by Keyword: Density

Bertran, O, Martí, D, Torras, J, Turon, P, Alemán, C, (2022). Computer simulations on oxidative stress-induced reactions in SARS-CoV-2 spike glycoprotein: a multi-scale approach Molecular Diversity 26, 3143-3155

Abstract Oxidative stress, which occurs when an organism is exposed to an adverse stimulus that results in a misbalance of antioxidant and pro-oxidants species, is the common denominator of diseases considered as a risk factor for SARS-CoV-2 lethality. Indeed, reactive oxygen species caused by oxidative stress have been related to many virus pathogenicity. In this work, simulations have been performed on the receptor binding domain of SARS-CoV-2 spike glycoprotein to study what residues are more susceptible to be attacked by ·OH, which is one of the most reactive radicals associated to oxidative stress. The results indicate that isoleucine (ILE) probably plays a crucial role in modification processes driven by radicals. Accordingly, QM/MM-MD simulations have been conducted to study both the ·OH-mediated hydrogen abstraction of ILE residues and the induced modification of the resulting ILE radical through hydroxylation or nitrosylation reactions. All in all, in silico studies show the importance of the chemical environment triggered by oxidative stress on the modifications of the virus, which is expected to help for foreseeing the identification or development of antioxidants as therapeutic drugs. Graphic abstract

JTD Keywords: atom abstraction, damage, density functionals, hydrogen abstraction, isoleucine, molecular dynamics, pathogenesis, protein, reactive oxygen species, receptor binding domain, residues, spike protein, Amino-acids, Hydrogen abstraction, Isoleucine, Molecular dynamics, Reactive oxygen species, Receptor binding domain, Spike protein

Riedelová, Z, Pereira, AD, Svoboda, J, Pop-Georgievski, O, Májek, P, Pecánková, K, Dycka, F, Rodriguez-Emmenegger, C, Riedel, T, (2022). The Relation Between Protein Adsorption and Hemocompatibility of Antifouling Polymer Brushes Macromolecular Bioscience 22, 2200247

Whenever an artificial surface comes into contact with blood, proteins are rapidly adsorbed onto its surface. This phenomenon, termed fouling, is then followed by a series of undesired reactions involving activation of complement or the coagulation cascade and adhesion of leukocytes and platelets leading to thrombus formation. Thus, considerable efforts are directed towards the preparation of fouling-resistant surfaces with the best possible hemocompatibility. Herein, a comprehensive hemocompatibility study after heparinized blood contact with seven polymer brushes prepared by surface-initiated atom transfer radical polymerization is reported. The resistance to fouling is quantified and thrombus formation and deposition of blood cellular components on the coatings are analyzed. Moreover, identification of the remaining adsorbed proteins is performed via mass spectroscopy to elucidate their influence on the surface hemocompatibility. Compared with an unmodified glass surface, the grafting of polymer brushes minimizes the adhesion of platelets and leukocytes and prevents the thrombus formation. The fouling from undiluted blood plasma is reduced by up to 99%. Most of the identified proteins are connected with the initial events of foreign body reaction towards biomaterial (coagulation cascade proteins, complement component, and inflammatory proteins). In addition, several proteins that are not previously linked with blood-biomaterial interaction are presented and discussed.

JTD Keywords: antifouling surfaces, biosensor, blood-plasma, coagulation, coatings, compatibility, glycoprotein, hemocompatibility, identification, methacrylate), ms identification, polymer brushes, protein adsorption, surface-chemistry, Antifouling surfaces, High-density-lipoprotein, Protein adsorption

Wauters, AC, Scheerstra, JF, Vermeijlen, IG, Hammink, R, Schluck, M, Woythe, L, Wu, HL, Albertazzi, L, Figdor, CG, Tel, J, Abdelmohsen, LKEA, van Hest, JCM, (2022). Artificial Antigen-Presenting Cell Topology Dictates T Cell Activation Acs Nano 16, 15072-15085

Nanosized artificial antigen-presenting cells (aAPCs), synthetic immune cell mimics that aim to activate T cells ex or in vivo, offer an effective alternative to cellular immunotherapies. However, comprehensive studies that delineate the effect of nano-aAPC topology, including nanoparticle morphology and ligand density, are lacking. Here, we systematically studied the topological effects of polymersome-based aAPCs on T cell activation. We employed an aAPC library created from biodegradable poly(ethylene glycol)-block-poly(d,l-lactide) (PEG-PDLLA) polymersomes with spherical or tubular shape and variable sizes, which were functionalized with αCD3 and αCD28 antibodies at controlled densities. Our results indicate that high ligand density leads to enhancement in T cell activation, which can be further augmented by employing polymersomes with larger size. At low ligand density, the effect of both polymersome shape and size was more pronounced, showing that large elongated polymersomes better activate T cells compared to their spherical or smaller counterparts. This study demonstrates the capacity of polymersomes as aAPCs and highlights the role of topology for their rational design.

