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3D-Printed SARS-CoV-2 RNA Genosensing Microfluidic System
(Wiley, 2022-02-05) González Crevillén, Agustín; Mayorga-Martinez, Carmen C.; Vaghasiya, Jayraj V.; Martin Pumera
Additive manufacturing technology, referred as 3D printing technology, is a growing research field with broad applications from nanosensors fabrication to 3D printing of buildings. Nowadays, the world is dealing with a pandemic and requires the use of simple sensing systems. Here, the strengths of fast screening by a lab-on-a-chip device through electrochemical detection using 3D printing technology for SARS-CoV-2 sensing are combined. This system comprises a PDMS microfluidic channel integrated with an electrochemical cell fully 3D-printed by a 3D printing pen (3D-PP). The 3D-PP genosensor is modified with an ssDNA probe that targeted the N gene sequence of SARS-CoV-2. The sensing mechanism relies on the electro-oxidation of adenines present in ssDNA when in contact with SARS-CoV-2 RNA. The hybridization between ssDNA and target RNA takes a place and ssDNA is desorbed from the genosensor surface, causing a decrease of the sensor signal. The developed SARS-CoV-2/3D-PP genosensor shows high sensitivity and fast response.
3D-printed Transmembrane Glycoprotein Cancer Biomarker Aptasensor
(Elsevier, 2021-08-21) González Crevillén, Agustín; Mayorga Martinez, Carmen C.; Zelenka, Jaroslav; Rimpelová, Silvie; Ruml, Tomáš; Pumera, Martin
Point-of-care, easy to manufacture, and low cost detection of cancer biomarkers is crucial for fighting the early stage disease. 3D printing allows delocalized printing at remote locations with updates/upgrades available globally via electronic files. Mucin 1 (MUC1) is a protein that is overexpressed in a number of epithelial cancers and is a key factor in advancement of the disease. Here we show the simple point-of-care 3D printing fabrication of a MUC1 aptasensor using a nanocarbon/polymer filament. Efficacy of the 3D-printed aptasensor is demonstrated by monitoring the expression and release of MUC1 in breast cancer cell cultures. Such a simple, low cost, and easy to locally fabricate cancer biosensor will have a large impact on the field of cancer diagnostics.
A comprehensive study of the molecular vibrations in solid-state benzylic amide [2]catenane
(Royal Society of Chemistry, 2019) Romero Muñiz, Carlos; Paredes Roibás, Denís; Hernanz, Antonio; Gavira Vallejo, José María
The interpretation of vibrational spectra is often complex but a detailed knowledge of the normal modes responsible for the experimental bands provides valuable information about the molecular structure of the sample. In this work we record and assign in detail the infrared (IR) spectrum of the benzylic amide [2]catenane, a complex molecular solid displaying crimped mechanical bonds like the links of a chain. In spite of the large size of the unit cell, we calculate all the vibrational modes of the catenane crystal using quantum first-principles calculations. The activity of each mode is also evaluated using the Born effective charges approach and a theoretical spectrum is constructed for comparison purposes. We find a remarkable agreement between the calculations and the experimental results without the need to apply any further empirical correction or fitting to the eigenfrequencies. A detailed description in terms of the usual internal coordinates is provided for over 1000 normal modes. This thorough analysis allows us to perform the complete assignment of the spectrum, revealing the nature of the most active modes responsible for the IR features. Finally, we compare the obtained results with those of Raman spectroscopy, studying the effects of the rule of mutual exclusion in vibrational spectroscopy according to the different levels of molecular symmetry embedded in this mechanically interlocked molecular compound.
A geometric model for non-uniform processes of morphogenesis
(Elsevier, 2022-09-23) León, Manuel de; Jiménez Morales, Víctor Manuel
In this paper we present an application of the groupoid theory to the study of relevant case of material evolution phenomena, the process of morphogenesis. Our theory is inspired by Walter Noll’s theories of continuous distributions and provides a unifying and very simple framework of these phenomena. We present the explicit equation, the morphogenesis equation, to calculate the material distributions associated to this phenomenon.
