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In Silico Antiprotozoal Evaluation of 1,4-Naphthoquinone Derivatives against Chagas and Leishmaniasis Diseases Using QSAR, Molecular Docking, and ADME Approaches
Chagas and leishmaniasis are two neglected diseases considered as public health problems worldwide, for which there is no effective, low-cost, and low-toxicity treatment for the host. Naphthoquinones are ligands with redox properties involved in oxidative biological processes with a wide variety of activities, including antiparasitic. In this work, in silico methods of quantitative structure–activity relationship (QSAR), molecular docking, and calculation of ADME (absorption, distribution, metabolism, and excretion) properties were used to evaluate naphthoquinone derivatives with unknown antiprotozoal activity. QSAR models were developed for predicting antiparasitic activity against Trypanosoma cruzi, Leishmania amazonensis, and Leishmania infatum, as well as the QSAR model for toxicity activity. Most of the evaluated ligands presented high antiparasitic activity. According to the docking results, the family of triazole derivatives presented the best affinity with the different macromolecular targets. The ADME results showed that most of the evaluated compounds present adequate conditions to be administered orally. Naphthoquinone derivatives show good biological activity results, depending on the substituents attached to the quinone ring, and perhaps the potential to be converted into drugs or starting molecules.
Journal Article
Adsorption and Vibrational Study of Folic Acid on Gold Nanopillar Structures Using Surface-Enhanced Raman Scattering Spectroscopy
This paper presents a study of adsorption and vibrational features of folic acid, using surface-enhanced Raman scattering (SERS). A gold-capped silicon nanopillar (Au NP) with a height of 600 nm and a width of 120 nm was utilized to study the vibrational features of FA molecules adsorbed on the nanopillars within the high electromagnetic field areas. The adsorption behaviour of folic acid and the band assignment of the main vibrations together with the optimized geometry of folic acid and folic acid in the presence of a cluster of 10 gold atoms were assessed using the density functional theory (B3LYP(6–31G(d))) and the scalar relativistic effective core potential with a double-zeta basis set (LANL2DZ). The vibrations obtained from the solid-state folic acid and the folic acid on a gold cluster were in accordance with those observed experimentally. The analysis of the main vibrations indicated that the interaction of folic acid with the Au NP occurred primarily through the nitrogen atoms, from their pteridine ring. Finally, the obtained adsorption isotherm for folic acid was deduced from the analysis of the SERS spectra and it followed a negative cooperative binding model.
Journal Article
Slipstreaming Mother Machine: A Microfluidic Device for Single-Cell Dynamic Imaging of Yeast
The yeast Saccharomyces cerevisiae is one of the most basic model organisms for studies of aging and other phenomena such as division strategies. These organisms have been typically studied with the use of microfluidic devices to keep cells trapped while under a flow of fresh media. However, all of the existing devices trap cells mechanically, subjecting them to pressures that may affect cell physiology. There is evidence mechanical pressure affects growth rate and the movement of intracellular components, so it is quite possible that it affects other physiological aspects such as aging. To allow studies with the lowest influence of mechanical pressure, we designed and fabricated a device that takes advantage of the slipstreaming effect. In slipstreaming, moving fluids that encounter a barrier flow around it forming a pressure gradient behind it. We trap mother cells in this region and force daughter cells to be in the negative pressure gradient region so that they are taken away by the flow. Additionally, this device can be fabricated using low resolution lithography techniques, which makes it less expensive than devices that require photolithography masks with resolution under 5 µm. With this device, it is possible to measure some of the most interesting aspects of yeast dynamics such as growth rates and Replicative Life Span. This device should allow future studies to eliminate pressure bias as well as extending the range of labs that can do these types of measurements.
Journal Article
Theoretical Vibrational Study of Metformin: A DFT-Based Analysis of Simulated Raman and SERS Spectra
Metformin (MET), a widely used antidiabetic drug, has attracted significant attention due to its potential applications beyond diabetes treatment. Understanding its molecular vibrations is crucial for spectroscopic characterization and interaction studies. This study presents a computational investigation of MET using Density Functional Theory (DFT) to analyze its vibrational properties, Raman spectra, and Surface-Enhanced Raman Scattering (SERS) behavior. Geometry optimization at the B3LYP/6-31G(d) level identified the most stable conformer, and a molecular electrostatic potential map highlighted key electron-rich sites for adsorption. Raman spectra were simulated using the B3LYP/6-31G(d) level, providing theoretical insights into ME T's vibrational modes. The interaction of MET with a gold cluster, modeled using the LanL2DZ basis set, revealed charge transfer effects influencing SERS enhancement. Theoretical Raman and SERS spectra, scaled for accuracy, closely matched experimental results, confirming MET's characteristic vibrational signatures. This combined approach offers valuable insights into MET's adsorption mechanisms and vibrational response, enhancing its potential application in electrochemical and spectroscopic sensing technologies.
