and 6 scale heights, respectively. Exoretrievals and PLATON retrievals favor stellar activity for WASP-25b, while the data for WASP-124b did not favor one model over another. For both planets the retrievals found a wide range in the depths where the atmosphere could be optically thick (& SIM;0.4 & mu;-0.2 bars for WASP-25b and 1.6 & mu;-32 bars for WASP-124b) and recovered a temperature that is consistent with the planets' equilibrium temperatures, but with wide uncertainties (up to & PLUSMN;430 K). For WASP-25b, the models also favor stellar spots that are & SIM;500-3000 K cooler than the surrounding photosphere. The fairly weak constraints on parameters are owing to the relatively low precision of the data, with an average precision of 840 and 1240 ppm per bin for WASP-25b and WASP-124b, respectively. However, some contribution might still be due to an inherent absence of absorption or scattering in the planets' upper atmospheres, possibly because of aerosols. We attempt to fit the strength of the sodium signals to the aerosol-metallicity trend proposed by McGruder et al., and find WASP-25b and WASP-124b are consistent with the prediction, though their uncertainties are too large to confidently confirm the trend.
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Vicuna, L., Fernandez, M. I., Vial, C., Valdebenito, P., Chaparro, E., Espinoza, K., et al. (2019). Adaptation to Extreme Environments in an Admixed Human Population from the Atacama Desert. Genome Biol. Evol., 11(9), 2468–2479.
Abstract: Inorganic arsenic (As) is a toxic xenobiotic and carcinogen associated with severe health conditions. The urban population from the Atacama Desert in northern Chile was exposed to extremely high As levels (up to 600 μmg/l) in drinking water between 1958 and 1971, leading to increased incidence of urinary bladder cancer (BC), skin cancer, kidney cancer, and coronary thrombosis decades later. Besides, the Andean Native-American ancestors of the Atacama population were previously exposed for millennia to elevated As levels in water (similar to 120 μg/l) for at least 5,000 years, suggesting adaptation to this selective pressure. Here, we performed two genome-wide selection tests-PBSn1 and an ancestry-enrichment test-in an admixed population from Atacama, to identify adaptation signatures to As exposure acquired before and after admixture with Europeans, respectively. The top second variant selected by PBSn1 was associated with LCE4A-C1orf68, a gene that may be involved in the immune barrier of the epithelium during BC. We performed association tests between the top PBSn1 hits and BC occurrence in our population. The strongest association (P = 0.012) was achieved by the LCE4A-C1orf68 variant. The ancestry-enrichment test detected highly significant signals (P = 1.3 x 10(-9)) mapping MAK16, a gene with important roles in ribosome biogenesis during the G1 phase of the cell cycle. Our results contribute to a better understanding of the genetic factors involved in adaptation to the pathophysiological consequences of As exposure.
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Vicuna, L., Norambuena, T., Miranda, J. P., Pereira, A., Mericq, V., Ongaro, L., et al. (2021). Novel loci and mapuche genetic ancestry are associated with pubertal growth traits in Chilean boys. Hum. Genet., 140(12), 1651–1661.
Abstract: Puberty is a complex developmental process that varies considerably among individuals and populations. Genetic factors explain a large proportion of the variability of several pubertal traits. Recent genome-wide association studies (GWAS) have identified hundreds of variants involved in traits that result from body growth, like adult height. However, they do not capture many genetic loci involved in growth changes over distinct growth phases. Further, such GWAS have been mostly performed in Europeans, but we do not know how these findings relate to other continental populations. In this study, we analyzed the genetic basis of three pubertal traits; namely, peak height velocity (PV), age at PV (APV) and height at APV (HAPV). We analyzed a cohort of 904 admixed Chilean children and adolescents with European and Mapuche Native American ancestries. Height was measured on roughly a 6-month basis from childhood to adolescence between 2006 and 2019. We predict that the difference in HAPV between an European and a Mapuche adolescent is 4.3 cm higher in the European (P = 0.042) and APV is 0.73 years later for the European compared with the Mapuche adolescent on average (P = 0.023). Further, by performing a GWAS on 774, 433 single-nucleotide polymorphisms, we identified a genetic signal harboring 3 linked variants significantly associated with PV in boys (P < 5 x 10(-8)). This signal has never been associated with growth-related traits.
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