A MIP-based flow-through fluoroimmunosensor as an alternative to immunosensors for the determination of digoxin serum samples
(Springer, 2009-01-09) Durand Alegría, Jesús Senén; Paniagua González, Gema; Fernández Hernando, Pilar
This work reports a comparative study of two automated flow-through fluorosensors for the determination of digoxin in serum samples: an immunosensor with an anti-digoxin polyclonal antibody as the reactive phase permanently immobilized on CPG, and a sensor with a selective reaction system based on a methacrylic molecularly imprinted polymer (MIP) synthesized by bulk polymerisation. The variables affecting the sensitivity and dynamic range of the sensors (e.g., the carrier and elution solutions, flow-rates, pH and reagent concentrations) were optimised and the binding characteristics of their reactive phases compared in a competitive fluorescent assay. Digoxin was reproducibly determined by both sensors at the mg L-1 level (detection limit= 1.20×10-3 mg L-1 and RSD= 4-7% for the immunosensor; detection limit= 1.7×10-5 mg L-1 and RSD= 1-2% for the MIP sensor). No cross reactivity with digoxinrelated compounds was seen for either sensor at a digoxin:interferent ratio of 1:100. The lifetime of the immunosensor was about 50 immunoassays; its shelf life, when unused, is about three months. The lifetime of the MIP sensor was over 18 months. Both sensors were used to determine the digoxin concentration of human serum samples with satisfactory results.
A morphological study of molecularly imprinted polymers using the scanning electron microscope
(Elsevier, 2006-01) Durand Alegría, Jesús Senén; Paniagua González, Gema; Fernández Hernando, Pilar
Molecular imprinting is an emerging technique for producing polymers with applications in affinity-based separation, in biomimetic sensors, in catalysis, etc. This variety of uses relies upon the production of polymers with different affinities, specificities, sensitivities and loading capacities. Research into the development of molecular imprinted polymers (MIPs) with new or improved morphologies – which involves modification of the polymerisation process – is therefore underway. This paper reports a comparative study of non-covalent MIPs synthesised by “bulk” polymerisation using digoxin as template. These were synthesised under different conditions, i.e., changing the functional monomers employed (methacrylic acid or 2-vinylpyridine), the porogens (acetonitrile or dichloromethane) used, and by altering the volume of the latter. The polymerisation process was allowed to proceed either under UV light or in a thermostat-controlled waterbath. The surface morphology (was determined by scanning electron microscopy) and the ability of the different polymers to selectively rebind the template was then evaluated.
A multinuclear magnetic resonance study of fluoro derivatives of hydroxybenzaldehydes
(2015-06-06) Claramunt, Rosa M.; Alkorta, Ibon; Elguero, José; Sanz del Castillo, Dionisia; Nieto Gómez, Carla Isabel; Claramunt, Rosa M.
A New Estimator: Median of the Distribution of the Mean in Robustness
(MDPI, 2023-06-14) García Pérez, Alfonso
In some statistical methods, the statistical information is provided in terms of the values used by classical estimators, such as the sample mean and sample variance. These estimations are used in a second stage, usually in a classical manner, to be combined into a single value, as a weighted mean. Moreover, in many applied studies, the results are given in these terms, i.e., as summary data. In all of these cases, the individual observations are unknown; therefore, computing the usual robustness estimators with them to replace classical non-robust estimations by robust ones is not possible. In this paper, the use of the median of the distribution 𝐹𝑥̲ of the sample mean is proposed, assuming a location-scale contaminated normal model, where the parameters of 𝐹𝑥̲ are estimated with the classical estimations provided in the first stage. The estimator so defined is called median of the distribution of the mean, 𝑀𝑑𝑀. This new estimator is applied in Mendelian randomization, defining the new robust inverse weighted estimator, RIVW.
