Performance of the PROSPECT leaf radiative transfer model version 4 for Norway spruce needles

Leaf optical properties (LOPs) are a key input parameter for vegetation canopy radiative transfer models. The uncertainty introduced in the measurement and/or the simulation of this spectral information determines a final reliability of the modelled canopy reflectance. The broad-leaf radiative transfer model PROSPECT version 3.01 has been previously applied for some needle-leaf type species (e.g. pine trees) to estimate biochemical parameters through its inversion. Nevertheless, in a particular case of Norway spruce (Picea abies (L.) Karst.) PROSPECT 3.01 showed a poor performance in near infrared wavelengths and had to be recalibrated. Therefore, the applicability of PROSPECT version 4, which has been recently released, is verified for this type of leaves in this experiment. Forward simulations of an optimized version of the original PROSPECT 4 suggest that it is possible to reduce the average RMSE of reflectance and transmittance from 8% to 3.5- 4 % in the near infrared domain. For this achievement, the absorption coefficients for chlorophyll and dry matter together with the refractive index had to be simultaneously optimized via model inversion using measured LOPs of Norway spruce needles

Valores sociales en los spots publicitarios de bebidas emitidos en España en el 2006

El objetivo principal de este artículo es señalar los valores sociales presentes en los spots de bebidas emitidos por televisión, en España, durante el año 2006. Se estudian los valores sociales que transmiten los anuncios al margen de su función comercial. En total, se han analizado 191 spots; para los que se detallan los valores atribuidos al producto y al consumidor. La salud, la juventud, la importancia de las relaciones sociales o de construirse una personalidad genuina son algunos de los principales valores e ideales transmitidos a través de los spots sometidos a estudio

The exoskeleton for gait rehabilitation ALICE: dynamic analysis and control system evaluation using Hamilton quaternions

