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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 María; Alkorta, Ibon; Elguero, J.; Sanz del Castillo, Dionisia; Nieto Gómez, Carla Isabel
A New Estimator: Median of the Distribution of the Mean in Robustness
(MDPI, 2023-06-14) García Pérez, Alfonso::virtual::3495::600; García Pérez, Alfonso; García Pérez, Alfonso; 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 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.
Abrupt environmental changes during the last glacial cycle in Western Mediterranean (Formentera Island, Balearic archipelago, Spain)
(Elsevier, 2022) Bardají Azcárate, Teresa; Roquero García-Casal, Elvira; Cabero del Río, Ana; Zazo Cardeña, Caridad; Goy Goy, José Luis; Dabrio, Cristino José; Machado, María J.; Silva Barroso, Pablo Gabriel; Martínez Graña, Antonio Miguel; Lario Gómez, Javier
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.
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.
Acrylamide-fat correlation in californian-style black olives using near-infrared spectroscopy
(MDPI, 2023-09-06) Montero Fernández, Ismael; Martín Tornero, Elísabet; Martín Vertedor, Daniel; Fernández Fernández, Antonio; Monago Maraña, Olga
Californian-style is one of the most important black table olive elaborations. During its processing, table olives produce acrylamide, a potential carcinogen compound generated during sterilization. In the present study, total fat and acrylamide content in Californian-style table olives were determined and a regression between them was performed (acrylamide concentration range: below limit of detection—2500 ng g−1 and 8–22% for total fat). Nowadays, there are fast and efficient new techniques, such as Near-Infrared Spectroscopy (NIRS) to measure fat content parameters. In that sense, NIRS was used to perform a fat content quantification model in olives in order to indirectly determine acrylamide content. Calibration models for fat quantification were obtained in defatted olive pastes from a unique variety and for olive pastes from different varieties. In the first case, best results were obtained since only one variety was used (R2 = 0.9694; RMSECV = 1.31%; and REP = 8.4%). However, in the second case, results were still acceptable R2 = 0.678, RMSECV = 2.3%, REP = 17.7% and RMSEV = 2.17%. Regression coefficients showed the most influence variables corresponded with fat. The determination coefficient for the fat and acrylamide correlation was high (r = 0.877), being an efficient approach to find out the contribution of fat degradation to acrylamide synthesis in table olives.
Amino-Functionalized Multiwall Carbon Nanotubes as Efficient Basic Catalysts for the Formation of γ-Lactams: Synthesis of N-1-Heptenyl-2-pyrrolidinone
(MDPI, 2022) Barrios Bermúdez, Niurka; Cerpa Naranjo, Arisbel; Rojas Cervantes, María Luisa
In this work, we prepared a series of N-functionalized carbon nanotubes by means of a process of acylation-amidation of commercial multiwall carbon nanotubes that were previously pre-oxidized with nitric acid. Three different amines, butylamine, N,N-dimethyl ethylenediamine, and ethylenediamine, were used in the process. The characterization of samples by several techniques probed the incorporation of nitrogen atoms to the carbon nanotubes, especially in the case of ethylenediamine. The solids were tested as catalysts in the synthesis of N-1-heptenyl-2-pyrrolidinone, included in the group of a γ-lactams, compounds that show important biological properties. The most active catalyst was that prepared with butylamine, which exhibited the highest SBET and Vpore values and contained an amount of nitrogen that was intermediate between that of the other two catalysts. A yield of 60% to N-1-heptenyl-2-pyrrolidinone was achieved after 3 h at 120 ◦C under free-solvent conditions. This catalyst could be used in four consecutive cycles without significant activity loss.
Ammonium acetate as a novel buffer for highly selective robust urinary HPLC-ICP-MS arsenic speciation methodology
(Elsevier, 2021-01-01) Rodríguez, P. F.; López Colón, José Luis; Mendoza, J. L. de; Martín Aranda, Rosa María
Ammonium acetate is employed in order to develop a novel HPLC-ICP-MS arsenic speciation methodology applicable to six arsenic species, i.e, AC, AB, AsIII, AsV, DMA and MMA. The most predominant species in the toxicological field are covered in a 30-min chromatogram with reproducible and repeatability peak area ratio. Moreover, typical problems from traditional methods are sorted out by using a robust, high-selective and 75ArCl+ interference-free methodology. Chromatographic and detector optimization ensures low LOQs for each species with acceptable precision and accuracy values obtained using four urinary arsenic speciation PTS enabling to be useful for sub ng mL−1 arsenic exposure assessments.