A novel approach to triplenegative breast cancer molecular classification reveals a luminal immune-positive subgroup with good prognoses
(Springer nature, 2019-02-07) Prado Vázquez, Guillermo; Gámez Pozo, Ángelo; Trilla Fuertes, Lucía; Zapater Moros, Andrea; Ferrer Gómez, María; Díaz Almirón, Mariana; López Vacas, Rocío; Maín, Paloma; Feliu Batlle, Jaime; Zamora Auñón, Pilar; Espinosa, Enrique; Fresno Vara, Juan Ángel; Martín Arevalillo, Jorge; Navarro Veguillas, Hilario
Triple-negative breast cancer is a heterogeneous disease characterized by a lack of hormonal receptors and HER2 overexpression. It is the only breast cancer subgroup that does not benefit from targeted therapies, and its prognosis is poor. Several studies have developed specific molecular classifications for triple-negative breast cancer. However, these molecular subtypes have had little impact in the clinical setting. Gene expression data and clinical information from 494 triple-negative breast tumors were obtained from public databases. First, a probabilistic graphical model approach to associate gene expression profiles was performed. Then, sparse k-means was used to establish a new molecular classification. Results were then verified in a second database including 153 triple-negative breast tumors treated with neoadjuvant chemotherapy. Clinical and gene expression data from 494 triple-negative breast tumors were analyzed. Tumors in the dataset were divided into four subgroups (luminal-androgen receptor expressing, basal, claudin-low and claudin-high), using the cancer stem cell hypothesis as reference. These four subgroups were defined and characterized through hierarchical clustering and probabilistic graphical models and compared with previously defined classifications. In addition, two subgroups related to immune activity were defined. This immune activity showed prognostic value in the whole cohort and in the luminal subgroup. The claudin-high subgroup showed poor response to neoadjuvant chemotherapy. Through a novel analytical approach we proved that there are at least two independent sources of biological information: cellular and immune. Thus, we developed two different and overlapping triple-negative breast cancer classifications and showed that the luminal immune-positive subgroup had better prognoses than the luminal immune-negative. Finally, this work paves the way for using the defined classifications as predictive features in the neoadjuvant scenario.
A pan-cheloniid turtle from the Middle Miocene of Portugal
(Wiley, 2024) Pérez García, Adán; Telles Antunes, Miguel
Currently, there is no information on the fossil record of Pan-Cheloniidae from the Neogene of the Iberian Peninsula. A well-preserved partial skeleton attributable to this lineage of turtles, from the Middle Miocene of Portugal, is presented here. It preserves much of the anterior half of its carapace, in which the plates remain articulated, as well as several articulated dorsal vertebrae, and an isolated cervical and a caudal vertebrae. The analysis of this Serravallian find shows that it cannot be attributed to a hitherto described taxon. Thus, a new member of Pan-Cheloniidae is defined, Lusochelys emilianoi gen. et sp. nov., improving the relatively limited knowledge about this lineage for the Middle Miocene global record. It represents the first generic and specific systematic attribution for a member of Pan-Chelonioidea in the Neogene record of the Iberian Peninsula.
A pressure indicator for the impact of Iberian wild goat on moss and soils in a Mediterranean climate
(Springer, 2021) Aroztegui Vélez, Javier; López‑Sánchez, Aida; Peláez Beato, Marta; Perea García-Calvo, Ramón; García Rodríguez, Manuel
In the Sierra de Guadarrama National Park (central Spain), the population of Iberian wild goat, also known as Spanish ibex (Capra pyrenaica) has grown strongly since its reintroduction three decades ago. The plant community is now under heavy browsing pressure due to this high population. A study of the presence of moss on rocks was used herein as the basis for the design of an indicator, named impact on mosses (im), to describe the environmental pressure exerted by the Iberian wild goat in terms of moss removal. Granite and gneiss zones at medium altitudes with continental Mediterranean climate are the most suitable areas for successful application of the indicator. The hypotheses to test are: (1) the indicator will discriminate between areas with different wild goat pressure levels, (2) wild goat pressure will explain a high proportion of moss loss variance, and (3) the im indicator will be useful to establish a mathematical model between wild goat pressure and moss loss. The proposed indicator was analyzed using both statistical and data science techniques. The results support the mentioned hypotheses. Specifically, statistically significant differences were found regarding the impact on mosses between areas with different levels of Iberian wild goat pressure. Thus, a high proportion of the variance was associated with wild goat pressure (80% for high-pressure areas, 56% for low-pressure areas). A modified parabolic function was fit to express the relationship between Iberian wild goat pressure and impact on mosses. In conclusion, the im indicator was shown to be a useful tool to assess pressure due to Iberian wild goat. Therefore, im can help assess and manage Iberian wild goat populations and determine their sustainable levels.