JTD Keywords: antibody density, artificial antigen-presenting cells, biodegradable polymersomes, design, expansion, immunotherapy, nano-immunotherapy, nanoparticle morphology, t cell activation, Biodegradable polymersomes, Nanoparticle morphology, Synthetic dendritic cells

Casanellas I, Samitier J, Lagunas A, (2022). Recent advances in engineering nanotopographic substrates for cell studies Frontiers In Bioengineering And Biotechnology 10, 1002967

Cells sense their environment through the cell membrane receptors. Interaction with extracellular ligands induces receptor clustering at the nanoscale, assembly of the signaling complexes in the cytosol and activation of downstream signaling pathways, regulating cell response. Nanoclusters of receptors can be further organized hierarchically in the cell membrane at the meso- and micro-levels to exert different biological functions. To study and guide cell response, cell culture substrates have been engineered with features that can interact with the cells at different scales, eliciting controlled cell responses. In particular, nanoscale features of 1-100 nm in size allow direct interaction between the material and single cell receptors and their nanoclusters. Since the first "contact guidance" experiments on parallel microstructures, many other studies followed with increasing feature resolution and biological complexity. Here we present an overview of the advances in the field summarizing the biological scenario, substrate fabrication techniques and applications, highlighting the most recent developments.Copyright © 2022 Casanellas, Samitier and Lagunas.

JTD Keywords: cell response, density, differentiation, lithography, micro, nanofabrication, nanopatterning, nanopatterns, nanoscale, nanotopography, organization, photolithography, Cell response, Nanofabrication, Nanopatterning, Nanotopography, Plasma-membrane, Receptor nanoclustering

Yazıcı N, Opar E, Kodal M, Tanören B, Sezen M, Özkoç G, (2022). A novel practical approach for monitoring the crosslink density of an ethylene propylene diene monomer compound: Complementary scanning acoustic microscopy and FIB-SEM-EDS analyses Polymers & Polymer Composites 30,

Tuning of the crosslink density (CLD) in the rubber compounds is very crucial for optimizing the physical and mechanical properties of the ultimate rubber products. Conventionally, CLD can be measured via rheological methods such as moving die rheometer (MDR), via mechanical tests such as temperature scanning stress relaxation analysis (TSSR), or via direct swelling experiments using Flory–Rehner approach. In the current study, two novel techniques, focused ion beam - scanning electron microscopy (FIB-SEM) processing, with simultaneous energy dispersive X-ray spectrometry (EDS) mapping analysis and scanning acoustic microscopy (SAM) were combined and correlated to conventional methods on a model recipe of ethylene propylene diene monomer (EPDM) compound having different sulphur contents. Depending on the applied technique, the increase in the crosslink density with sulphur content was found to be 1.7 fold for the Flory–Rehner approach and 1.2 fold for both TSSR and MDR. It is directly monitored from the FIB-SEM-EDS analysis that the sulphur distribution and agglomeration behavior increased in line with ZnO content, which is an indirect indication of the rise in crosslink density. The impedance maps of the crosslinked samples obtained through SAM analysis revealed that the impedance of the samples increased with the increasing sulphur content, which can be attributed to higher level of crosslink density. A quantified correlation was obtained between SAM images and the crosslink density of the samples. It was shown that SAM is a promising tool for practical and non-destructive analysis for determining the formation of crosslink density of the rubbers. © The Author(s) 2022.

JTD Keywords: blends, compressibility, crosslink density, cure characteristics, ethylene propylene diene monomer, focused ion beam, mechanical-properties, morphology, natural-rubber, particles, scanning acoustic microscopy, scanning electron microscopy, sulfur, thermal-stability, vulcanization, Composite soft materials, Cross-link densities, Crosslink density, Crosslinking, Density (specific gravity), Ethylene, Ethylene propylene diene monomer, Flory-rehner, Focused ion beam - scanning electron microscopy, Focused ion beam-scanning electron microscopies, Ii-vi semiconductors, Monomers, Moving die rheometers, Physical and mechanical properties, Propylene, Relaxation analysis, Rubber, Scanning acoustic microscopy, Scanning electron microscopy, Stress relaxation, Sulfur contents, Temperature scanning stress relaxations, Zinc oxide

Noguchi, H, Tozzi, C, Arroyo, M, (2022). Binding of anisotropic curvature-inducing proteins onto membrane tubes Soft Matter 18, 3384-3394

We studied how anisotropic proteins are orientationally ordered and change the radius of membrane tubes using mean-field theory with an orientation-dependent excluded volume interaction.

JTD Keywords: bar, density, driven, generation, inclusions, invagination, mechanisms, monte-carlo, tubulation, Mediated aggregation

Lozano-Hernández, N, Llanos, GP, Comet, CS, del Valle, LJ, Puiggali, J, Fontdecaba, E, (2022). Micro- and Nanotexturization of Liquid Silicone Rubber Surfaces by Injection Molding Using Hybrid Polymer Inlays Macromolecular Materials And Engineering 307, 2100741

Micro- and nanotexturization of surfaces can give to the parts different advanced functionalities, such as superhydrophobicity, self-cleaning, or antibacterial capabilities. These advanced properties in combination with the biocompatibility of Liquid Silicone Rubber are an interesting approach for obtaining high-performance medical devices. The industrial production of surface textures in polymeric materials is through the replication technique, and the best option to attain a high production rate is injection molding. Moreover, its low viscosity during processing can provide an accurate replication capacity by the easy filling by capillarity of the microtextures. An innovative replicating technique for Liquid Silicone Rubber is presented by studying the replication of different shaped textures within a diameter range of between 2 and 50 mu m. The copying process consists in the overmolding of a textured polymeric inlay obtained by nanoimprint lithography. At the end of the process, a textured part is obtained, while the imprinted film remains in the mold. The injection molding parameters are optimized to increase the replication accuracy, and their effect on texture replicability is analyzed and discussed. Finally, it is shown that the textured surfaces improve their wettability behavior, which is a necessary and important characteristic in the development of biomedical devices.