[EN] A robotic exoskeleton is an electromechanical device that can be worn by a person to increase its physical capacity, to assist locomotion or for gait rehabilitation processes. In the case of rehabilitation exoskeletons, the control system is required to be smooth and capable to match accurately with the patients’ evolution in order to optimize the eciency of their recovery, this implies the design of robust and precise controllers. In this paper, kinematic analysis, dynamic analysis and control system evaluation for ALICE rehabilitation exoskeleton is presented. Among the control techniques used are: the PD controller, adaptive PD, and the sliding mode controller. In addition, a stability analysis using the Lyapunov criterion is performed. To test the performance of the controllers, gait data obtained by the ONCE School of  Physiotherapy in Madrid, which correspond to healthy people and people with multiple sclerosis, are used. MATLAB as simulation software and programming language is used.[ES] Un exoesqueleto robótico es un dispositivo electromecánico utilizado para aumentar la capacidad física de una persona, como ayuda a la locomoción o para procesos de rehabilitación de la marcha. En el caso de los exoesqueletos de rehabilitación se requiere que el sistema de control sea capaz de adaptarse adecuadamente a la evolución del paciente con el fin de optimizar su recuperación, esto implica el diseño de controladores robustos y precisos. En este trabajo se presenta el análisis cinemático, análisis dinámico y evaluación del sistema de control del exoesqueleto de rehabilitación ALICE. Dentro de las técnicas de control presentadas se encuentran: el controlador PD, PD adaptativo, y el controlador en modo deslizante. Además, se realiza un análisis de estabilidad utilizando el criterio de Lyapunov. Para probar el rendimiento de los reguladores, se utiliza un conjunto de datos de la Escuela de Fisioterapia de la ONCE de Madrid, correspondiente a personas sanas y personas con esclerosis múltiple. Se utiliza MATLAB como software de simulación y lenguaje de programación.Manuel Cardona agradece a la Fundación Carolina y a la Universidad Politécnica de Madrid, España, por el apoyo para la realización de esta investigación gracias a la beca de Doctorado otorgada en el marco del convenio con la Universidad Don Bosco, El Salvador.Cardona, M.; Serrano, F.; Martín, JA.; Rausell, E.; Saltaren, R.; García-Cena, C. (2020). El exoesqueleto de rehabilitación de la marcha ALICE: análisis dinámico y evaluación del sistema de control utilizando cuaternios de Hamilton. Revista Iberoamericana de Automática e Informática industrial. 18(1):48-57. https://doi.org/10.4995/riai.2020.12558OJS4857181Abolvafaei, M., Ganjefar, S., 2019. Maximum power extraction from a wind turbine using second-order fast terminal sliding mode control. Renewable Energy 139, 1437 - 1446. https://doi.org/10.1016/j.renene.2019.03.044Arnold, E. M., Ward, S. R., Lieber, R. L., Delp, S. L., 2010. A model of the lower limb for analysis of human movement.Cardona, M., Destarac, M. A., García, C. E., Nov 2017. Exoskeleton robots for rehabilitation: State of the art and future trends. In: 2017 IEEE 37th Central America and Panama Convention (CONCAPAN XXXVII). pp. 1-6. https://doi.org/10.1109/CONCAPAN.2017.8278480Cardona, M., García Cena, C. E., 2019a. Biomechanical analysis of the lower limb: A full-body musculoskeletal model for muscle-driven simulation. IEEE Access 7, 92709-92723. https://doi.org/10.1109/ACCESS.2019.2927515Cardona, M., García Cena, C. E., October 2019b. Musculoskeletal modeling as a tool for biomechanical analysis of normal and pathological gait. VIII Latin American Conference on Biomedical Engineering and XLII National Conference on Biomedical Engineering. CLAIB 2019. IFMBE Proceedings, Springer 75, 955-963. https://doi.org/10.1007/978-3-030-30648-9_124Chong, L., Jianfeng, S., Linhong, J., 2013. Lower limb rehabilitation robots: A review. In: World Congress on Medical Physics and Biomedical Engineering. IFMBE Proceedings. Vol. 39. p. 2042-2045. https://doi.org/10.1007/978-3-642-29305-4_536Eker, I., 2010. Second-order sliding mode control with experimental application. ISA Transactions 49 (3), 394 - 405. https://doi.org/10.1016/j.isatra.2010.03.010He, W., Li, Z., Dong, Y., Zhao, T., Jan 2019. Design and adaptive control for an upper limb robotic exoskeleton in presence of input saturation. IEEE Transactions on Neural Networks and Learning Systems 30 (1), 97-108. DOI: 10.1109/TNNLS.2018.2828813 https://doi.org/10.1109/TNNLS.2018.2828813Kapandji, A., 2010. Fisiología Articular, 6th Edition. Vol. 2. Editorial Panamericana, France.Maciejasz, P., Eschweiler, J., Gerlach-Hahn, K., et.al., 2014. "A survey on robotic devices for upper limb rehabilitation". https://doi.org/10.1186/1743-0003-11-3Proietti, T., Jarrasse, N., Roby-Brami, A., Morel, G., April 2015. Adaptive control of a robotic exoskeleton for neurorehabilitation. In: 2015 7th International IEEE/EMBS Conference on Neural Engineering (NER). pp. 803-806. https://doi.org/10.1109/NER.2015.7146745Reinkensmeyer, D. J., 2003. How to retrain movement after neurologic injury: a computational rationale for incorporating robot (or therapist) assistance. In: Proceedings of the 25th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (IEEE Cat. No.03CH37439). Vol. 2. pp. 1479-1482 Vol.2.Reinkensmeyer, D. J., Aoyagi, D., Emken, J., Galvez, J., Ichinose W, W., etal, Aug-Sep 2006. Tools for understanding and optimizing robotic gait training. J Rehabil Res Dev 43 (5), 657-70. https://doi.org/10.1682/JRRD.2005.04.0073Riener, R., Guidali, M., Keller, U., Duschau-Wicke, A., et.al., 2014. "a survey on robotic devices for upper limb rehabilitation".Serrano, F. E., Rossell, J. M., 2015. Complete kinematic analysis of the stewartgough platform by unit quaternions. Mechanics and Control (Vol, 34, no. 4), 59-69.Spong, M., Hutchinson, S., Vidyasagar, M., 2006. Robot Modeling and Control. John Wiley and Sons.Wang, J.-Y., Liang, H.-Z., Sun, Z.-W., Wu, S.-N., Zhang, S.-J., 2013. Relative motion coupled control based on dual quaternion. Aerospace Science and Technology 25 (1), 102 - 113. https://doi.org/10.1016/j.ast.2011.12.013Wu, Q., Chen, B., Wu, H., 2019. Rbfn-based adaptive backstepping sliding mode control of an upper-limb exoskeleton with dynamic uncertainties. IEEE Access 7, 134635-134646. https://doi.org/10.1109/ACCESS.2019.2941973Yakub, F., Khudzari, A., Mori, Y., March 2014. "recent trends for practical rehabilitation robotics, current challenges and the future". https://doi.org/10.1097/MRR.0000000000000035Yang, Z., Zhu, Y., Yang, X., Zhang, Y., Aug 2009. Impedance control of exoskeleton suit based on adaptive rbf neural network. In: 2009 International Conference on Intelligent Human-Machine Systems and Cybernetics. Vol. 1. pp. 182-187. https://doi.org/10.1109/IHMSC.2009.54Zhou, W., Chen, W., Liu, H., Li, X., 2015. A new forward kinematic algorithm for a general stewart platform. Mechanism and Machine Theory 87, 177 - 190. https://doi.org/10.1016/j.mechmachtheory.2015.01.002Özgur, E., Mezouar, Y., 2016. Kinematic modeling and control of a robot arm ¨ using unit dual quaternions. Robotics and Autonomous Systems 77, 66 - 73. https://doi.org/10.1016/j.robot.2015.12.005Ilyas Eker, 2010. Second-order sliding mode control with experimental application. ISA Transactions 49 (3), 394 - 405. https://doi.org/10.1016/j.isatra.2010.03.01