A semi-mechanistic model for predicting daily variations in species-level live fuel moisture content
(Elsevier, 2022) Balaguer Romano, Rodrigo
Live Fuel Moisture Content (LFMC) is one of the main factors affecting forest ignitability as it determines the availability of existing live fuel to burn. Currently, LFMC is monitored through spectral vegetation indices or inferred from meteorological drought indices. While useful, neither approach provides mechanistic insights into species-specific LFMC variation and they are limited in the ability to forecast LFMC under altered future climates. Here, we developed a semi-mechanistic model to predict daily variation in LFMC across woody species from different functional types by adjusting a soil water balance model which estimates predawn leaf water potential (Ψpd). Our overarching goal was to balance the trade-off between biological realism, which enhances model applicability, and parameterization complexity, which may limit its value within operational settings. After calibration, model predictions were validated against a dataset comprising 1659 LFMC observations across peninsular Spain, belonging to different functional types and from contrasting climates. The overall goodness of fit for our model (R2 = 0.5) was better than that obtained by an existing models based on drought indices (R2 = 0.3) or spectral vegetation indices (R2 = 0.1). We observed the best predictive performance for seeding shrubs (R2 = 0.6) followed by trees (R2 = 0.5) and resprouting shrubs (R2 = 0.4). Through its relatively simple parameterization, the approach developed here may pave the way for a new generation of process-based models that can be used for operational purposes within fire risk mitigation scenarios.
A sparse Bayesian representation for super-resolution of cardiac MR images
(Elsevier, 2017-02) Velasco, Nelson F.; Rueda Olarte, Andrea del Pilar; Romero, Eduardo C.; Santa Marta Pastrana, Cristina María
High-quality cardiac magnetic resonance (CMR) images can be hardly obtained when intrinsic noise sources are present, namely heart and breathing movements. Yet heart images may be acquired in real time, the image quality is really limited and most sequences use ECG gating to capture images at each stage of the cardiac cycle during several heart beats. This paper presents a novel super-resolution algorithm that improves the cardiac image quality using a sparse Bayesian approach. The high-resolution version of the cardiac image is constructed by combining the information of the low-resolution series –observations from different non-orthogonal series composed of anisotropic voxels – with a prior distribution of the high-resolution local coefficients that enforces sparsity. In addition, a global prior, extracted from the observed data, regularizes the solution. Quantitative and qualitative validations were performed in synthetic and real images w.r.t to a baseline, showing an average increment between 2.8 and 3.2 dB in the Peak Signal-to-Noise Ratio (PSNR), between 1.8% and 2.6% in the Structural Similarity Index (SSIM) and 2.% to 4% in quality assessment (IL-NIQE). The obtained results demonstrated that the proposed method is able to accurately reconstruct a cardiac image, recovering the original shape with less artifacts and low noise.