JTD Keywords: Cross-linking density, Injection molding, Microtextures, Nanoimprint lithography, Polymeric inlays, Silicone rubber, Stamp, Wettability

Andrian, T, Pujals, S, Albertazzi, L, (2021). Quantifying the effect of PEG architecture on nanoparticle ligand availability using DNA-PAINT Nanoscale Advances 3, 6876-6881

The importance of PEG architecture on nanoparticle (NP) functionality is known but still difficult to investigate, especially at a single particle level. Here, we apply DNA Point Accumulation for Imaging in Nanoscale Topography (DNA-PAINT), a super-resolution microscopy (SRM) technique, to study the surface functionality in poly(lactide-co-glycolide)-poly(ethylene glycol) (PLGA-PEG) NPs with different PEG structures. We demonstrated how the length of the PEG spacer can influence the accessibility of surface chemical functionality, highlighting the importance of SRM techniques to support the rational design of functionalized NPs.

JTD Keywords: chain-length, density, plga, surface, systems, Chain-length, Density, Dna, Microscopy technique, Nanoparticles, Nanoscale topography, Paint, Peg spacers, Plga, Poly lactide-co-glycolide, Poly-lactide-co-glycolide, Polyethylene glycols, Polylactide-co-glycolide, Single-particle, Super-resolution microscopy, Superresolution microscopy, Surface, Surface chemicals, Surface functionalities, Systems

Riera, Roger, Hogervorst, Tim P., Doelman, Ward, Ni, Yan, Pujals, Silvia, Bolli, Evangelia, Codée, Jeroen DC., van Kasteren, Sander I., Albertazzi, Lorenzo, (2021). Single-molecule imaging of glycan–lectin interactions on cells with Glyco-PAINT Nature Chemical Biology 17, 1281-1288

Most lectins bind carbohydrate ligands with relatively low affinity, making the identification of optimal ligands challenging. Here we introduce a point accumulation in nanoscale topography (PAINT) super-resolution microscopy method to capture weak glycan-lectin interactions at the single-molecule level in living cells (Glyco-PAINT). Glyco-PAINT exploits weak and reversible sugar binding to directly achieve single-molecule detection and quantification in cells and is used to establish the relative kon and koff rates of a synthesized library of carbohydrate-based probes, as well as the diffusion coefficient of the receptor-sugar complex. Uptake of ligands correlates with their binding affinity and residence time to establish structure-function relations for various synthetic glycans. We reveal how sugar multivalency and presentation geometry can be optimized for binding and internalization. Overall, Glyco-PAINT represents a powerful approach to study weak glycan-lectin interactions on the surface of living cells, one that can be potentially extended to a variety of lectin-sugar interactions.© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.

JTD Keywords: dc-sign, density, dimerization, endocytosis, lateral mobility, ligand-binding, mannose receptor, proteins, recognition, Animal, Animals, Cell membrane, Cell membrane permeability, Chemistry, Cho cell line, Cho cells, Cricetulus, Cysteine-rich domain, Kinetics, Lectin, Lectins, Ligand, Ligands, Molecular library, Multivariate analysis, Polysaccharide, Polysaccharides, Procedures, Protein binding, Single molecule imaging, Small molecule libraries, Structure activity relation, Structure-activity relationship

Morgado, A, Najera, F, Lagunas, A, Samitier, J, Vida, Y, Perez-Inestrosa, E, (2021). Slightly congested amino terminal dendrimers. The synthesis of amide-based stable structures on a large scale Polymer Chemistry 12, 5168-5177

Nowadays, amino terminal dendrimers are appealing materials for biological applications due to their multivalence and the versatile conjugation of the amino groups. However, the high reactivity of these terminal groups can be decreased by steric hindrance, limiting their possible bioapplications. Herein, we report the divergent synthesis of slightly sterically hindered amino terminal polyamide dendrimers. A simple and unique AB(2) scaffold has been chosen to build the dendritic structures, where only amide bonds have been used as the connecting unit. The 1-7 relative positions of the amino groups in the AB(2) monomers avoid the steric congestion of the macromolecules, allowing the construction of robust dendrimers up to the fifth generation. The construction of the dendrimers is based on two well-established reactions, using simple and cheap reactants, with yields above 90% on a gram scale and easy purification procedures. This synthetic methodology constitutes an easy and efficient way for the preparation of stable and aqueous soluble dendrimers on a gram scale, representing a substantial improvement over the synthesis of this kind of aliphatic polyamide amino terminal dendrimer. The prepared structures were completely characterized and evaluated by size exclusion chromatography, diffusion ordered spectroscopy and atomic force microscopy to determine their size. Molecular dynamics simulations were also carried out and the values obtained were consistent with the experimentally determined values.