Journal Article
The Red Radio Ring: a gravitationally lensed hyperluminous infrared radio galaxy at z=2.553 discovered through citizen science
We report the discovery of a gravitationally lensed hyperluminous infrared galaxy (L_IR~10^13 L_sun) with strong radio emission (L_1.4GHz~10^25 W/Hz) at z=2.553. The source was identified in the citizen science project SpaceWarps through the visual inspection of tens of thousands of iJKs colour composite images of Luminous Red Galaxies (LRGs), groups and clusters of galaxies and quasars. Appearing as a partial Einstein ring (r_e~3\") around an LRG at z=0.2, the galaxy is extremely bright in the sub-millimetre for a cosmological source, with the thermal dust emission approaching 1 Jy at peak. The redshift of the lensed galaxy is determined through the detection of the CO(3-2) molecular emission line with the Large Millimetre Telescope's Redshift Search Receiver and through [OIII] and H-alpha line detections in the near-infrared from Subaru/IRCS. We have resolved the radio emission with high resolution (300-400 mas) eMERLIN L-band and JVLA C-band imaging. These observations are used in combination with the near-infrared imaging to construct a lens model, which indicates a lensing magnification of ~10x. The source reconstruction appears to support a radio morphology comprised of a compact (<250 pc) core and more extended component, perhaps indicative of an active nucleus and jet or lobe.
Paper
Spectroscopic Quantification of Projection Effects in the SDSS redMaPPer Galaxy Cluster Catalogue
Projection effects, whereby galaxies along the line-of-sight to a galaxy cluster are mistakenly associated with the cluster halo, present a significant challenge for optical cluster cosmology. We use statistically representative spectral coverage of luminous galaxies to investigate how projection effects impact the low-redshift limit of the Sloan Digital Sky Survey (SDSS) redMaPPer galaxy cluster catalogue. Spectroscopic redshifts enable us to differentiate true cluster members from false positives and determine the fraction of candidate cluster members viewed in projection. Our main results can be summarized as follows: first, we show that a simple double-Gaussian model can be used to describe the distribution of line-of-sight velocities in the redMaPPer sample; second, the incidence of projection effects is substantial, accounting for \\(\\sim 16\\) per cent of the weighted richness for the lowest richness objects; third, projection effects are a strong function of richness, with the contribution in the highest richness bin being several times smaller than for low-richness objects; fourth, our measurement has a similar amplitude to state-of-the-art models, but finds a steeper dependence of projection effects on richness than these models; and fifth, the slope of the observed velocity dispersion--richness relation, corrected for projection effects, implies an approximately linear relationship between the true, three-dimensional halo mass and three-dimensional richness. Our results provide a robust, empirical description of the impact of projection effects on the SDSS redMaPPer cluster sample and exemplify the synergies between optical imaging and spectroscopic data for studies of galaxy cluster astrophysics and cosmology.
Paper
Combination of cluster number counts and two-point correlations: Validation on Mock Dark Energy Survey
We present a method of combining cluster abundances and large-scale two-point correlations, namely galaxy clustering, galaxy--cluster cross-correlations, cluster auto-correlations, and cluster lensing. This data vector yields comparable cosmological constraints to traditional analyses that rely on small-scale cluster lensing for mass calibration. We use cosmological survey simulations designed to resemble the Dark Energy Survey Year One (DES-Y1) data to validate the analytical covariance matrix and the parameter inferences. The posterior distribution from the analysis of simulations is statistically consistent with the absence of systematic biases detectable at the precision of the DES Y1 experiment. We compare the \\(\\chi^2\\) values in simulations to their expectation and find no significant difference. The robustness of our results against a variety of systematic effects is verified using a simulated likelihood analysis of a Dark Energy Survey Year 1-like data vectors. This work presents the first-ever end-to-end validation of a cluster abundance cosmological analysis on galaxy catalog-level simulations.