A stochastic ordering based on the canonical transformation of skew-normal vectors
(Springer, 2018-04-25) Martín Arevalillo, Jorge; Navarro Veguillas, Hilario
In this paper, we define a new skewness ordering that enables stochastic comparisons for vectors that follow a multivariate skew-normal distribution. The new ordering is based on the canonical transformation associated with the multivariate skew-normal distribution and on the well-known convex transform order applied to the only skewed component of such canonical transformation. We examine the connection between the proposed ordering and the multivariate convex transform order studied by Belzunce et al. (TEST 24(4):813–834, 2015). Several standard skewness measures like Mardia’s and Malkovich–Afifi’s indices are revisited and interpreted in connection with the new ordering; we also study its relationship with the J-divergence between skew-normal and normal random vectors and with the Negentropy. Some artificial data are used in simulation experiments to illustrate the theoretical discussion; a real data application is provided as well.
Abelian Actions on Pseudo-real Riemann Surfaces
(Springer, 2023-04-08) Bujalance García, Emilio; Cirre Torres, Francisco Javier; J. Rodríguez
A compact Riemann surface is called pseudo-real if it admits orientation-reversing automorphisms but none of them has order two. In this paper, we find necessary and sufficient conditions for the existence of an action on a pseudo-real surface of genus g 2 of an abelian group containing orientation-reversing automorphisms. Several consequences are obtained, such as the solution of the minimum genus problem for such abelian actions.
Abrupt environmental changes during the last glacial cycle in Western Mediterranean (Formentera Island, Balearic archipelago, Spain)
(Elsevier, 2022) Bardají, Teresa; Roquero García-Casal, Elvira; Cabero del Río, Ana; Zazo Cardeña, Caridad; Goy Goy, José Luis; Dabrio, Cristino José; Machado, María J.; Silva, Pablo Gabriel; Martínez Graña, Antonio Miguel; Lario Gómez, Javier; https://orcid.org/0000-0003-2988-8077
A sedimentary sequence covering the entire last glacial cycle (period between Terminations I and II) outcrops along the south-eastern coast of Formentera Island. A detailed geomorphological, geological and sedimentological study, supported by geochemical, soil and soil-morphology analyses, magnetic susceptibility, phytolite content and luminescence dating (TL, OSL) allowed to reconstruct the environmental evolution of this coastal setting, and to frame it within the evolutionary pattern of the North Atlantic climate variability. Three highstands of sea level are identified in this island for MIS 5e, and a fourth one is attributed to MIS5a. MIS5 – MIS4 transition is characterized by soil development under a moist-warm climate and a descending sea level scenario. Aeolian units (72 ± 7 ka BP) developed during MIS4 under prevailing northerly winds that persisted until the beginning of MIS3, when new aeolian dunes (54 ± 5 ka BP) developed after a major sea-level lowstand. A sudden shift in prevailing winds occur within MIS3, when aeolian units (51 ± 4 ka BP) grew under the influence of S-SW winds and moister climate, evidenced by a dense root bioturbation. The greater influence of northerly winds is attributed to the weakening of Atlantic Meridional Overturning Current (AMOC) in North Atlantic, and enhancement of westerlies in NW Europe during colder periods. Periods of prevailing southerly winds and moister climate correlate well with warm Greenland Interstadials, and reinforcement of AMOC. Between 50 and 40ka, alluvial/colluvial sedimentary units punctuated by soil and calcrete development, witness the climatic variability recorded along this period in the North Atlantic. A sedimentary hiatus with erosion and calcrete development characterizes the transit between MIS3 and MIS2. Finally, a reddish alluvial sedimentary unit records a short span of humid and warm climate (soil development, peak in magnetic susceptibility, phytolite content) within MIS 2 (20 ± 2 ka BP – 17 + 2.4/-2.2) that contrast with the general climatic trend recorded in Western Mediterranean during the Last Glacial Maximum.