JTD Keywords: Density, Discovery, Pamam dendrimers, Polymers

Andrian, T, Delcanale, P, Pujals, S, Albertazzi, L, (2021). Correlating Super-Resolution Microscopy and Transmission Electron Microscopy Reveals Multiparametric Heterogeneity in Nanoparticles Nano Letters 21, 5360-5368

The functionalization of nanoparticles with functional moieties is a key strategy to achieve cell targeting in nanomedicine. The interplay between size and ligand number is crucial for the formulation performance and needs to be properly characterized to understand nanoparticle structure-activity relations. However, there is a lack of methods able to measure both size and ligand number at the same time and at the single particle level. Here, we address this issue by introducing a correlative light and electron microscopy (CLEM) method combining super-resolution microscopy (SRM) and transmission electron microscopy (TEM) imaging. We apply our super-resCLEM method to characterize the relationship between size and ligand number and density in PLGA-PEG nanoparticles. We highlight how heterogeneity found in size can impact ligand distribution and how a significant part of the nanoparticle population goes completely undetected in the single-technique analysis. Super-resCLEM holds great promise for the multiparametric analysis of other parameters and nanomaterials.

JTD Keywords: cellular uptake, correlative light and electron microscopy (clem), density, electron microscopy (em), functionalization, heterogeneity, nanomedicine, nanoparticles, pegylation, plga, progress, quantification, size, Correlative light and electron microscopy (clem), Electron microscopy (em), Heterogeneity, Nanomedicine, Nanoparticles, Physicochemical characterization, Super-resolution microscopy (srm)

Rodríguez-Pereira, Cristina, Lagunas, Anna, Casanellas, Ignasi, Vida, Yolanda, Pérez-Inestrosa, Ezequiel, Andrades, José A., Becerra, José, Samitier, Josep, Blanco, Francisco J., Magalhães, Joana, (2020). RGD-dendrimer-poly(L-lactic) acid nanopatterned substrates for the early chondrogenesis of human mesenchymal stromal cells derived from osteoarthritic and healthy donors Materials 13, (10), 2247

Aiming to address a stable chondrogenesis derived from mesenchymal stromal cells (MSCs) to be applied in cartilage repair strategies at the onset of osteoarthritis (OA), we analyzed the effect of arginine–glycine–aspartate (RGD) density on cell condensation that occurs during the initial phase of chondrogenesis. For this, we seeded MSC-derived from OA and healthy (H) donors in RGD-dendrimer-poly(L-lactic) acid (PLLA) nanopatterned substrates (RGD concentrations of 4 × 10−9, 10−8, 2.5 × 10−8, and 10−2 w/w), during three days and compared to a cell pellet conventional three-dimensional culture system. Molecular gene expression (collagens type-I and II–COL1A1 and COL2A1, tenascin-TNC, sex determining region Y-box9-SOX9, and gap junction protein alpha 1–GJA1) was determined as well as the cell aggregates and pellet size, collagen type-II and connexin 43 proteins synthesis. This study showed that RGD-tailored first generation dendrimer (RGD-Cys-D1) PLLA nanopatterned substrates supported the formation of pre-chondrogenic condensates from OA- and H-derived human bone marrow-MSCs with enhanced chondrogenesis regarding the cell pellet conventional system (presence of collagen type-II and connexin 43, both at the gene and protein level). A RGD-density dependent trend was observed for aggregates size, in concordance with previous studies. Moreover, the nanopatterns’ had a higher effect on OA-derived MSC morphology, leading to the formation of bigger and more compact aggregates with improved expression of early chondrogenic markers.

JTD Keywords: Cell condensation, Gap junctions, RGD-density, Chondrogenic differentiation, Osteoarthritis

Estrada, L., Torres, A., Sarlabous, L., Jané, R., (2018). Onset and offset estimation of the neural inspiratory time in surface diaphragm electromyography: A pilot study in healthy subjects IEEE Journal of Biomedical and Health Informatics 22, (1), 67-76

This study evaluates the onset and offset of neural inspiratory time estimated from surface diaphragm electromyographic (EMGdi) recordings. EMGdi and airflow signals were recorded in ten healthy subjects according to two respiratory protocols based on respiratory rate (RR) increments, from 15 to 40 breaths per minute (bpm), and fractional inspiratory time (Ti/Ttot) decrements, from 0.54 to 0.18. The analysis of diaphragm electromyographic (EMGdi) signal amplitude is an alternative approach for the quantification of neural respiratory drive (NRD). The EMGdi amplitude was estimated using the fixed sample entropy computed over a 250 ms moving window of the EMGdi signal (EMGdifse). The neural onset was detected through a dynamic threshold over the EMGdifse using the kernel density estimation method, while neural offset was detected by finding when the EMGdifse had decreased to 70 % of the peak value reached during inspiration. The Bland-Altman analysis between airflow and neural onsets showed a global bias of 46 ms in the RR protocol and 22 ms in the Ti/Ttot protocol. The Bland-Altman analysis between airflow and neural offsets reveals a global bias of 11 ms in the RR protocol and -2 ms in the Ti/Ttot protocol. The relationship between pairs of RR values (Pearson’s correlation coefficient of 0.99, Bland- Altman limits of -2.39 to 2.41 bpm, and mean bias of 0.01 bpm) and between pairs of Ti/Ttot values (Pearson’s correlation coefficient of 0.86, Bland-Altman limits of -0.11 to 0.10, and mean bias of -0.01) showed a good agreement. In conclusion, we propose a method for determining neural onset and neural offset based on non-invasive recordings of the electrical activity of the diaphragm that requires no filtering of cardiac muscle interference.