Paper
CODEX Weak Lensing Mass Catalogue and implications on the mass-richness relation
The COnstrain Dark Energy with X-ray clusters (CODEX) sample contains the largest flux limited sample of X-ray clusters at \\(0.35 < z < 0.65\\). It was selected from ROSAT data in the 10,000 square degrees of overlap with BOSS, mapping a total number of 2770 high-z galaxy clusters. We present here the full results of the CFHT CODEX program on cluster mass measurement, including a reanalysis of CFHTLS Wide data, with 25 individual lensing-constrained cluster masses. We employ \\(lensfit\\) shape measurement and perform a conservative colour-space selection and weighting of background galaxies. Using the combination of shape noise and an analytic covariance for intrinsic variations of cluster profiles at fixed mass due to large scale structure, miscentring, and variations in concentration and ellipticity, we determine the likelihood of the observed shear signal as a function of true mass for each cluster. We combine 25 individual cluster mass likelihoods in a Bayesian hierarchical scheme with the inclusion of optical and X-ray selection functions to derive constraints on the slope \\(\\alpha\\), normalization \\(\\beta\\), and scatter \\(\\sigma_{\\ln \\lambda | \\mu}\\) of our richness-mass scaling relation model in log-space: \\(\\left<\\ln \\lambda | \\mu \\right> = \\alpha \\mu + \\beta\\), with \\(\\mu = \\ln (M_{200c}/M_{\\mathrm{piv}})\\), and \\(M_{\\mathrm{piv}} = 10^{14.81} M_{\\odot}\\). We find a slope \\(\\alpha = 0.49^{+0.20}_{-0.15}\\), normalization \\( \\exp(\\beta) = 84.0^{+9.2}_{-14.8}\\) and \\(\\sigma_{\\ln \\lambda | \\mu} = 0.17^{+0.13}_{-0.09}\\) using CFHT richness estimates. In comparison to other weak lensing richness-mass relations, we find the normalization of the richness statistically agreeing with the normalization of other scaling relations from a broad redshift range (\\(0.0
Paper
Synthetic Galaxy Clusters and Observations Based on Dark Energy Survey Year 3 Data
We develop a novel data-driven method for generating synthetic optical observations of galaxy clusters. In cluster weak lensing, the interplay between analysis choices and systematic effects related to source galaxy selection, shape measurement and photometric redshift estimation can be best characterized in end-to-end tests going from mock observations to recovered cluster masses. To create such test scenarios, we measure and model the photometric properties of galaxy clusters and their sky environments from the Dark Energy Survey Year 3 (DES Y3) data in two bins of cluster richness \\(\\lambda\\in[30;\\,45)\\), \\(\\lambda\\in[45;\\,60)\\) and three bins in cluster redshift (\\(z\\in[0.3;\\,0.35)\\), \\(z\\in[0.45;\\,0.5)\\) and \\(z\\in[0.6;\\,0.65)\\). Using deep-field imaging data we extrapolate galaxy populations beyond the limiting magnitude of DES Y3 and calculate the properties of cluster member galaxies via statistical background subtraction. We construct mock galaxy clusters as random draws from a distribution function, and render mock clusters and line-of-sight catalogs into synthetic images in the same format as actual survey observations. Synthetic galaxy clusters are generated from real observational data, and thus are independent from the assumptions inherent to cosmological simulations. The recipe can be straightforwardly modified to incorporate extra information, and correct for survey incompleteness. New realizations of synthetic clusters can be created at minimal cost, which will allow future analyses to generate the large number of images needed to characterize systematic uncertainties in cluster mass measurements.
Paper
Measuring Cosmological Parameters with Type Ia Supernovae in redMaGiC galaxies
Current and future cosmological analyses with Type Ia Supernovae (SNe Ia) face three critical challenges: i) measuring redshifts from the supernova or its host galaxy; ii) classifying SNe without spectra; and iii) accounting for correlations between the properties of SNe Ia and their host galaxies. We present here a novel approach that addresses each challenge. In the context of the Dark Energy Survey (DES), we analyze a SNIa sample with host galaxies in the redMaGiC galaxy catalog, a selection of Luminous Red Galaxies. Photo-\\(z\\) estimates for these galaxies are expected to be accurate to \\(\\sigma_{\\Delta z/(1+z)}\\sim0.02\\). The DES-5YR photometrically classified SNIa sample contains approximately 1600 SNe and 125 of these SNe are in redMaGiC galaxies. We demonstrate that redMaGiC galaxies almost exclusively host SNe Ia, reducing concerns with classification uncertainties. With this subsample, we find similar Hubble scatter (to within \\(\\sim0.01\\) mag) using photometric redshifts in place of spectroscopic redshifts. With detailed simulations, we show the bias due to using photo-\\(z\\)s from redMaGiC host galaxies on the measurement of the dark energy equation-of-state \\(w\\) is up to \\(\\Delta w \\sim 0.01-0.02\\). With real data, we measure a difference in \\(w\\) when using redMaGiC photometric redshifts versus spectroscopic redshifts of \\(\\Delta w = 0.005\\). Finally, we discuss how SNe in redMaGiC galaxies appear to be a more standardizable population due to a weaker relation between color and luminosity (\\(\\beta\\)) compared to the DES-3YR population by \\(\\sim5\\sigma\\); this finding is consistent with predictions that redMaGiC galaxies exhibit lower reddening ratios (\\(\\textrm{R}_\\textrm{V}\\)) than the general population of SN host galaxies. These results establish the feasibility of performing redMaGiC SN cosmology with photometric survey data in the absence of spectroscopic data.
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