Absorbing Markov decision processes
(EDP Sciences, 2024-02-09) Dufour, François; Prieto Rumeau, Tomás
In this paper, we study discrete-time absorbing Markov Decision Processes (MDP) with measurable state space and Borel action space with a given initial distribution. For such models, solutions to the characteristic equation that are not occupation measures may exist. Several necessary and sufficient conditions are provided to guarantee that any solution to the characteristic equation is an occupation measure. Under the so-called continuity-compactness conditions, we first show that a measure is precisely an occupation measure if and only if it satisfies the characteristic equation and an additional absolute continuity condition. Secondly, it is shown that the set of occupation measures is compact in the weak-strong topology if and only if the model is uniformly absorbing. Several examples are provided to illustrate our results.
Accurate and efficient calculation of multicomponent thermal diffusion coefficients and partial thermal conductivity based on kinetic theory
(Elsevier, 2022-03-25) Córdoba, Oscar; Arias Zugasti, Manuel
The calculation of the multicomponent thermal diffusion coefficients and partial thermal conductivity of polyatomic gas mixtures, with large numbers of components, based on the Kinetic Theory of Gases is revisited. The terms involving inelastic collisions and relaxation times for various internal degrees of freedom are considered, in addition to the classical Chapman-Enskog expressions. For polar gases, the resonant exchange of rotational energy is also accounted for. The present work is the natural extension of the algorithms shown in Combust. and Flame 163 (2016) 540-55 for the calculation of the Fick’s law multicomponent diffusion coefficients, of which it makes use. This work presents a new iterative algorithm for the calculation of the multicomponent thermal diffusion coefficients and partial thermal conductivity. This new algorithm has been implemented in the C++ library MuTLib (Multicomponent Transport Library), available for the transport properties calculations in third party applications and included in the additional material of this publication. The algorithm performance improvements are shown in two different flames: a hydrogen premixed flame and a methane diffusion flame. The results are successfully compared against the library package EGLib (Ern-Giovangigli Library, which considers the same physical effects as this work), and to the well known mixture averaged approximation.
Accurate Test of Chiral Dynamics in the → 𝛾 ⁢𝑝 →𝜋0⁢𝑝 Reaction
(American Physical Society, 2013-08-07) Hornidge, D; Aguar Bartolomé, P.; J. R. M. Annand,; Fernández Ramírez, César; et al.
A precision measurement of the differential cross sections 𝑑⁢𝜎/𝑑⁢𝛺 and the linearly polarized photon asymmetry 𝛴 ≡(𝑑⁢𝜎⊥ −𝑑⁢𝜎∥)/(𝑑⁢𝜎⊥ +𝑑⁢𝜎∥) for the →𝛾⁢𝑝 →𝜋0⁢𝑝 reaction in the near-threshold region has been performed with a tagged photon beam and almost 4⁢𝜋 detector at the Mainz Microtron. The Glasgow-Mainz photon tagging facility along with the Crystal Ball/TAPS multiphoton detector system and a cryogenic liquid hydrogen target were used. These data allowed for a precise determination of the energy dependence of the real parts of the 𝑆- and all three 𝑃-wave amplitudes for the first time and provide the most stringent test to date of the predictions of chiral perturbation theory and its energy region of agreement with experiment.
Acidic porous carbons involved in the green and selective synthesis of benzodiazepines
(Elsevier, 2020-11-01) Godino Ojer, Marina; Matos, Ines; Bernardo, M.; Carvalho, R.; G.P. Soares, Olívia Salomé; Durán Valle, C.; Fonseca, I.M.; Pérez Mayoral, María Elena
Eco-sustainable and recyclable porous carbons are reported as metal-free catalysts for the synthesis of benzodiazepines for the first time. The porous carbons were able to efficiently catalyse the synthesis of benzodiazepine 1 from o-phenylendiamine 2 and acetone 3 under mild conditions. Both acidic functions and the porosity of the catalysts were determinant features. High conversion values were obtained when using HNO3 oxidized carbons. The highest selectivity to benzodiazepine 1 was obtained in the presence of the most microporous catalyst N-N, which is indicative of the great influence of porous properties. Stronger acid sites and high microporosity of the carbon treated with H2SO4 yield benzodiazepine 1 with total selectivity.

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