JTD Keywords: Kernel density estimation (KDE),, Surface diaphragm electromyographic,, (EMGdi) signal,, Inspiratory time,, Neural respiratory drive (NRD),, Neural inspiratory time,, Fixed sample entropy (fSampEn)

Bosch, M., Castro, J., Sur, M., Hayashi, Y., (2017). Photomarking relocalization technique for correlated two-photon and electron microcopy imaging of single stimulated synapses Synapse Development - Methods and Protocols (Methods in Molecular Biology) (ed. Poulopoulos , A.), Humana Press (New York, USA) 1538, 185-214

Synapses learn and remember by persistent modifications of their internal structures and composition but, due to their small size, it is difficult to observe these changes at the ultrastructural level in real time. Two-photon fluorescence microscopy (2PM) allows time-course live imaging of individual synapses but lacks ultrastructural resolution. Electron microscopy (EM) allows the ultrastructural imaging of subcellular components but cannot detect fluorescence and lacks temporal resolution. Here, we describe a combination of procedures designed to achieve the correlated imaging of the same individual synapse under both 2PM and EM. This technique permits the selective stimulation and live imaging of a single dendritic spine and the subsequent localization of the same spine in EM ultrathin serial sections. Landmarks created through a photomarking method based on the 2-photon-induced precipitation of an electrodense compound are used to unequivocally localize the stimulated synapse. This technique was developed to image, for the first time, the ultrastructure of the postsynaptic density in which long-term potentiation was selectively induced just seconds or minutes before, but it can be applied for the study of any biological process that requires the precise relocalization of micron-wide structures for their correlated imaging with 2PM and EM.

JTD Keywords: Correlated imaging, DAB, Dendritic spine, Photobranding, Photoetching, Photomarking, Postsynaptic density, Serial-section transmission electron microscopy, Synapse, Time-lapse live two-photon fluorescence microscopy

Aragonès, A. C., Aravena, D., Cerdá, J. I., Acís-Castillo, Z., Li, H., Real, J. A., Sanz, F., Hihath, J., Ruiz, E., Díez-Pérez, I., (2016). Large conductance switching in a single-molecule device through room temperature spin-dependent transport Nano Letters 16, (1), 218-226

Controlling the spin of electrons in nanoscale electronic devices is one of the most promising topics aiming at developing devices with rapid and high density information storage capabilities. The interface magnetism or spinterface resulting from the interaction between a magnetic molecule and a metal surface, or vice versa, has become a key ingredient in creating nanoscale molecular devices with novel functionalities. Here, we present a single-molecule wire that displays large (>10000%) conductance switching by controlling the spin-dependent transport under ambient conditions (room temperature in a liquid cell). The molecular wire is built by trapping individual spin crossover FeII complexes between one Au electrode and one ferromagnetic Ni electrode in an organic liquid medium. Large changes in the single-molecule conductance (>100-fold) are measured when the electrons flow from the Au electrode to either an α-up or a β-down spin-polarized Ni electrode. Our calculations show that the current flowing through such an interface appears to be strongly spin-polarized, thus resulting in the observed switching of the single-molecule wire conductance. The observation of such a high spin-dependent conductance switching in a single-molecule wire opens up a new door for the design and control of spin-polarized transport in nanoscale molecular devices at room temperature.

JTD Keywords: Density functional calculations, Magnetoresistance, Single-molecule junctions, Spin orbit coupling, Spin-crossover complexes, Spinterface, STM break-junction

Blanchard, R., Morin, C., Malandrino, A., Vella, A., Sant, Z., Hellmich, C., (2016). Patient-specific fracture risk assessment of vertebrae: A multiscale approach coupling X-ray physics and continuum micromechanics International Journal for Numerical Methods in Biomedical Engineering , 32, (9), e02760