An experimental and theoretical NMR study of NH-benzimidazoles in solution and in the solid state: proton transfer and tautomerism
(Beilstein-Institut, 2014) Nieto Gómez, Carla Isabel
This paper reports the 1H, 13C and 15N NMR experimental study of five benzimidazoles in solution and in the solid state (13C and 15N CPMAS NMR) as well as the theoretically calculated (GIAO/DFT) chemical shifts. We have assigned unambiguously the "tautomeric positions" (C3a/C7a, C4/C7 and C5/C6) of NH-benzimidazoles that, in some solvents and in the solid state, appear different (blocked tautomerism). In the case of 1H-benzimidazole itself we have measured the prototropic rate in HMPA-d18.
An extreme wave event in eastern Yucatan, Mexico: Evidence of a palaeotsunami event during the Mayan times
(Wiley Online Library, 2020) Spencer, Chris; Bardají Azcárate, Teresa; Marchante Ortega, Ángel; Garduño Monroy, Victor Hugo; Macias, Jorge; Ortega, Sergio; Lario Gómez, Javier::virtual::2800::600; Lario Gómez, Javier; Lario Gómez, Javier; Lario Gómez, Javier
The Yucatan Peninsula, Mexico, has typically been considered a tectonically stable region with little significant seismic activity. The region though, is one that is regularly affected by hurricanes. A detailed survey of ca 100 km of the eastern Yucatan and Cozumel coast identified the presence of ridges containing individual boulders measuring >1 m in length. The boulder ridges reach 5 m in height and their origin is associated with extreme wave event activity. Previously modelled tsunami waves from known seismically active zones in the region (Muertos Thrust Belt and South Caribbean Deformed Belt) are not of sufficient scale in the area of the Yucatan Peninsula to have produced the boulder ridges recorded in this study. The occurrence of hurricanes in this region is more common, but two of the most destructive (Hurricane Gilbert 1988 and Hurricane Wilma 2005) produced coastal waves too small to have created the ridges recorded here. In this paper, a new tsunami model with a source area located on the Motagua/Swan Island Fault System has been generated that indicates a tsunami event may have caused the extreme wave events that resulted in the deposition of the boulder ridges.
An optical sensor for the determination of digoxin in serum samples based on a molecularly imprinted polymer membrane.
(Elsevier, 2009-04) Durand Alegría, Jesús Senén; Paniagua González, Gema::virtual::2768::600; Fernández Hernando, Pilar::virtual::2769::600; Paniagua González, Gema; Fernández Hernando, Pilar; Paniagua González, Gema; Fernández Hernando, Pilar; Paniagua González, Gema; Fernández Hernando, Pilar
This paper reports the synthesis and testing of a molecularly imprinted polymer membrane for digoxin analysis. Digoxin-specific bulk polymer was obtained by the UV initiated co-polymerisation of methacrylic acid and ethylene glycol dimethacrylate in acetonitrile as porogen. After extracting the template analyte, the ground polymer particles were mixed with plasticizer polyvinyl chloride to form a MIP membrane. A reference polymer membrane was prepared from the same mixture of monomers but with no template. The resultant membrane morphologies were examined by scanning electron microscopy. The imprinted membrane was tested as the recognition element in a digoxin-sensitive fluorescence sensor; sensor response was measured using standard solutions of digoxin at concentrations of up to 4 × 10−3 mg L−1. The detection limit was 3.17 × 10−5 mg L−1. Within- and between-day relative standard deviations RSD (n = 5) were in the range 4.5–5.5% and 5.5–6.5% respectively for 0 and 1 × 10−3 mg L−1 digoxin concentrations. A selectivity study showed that compounds of similar structure to digoxin did not significantly interfere with detection for interferent concentrations at 10, 30 and 100 times higher than the digoxin concentration. This simply manufactured MIP membrane showed good recognition characteristics, a high affinity for digoxin, and provided satisfactory results in analyses of this analyte in human serum.
Analytical technique and chemometrics approaches in authenticating and identifying adulteration of paprika powder using fingerprints: a review.
(Elsevier, 2022) Durán Merás, Isabel; Muñoz de la Peña, Arsenio; Galeano Díaz, Teresa; Monago Maraña, Olga
Paprika powder authentication has gained interest in recent decades along with increases in its consumption. There are different Protected Designation of Origins (PDOs) around the world, some of them are from Spain, and it is important to assure the quality parameters that they offer and to provide a guaranty about their quality and authentication. This review covers the latest advances concerning the targeted and untargeted methodologies. These methodologies have been developed to ensure paprika powder authenticity, corroborating that it belongs or not to a certain PDO and that it complies with the regulations and legal standards for its consumption, as well as detection of possible adulterations, mainly with Sudan dyes, which are illegal colorants. Differences between spectroscopic and non-spectroscopic methods have been emphasized. As observed from the literature, paprika powder has not been extensively studied, but the number of papers has been increasing in recent years.

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