Summary: While in clinical settings, bone mineral density measured by computed tomography (CT) remains the key indicator for bone fracture risk, there is an ongoing quest for more engineering mechanics-based approaches for safety analyses of the skeleton. This calls for determination of suitable material properties from respective CT data, where the traditional approach consists of regression analyses between attenuation-related grey values and mechanical properties. We here present a physics-oriented approach, considering that elasticity and strength of bone tissue originate from the material microstructure and the mechanical properties of its elementary components. Firstly, we reconstruct the linear relation between the clinically accessible grey values making up a CT, and the X-ray attenuation coefficients quantifying the intensity losses from which the image is actually reconstructed. Therefore, we combine X-ray attenuation averaging at different length scales and over different tissues, with recently identified 'universal' composition characteristics of the latter. This gives access to both the normally non-disclosed X-ray energy employed in the CT-device and to in vivo patient-specific and location-specific bone composition variables, such as voxel-specific mass density, as well as collagen and mineral contents. The latter feed an experimentally validated multiscale elastoplastic model based on the hierarchical organization of bone. Corresponding elasticity maps across the organ enter a finite element simulation of a typical load case, and the resulting stress states are increased in a proportional fashion, so as to check the safety against ultimate material failure. In the young patient investigated, even normal physiological loading is probable to already imply plastic events associated with the hydrated mineral crystals in the bone ultrastructure, while the safety factor against failure is still as high as five.

JTD Keywords: Bone, Bone mass density, Continuum micromechanics, Elastoplasticity, Spine, Strength, X-ray physics

Arcentales, A., Voss, A., Caminal, P., Bayes-Genis, A., Domingo, M. T., Giraldo, B. F., (2013). Characterization of patients with different ventricular ejection fractions using blood pressure signal analysis CinC 2013 Computing in Cardiology Conference (CinC) , IEEE (Zaragoza, Spain) , 795-798

Ischemic and dilated cardiomyopathy are associated with disorders of myocardium. Using the blood pressure (BP) signal and the values of the ventricular ejection fraction, we obtained parameters for stratifying cardiomyopathy patients as low- and high-risk. We studied 48 cardiomyopathy patients characterized by NYHA ≥2: 19 patients with dilated cardiomyopathy (DCM) and 29 patients with ischemic cardiomyopathy (ICM). The left ventricular ejection fraction (LVEF) percentage was used to classify patients in low risk (LR: LVEF > 35%, 17 patients) and high risk (HR: LVEF ≤ 35%, 31 patients) groups. From the BP signal, we extracted the upward systolic slope (BPsl), the difference between systolic and diastolic BP (BPA), and systolic time intervals (STI). When we compared the LR and HR groups in the time domain analysis, the best parameters were standard deviation (SD) of 1=STI, kurtosis (K) of BPsl, and K of BPA. In the frequency domain analysis, very low frequency (VLF) and high frequency (HF) bands showed statistically significant differences in comaprisons of LR and HR groups. The area under the curve of power spectral density was the best parameter in all classifications, and particularly in the very-low-and high- frequency bands (p <; 0.001). These parameters could help to improve the risk stratification of cardiomyopathy patients.

JTD Keywords: blood pressure measurement, cardiovascular system, diseases, medical disorders, medical signal processing, statistical analysis, time-domain analysis, BP signal, HR groups, LR groups, blood pressure signal analysis, cardiomyopathy patients, diastolic BP, dilated cardiomyopathy, frequency domain analysis, high-frequency bands, ischemic cardiomyopathy, left ventricular ejection fraction, low-frequency bands, myocardium disorders, patient characterization, power spectral density curve, standard deviation, statistical significant differences, systolic BP, systolic slope, systolic time intervals, time domain analysis, ventricular ejection fraction, Abstracts, Databases, Parameter extraction, Telecommunication standards, Time-frequency analysis

Udina, S., Carmona, M., Pardo, A., Calaza, C., Santander, J., Fonseca, L., Marco, S., (2012). A micromachined thermoelectric sensor for natural gas analysis: Multivariate calibration results Sensors and Actuators B: Chemical 166-167, 338-348

The potential use of a micromachined thermopile based sensor device for analyzing natural gas is explored. The sensor consists of a thermally isolated hotplate which is heated by the application of a sequence of programmed voltages to an integrated heater. Once the hotplate reaches a stationary temperature, the thermopile provides a signal proportional to the hotplate temperature. These signals are processed in order to determine different natural gas properties. Sensor response is mainly dependent on the thermal conductivity of the surrounding gas at different temperatures. Seven predicted properties (normal density, Superior Heating Value, Wobbe index and the concentrations of methane, ethane, carbon dioxide and nitrogen) are calibrated against sensor signals by using multivariate regression, in particular Partial Least Squares. Experimental data have been used for calibration and validation. Results show property prediction capability with reasonable accuracy except for prediction of carbon dioxide concentration. A detailed uncertainty analysis is provided to better understand the metrological limits of the system. These results imply for the first time the possibility of designing unprecedented low-cost natural gas analyzers. The concept may be extended to other constrained gas mixtures (e.g. of a known number of components) to enable low-cost multicomponent gas analyzers.

JTD Keywords: Gas sensor, Natural gas, MEMS, Superior Heating Value, density, PLS

Solà, J., Fiz, J. A., Morera, J., Jané, R., (2012). Multiclass classification of subjects with sleep apnoea-hypopnoea syndrome through snoring analysis Medical Engineering and Physics , 34, (9), 1213-1220

The gold standard for diagnosing sleep apnoea-hypopnoea syndrome (SAHS) is polysomnography (PSG), an expensive, labour-intensive and time-consuming procedure. Accordingly, it would be very useful to have a screening method to allow early assessment of the severity of a subject, prior to his/her referral for PSG. Several differences have been reported between simple snorers and SAHS patients in the acoustic characteristics of snoring and its variability. In this paper, snores are fully characterised in the time domain, by their sound intensity and pitch, and in the frequency domain, by their formant frequencies and several shape and energy ratio measurements. We show that accurate multiclass classification of snoring subjects, with three levels of SAHS, can be achieved on the basis of acoustic analysis of snoring alone, without any requiring information on the duration or the number of apnoeas. Several classification methods are examined. The best of the approaches assessed is a Bayes model using a kernel density estimation method, although good results can also be obtained by a suitable combination of two binary logistic regression models. Multiclass snore-based classification allows early stratification of subjects according to their severity. This could be the basis of a single channel, snore-based screening procedure for SAHS.

JTD Keywords: Bayes classifier, Kernel density estimation, Sleep apnoea, Snoring

Garde, A., Giraldo, B.F., Jané, R., Latshang, T.D., Turk, A.J., Hess, T., Bosch, M-.M., Barthelmes, D., Hefti, J.P., Maggiorini, M., Hefti, U., Merz, T.M., Schoch, O.D., Bloch, K.E., (2012). Periodic breathing during ascent to extreme altitude quantified by spectral analysis of the respiratory volume signal Engineering in Medicine and Biology Society (EMBC) 34th Annual International Conference of the IEEE , IEEE (San Diego, USA) , 707-710

High altitude periodic breathing (PB) shares some common pathophysiologic aspects with sleep apnea, Cheyne-Stokes respiration and PB in heart failure patients. Methods that allow quantifying instabilities of respiratory control provide valuable insights in physiologic mechanisms and help to identify therapeutic targets. Under the hypothesis that high altitude PB appears even during physical activity and can be identified in comparison to visual analysis in conditions of low SNR, this study aims to identify PB by characterizing the respiratory pattern through the respiratory volume signal. A number of spectral parameters are extracted from the power spectral density (PSD) of the volume signal, derived from respiratory inductive plethysmography and evaluated through a linear discriminant analysis. A dataset of 34 healthy mountaineers ascending to Mt. Muztagh Ata, China (7,546 m) visually labeled as PB and non periodic breathing (nPB) is analyzed. All climbing periods within all the ascents are considered (total climbing periods: 371 nPB and 40 PB). The best crossvalidated result classifying PB and nPB is obtained with Pm (power of the modulation frequency band) and R (ratio between modulation and respiration power) with an accuracy of 80.3% and area under the receiver operating characteristic curve of 84.5%. Comparing the subjects from 1st and 2nd ascents (at the same altitudes but the latter more acclimatized) the effect of acclimatization is evaluated. SaO2 and periodic breathing cycles significantly increased with acclimatization (p-value <; 0.05). Higher Pm and higher respiratory frequencies are observed at lower SaO2, through a significant negative correlation (p-value <; 0.01). Higher Pm is observed at climbing periods visually labeled as PB with >; 5 periodic breathing cycles through a significant positive correlation (p-value <; 0.01). Our data demonstrate that quantification of the respiratory volum- signal using spectral analysis is suitable to identify effects of hypobaric hypoxia on control of breathing.

JTD Keywords: Frequency domain analysis, Frequency modulation, Heart, Sleep apnea, Ventilation, Visualization, Cardiology, Medical disorders, Medical signal processing, Plethysmography, Pneumodynamics, Sensitivity analysis, Sleep, Spectral analysis, Cheyne-Stokes respiration, Climbing periods, Dataset, Heart failure patients, High altitude PB, High altitude periodic breathing, Hypobaric hypoxia, Linear discriminant analysis, Pathophysiologic aspects, Physical activity, Physiologic mechanisms, Power spectral density, Receiver operating characteristic curve, Respiratory control, Respiratory frequency, Respiratory inductive plethysmography, Respiratory pattern, Respiratory volume signal, Sleep apnea, Spectral analysis, Spectral parameters

Garde, A., Sörnmo, L., Jané, R., Giraldo, B. F., (2010). Correntropy-based spectral characterization of respiratory patterns in patients with chronic heart failure IEEE Transactions on Biomedical Engineering 57, (8), 1964-1972

A correntropy-based technique is proposed for the characterization and classification of respiratory flow signals in chronic heart failure (CHF) patients with periodic or nonperiodic breathing (PB or nPB, respectively) and healthy subjects. The correntropy is a recently introduced, generalized correlation measure whose properties lend themselves to the definition of a correntropy-based spectral density (CSD). Using this technique, both respiratory and modulation frequencies can be reliably detected at their original positions in the spectrum without prior demodulation of the flow signal. Single-parameter classification of respiratory patterns is investigated for three different parameters extracted from the respiratory and modulation frequency bands of the CSD, and one parameter defined by the correntropy mean. The results show that the ratio between the powers in the modulation and respiratory frequency bands provides the best result when classifying CHF patients with either PB or nPB, yielding an accuracy of 88.9%. The correntropy mean offers excellent performance when classifying CHF patients versus healthy subjects, yielding an accuracy of 95.2% and discriminating nPB patients from healthy subjects with an accuracy of 94.4%.

JTD Keywords: Autoregressive (AR) modeling, Chronic heart failure (CHF), Correntropy spectral density (CSD), Linear classification, Periodic breathing (PB)

Garde, A., Sörnmo, L., Jané, R., Giraldo, B. F., (2010). Correntropy-based nonlinearity test applied to patients with chronic heart failure Engineering in Medicine and Biology Society (EMBC) 32nd Annual International Conference of the IEEE , IEEE (Buenos Aires, Argentina) , 2399-2402

In this study we propose the correntropy function as a discriminative measure for detecting nonlinearities in the respiratory pattern of chronic heart failure (CHF) patients with periodic or nonperiodic breathing pattern (PB or nPB, respectively). The complexity seems to be reduced in CHF patients with higher risk level. Correntropy reflects information on both, statistical distribution and temporal structure of the underlying dataset. It is a suitable measure due to its capability to preserve nonlinear information. The null hypothesis considered is that the analyzed data is generated by a Gaussian linear stochastic process. Correntropy is used in a statistical test to reject the null hypothesis through surrogate data methods. Various parameters, derived from the correntropy and correntropy spectral density (CSD) to characterize the respiratory pattern, presented no significant differences when extracted from the iteratively refined amplitude adjusted Fourier transform (IAAFT) surrogate data. The ratio between the powers in the modulation and respiratory frequency bands R was significantly different in nPB patients, but not in PB patients, which reflects a higher presence of nonlinearities in nPB patients than in PB patients.

JTD Keywords: Practical, Theoretical or Mathematical, Experimental/cardiology diseases, Fourier transforms, Medical signal processing, Pattern classification, Pneumodynamics, Spectral analysis, Statistical analysis, Stochastic processes/ correntropy based nonlinearity test, Chronic heart failure, Correntropy function, Respiratory pattern nonlinearities, CHF patients, Nonperiodic breathing pattern, Dataset statistical distribution, Dataset temporal structure, Nonlinear information, Null hypothesis, Gaussian linear stochastic process, Statistical test, Correntropy spectral density, Iteratively refined amplitude adjusted Fourier transform, Surrogate data, Periodic breathing pattern

Correa, L. S., Laciar, E., Mut, V., Giraldo, B. F., Torres, A., (2010). Multi-parameter analysis of ECG and Respiratory Flow signals to identify success of patients on weaning trials Engineering in Medicine and Biology Society (EMBC) 32nd Annual International Conference of the IEEE , IEEE (Buenos Aires, Argentina) -----, 6070-6073

Statistical analysis, power spectral density, and Lempel Ziv complexity, are used in a multi-parameter approach to analyze four temporal series obtained from the Electrocardiographic and Respiratory Flow signals of 126 patients on weaning trials. In which, 88 patients belong to successful group (SG), and 38 patients belong to failure group (FG), i.e. failed to maintain spontaneous breathing during trial. It was found that mean values of cardiac inter-beat and breath durations give higher values for SG than for FG; Kurtosis coefficient of the spectrum of the rapid shallow breathing index is higher for FG; also Lempel Ziv complexity mean values associated with the respiratory flow signal are bigger for FG. Patients were then classified with a pattern recognition neural network, obtaining 80% of correct classifications (81.6% for FG and 79.5% for SG).

JTD Keywords: Electrocardiography, Medical signal processing, Neural nets, Pattern recognition, Pneumodynamics, Signal classification, Statistical analysis, ECG, Kurtosis coefficient, Lempel Ziv complexity, Breath durations, Cardiac interbeat durations, Electrocardiography, Multiparameter analysis, Pattern recognition neural network, Power spectral density, Respiratory flow signals, Signal classification, Spontaneous breathing, Statistical analysis, Weaning trials

Arcentales, A., Giraldo, B. F., Caminal, P., Diaz, I., Benito, S., (2010). Spectral analysis of the RR series and the respiratory flow signal on patients in weaning process Engineering in Medicine and Biology Society (EMBC) 32nd Annual International Conference of the IEEE , IEEE (Buenos Aires, Argentina) , 2485-2488

A considerable number of patients in weaning process have problems to keep spontaneous breathing during the trial and after it. This study proposes to extract characteristic parameters of the RR series and respiratory flow signal according to the patients' condition in weaning test. Three groups of patients have been considered: 93 patients with successful trials (group S), 40 patients that failed to maintain spontaneous breathing (group F), and 21 patients who had successful weaning trials, but that had to be reintubated before 48 hours (group R). The characterization was performed using spectral analysis of the signals, through the power spectral density, cross power spectral density and Coherence method. The parameters were extracted on the three frequency bands (VLF, LF and HF), and the principal statistical differences between groups were obtained in bands of VLF and HF. The results show an accuracy of 76.9% in the classification of the groups S and F.

JTD Keywords: Biomedical measurement, Electrocardiography, Medical signal processing, Pneumodynamics, Spectral analysis, RR series, Coherence method, Cross power spectral density, Electrocardiography, Principal statistical differences, Respiratory flow signal, Spectral analysis, Spontaneous breathing, Weaning test