Composite structural motifs of binding sites for delineating biological functions of proteins

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs which represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures.Comment: 34 pages, 7 figure

Severe hematopoietic stem cell inflammation compromises chronic granulomatous disease gene therapy

X-linked chronic granulomatous disease (CGD) is associated with defective phagocytosis, life-threatening infections, and inflammatory complications. We performed a clinical trial of lentivirus-based gene therapy in four patients (NCT02757911). Two patients show stable engraftment and clinical benefits, whereas the other two have progressively lost gene-corrected cells. Single-cell transcriptomic analysis reveals a significantly lower frequency of hematopoietic stem cells (HSCs) in CGD patients, especially in the two patients with defective engraftment. These two present a profound change in HSC status, a high interferon score, and elevated myeloid progenitor frequency. We use elastic-net logistic regression to identify a set of 51 interferon genes and transcription factors that predict the failure of HSC engraftment. In one patient, an aberrant HSC state with elevated CEBPβ expression drives HSC exhaustion, as demonstrated by low repopulation in a xenotransplantation model. Targeted treatments to protect HSCs, coupled to targeted gene expression screening, might improve clinical outcomes in CGD

Structure-guided selection of specificity determining positions in the human kinome

Background: The human kinome contains many important drug targets. It is well-known that inhibitors of protein kinases bind with very different selectivity profiles. This is also the case for inhibitors of many other protein families. The increased availability of protein 3D structures has provided much information on the structural variation within a given protein family. However, the relationship between structural variations and binding specificity is complex and incompletely understood. We have developed a structural bioinformatics approach which provides an analysis of key determinants of binding selectivity as a tool to enhance the rational design of drugs with a specific selectivity profile. Results: We propose a greedy algorithm that computes a subset of residue positions in a multiple sequence alignment such that structural and chemical variation in those positions helps explain known binding affinities. By providing this information, the main purpose of the algorithm is to provide experimentalists with possible insights into how the selectivity profile of certain inhibitors is achieved, which is useful for lead optimization. In addition, the algorithm can also be used to predict binding affinities for structures whose affinity for a given inhibitor is unknown. The algorithm’s performance is demonstrated using an extensive dataset for the human kinome. Conclusion: We show that the binding affinity of 38 different kinase inhibitors can be explained with consistently high precision and accuracy using the variation of at most six residue positions in the kinome binding site. We show for several inhibitors that we are able to identify residues that are known to be functionally important

Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification

Identification of catalytic residues (CR) is essential for the characterization of enzyme function. CR are, in general, conserved and located in the functional site of a protein in order to attain their function. However, many non-catalytic residues are highly conserved and not all CR are conserved throughout a given protein family making identification of CR a challenging task. Here, we put forward the hypothesis that CR carry a particular signature defined by networks of close proximity residues with high mutual information (MI), and that this signature can be applied to distinguish functional from other non-functional conserved residues. Using a data set of 434 Pfam families included in the catalytic site atlas (CSA) database, we tested this hypothesis and demonstrated that MI can complement amino acid conservation scores to detect CR. The Kullback-Leibler (KL) conservation measurement was shown to significantly outperform both the Shannon entropy and maximal frequency measurements. Residues in the proximity of catalytic sites were shown to be rich in shared MI. A structural proximity MI average score (termed pMI) was demonstrated to be a strong predictor for CR, thus confirming the proposed hypothesis. A structural proximity conservation average score (termed pC) was also calculated and demonstrated to carry distinct information from pMI. A catalytic likeliness score (Cls), combining the KL, pC and pMI measures, was shown to lead to significantly improved prediction accuracy. At a specificity of 0.90, the Cls method was found to have a sensitivity of 0.816. In summary, we demonstrate that networks of residues with high MI provide a distinct signature on CR and propose that such a signature should be present in other classes of functional residues where the requirement to maintain a particular function places limitations on the diversification of the structural environment along the course of evolution

Characterization of pathogenic germline mutations in human Protein Kinases

Background Protein Kinases are a superfamily of proteins involved in crucial cellular processes such as cell cycle regulation and signal transduction. Accordingly, they play an important role in cancer biology. To contribute to the study of the relation between kinases and disease we compared pathogenic mutations to neutral mutations as an extension to our previous analysis of cancer somatic mutations. First, we analyzed native and mutant proteins in terms of amino acid composition. Secondly, mutations were characterized according to their potential structural effects and finally, we assessed the location of the different classes of polymorphisms with respect to kinase-relevant positions in terms of subfamily specificity, conservation, accessibility and functional sites.<p></p> Results Pathogenic Protein Kinase mutations perturb essential aspects of protein function, including disruption of substrate binding and/or effector recognition at family-specific positions. Interestingly these mutations in Protein Kinases display a tendency to avoid structurally relevant positions, what represents a significant difference with respect to the average distribution of pathogenic mutations in other protein families.<p></p> Conclusions Disease-associated mutations display sound differences with respect to neutral mutations: several amino acids are specific of each mutation type, different structural properties characterize each class and the distribution of pathogenic mutations within the consensus structure of the Protein Kinase domain is substantially different to that for non-pathogenic mutations. This preferential distribution confirms previous observations about the functional and structural distribution of the controversial cancer driver and passenger somatic mutations and their use as a proxy for the study of the involvement of somatic mutations in cancer development.<p></p&gt

Improving Cry8Ka toxin activity towards the cotton boll weevil (Anthonomus grandis)

<p>Abstract</p> <p>Background</p> <p>The cotton boll weevil (<it>Anthonomus grandis</it>) is a serious insect-pest in the Americas, particularly in Brazil. The use of chemical or biological insect control is not effective against the cotton boll weevil because of its endophytic life style. Therefore, the use of biotechnological tools to produce insect-resistant transgenic plants represents an important strategy to reduce the damage to cotton plants caused by the boll weevil. The present study focuses on the identification of novel molecules that show improved toxicity against the cotton boll weevil. <it>In vitro </it>directed molecular evolution through DNA shuffling and phage display screening was applied to enhance the insecticidal activity of variants of the Cry8Ka1 protein of <it>Bacillus thuringiensis</it>.</p> <p>Results</p> <p>Bioassays carried out with <it>A. grandis </it>larvae revealed that the LC₅₀of the screened mutant Cry8Ka5 toxin was 3.15-fold higher than the wild-type Cry8Ka1 toxin. Homology modelling of Cry8Ka1 and the Cry8Ka5 mutant suggested that both proteins retained the typical three-domain Cry family structure. The mutated residues were located mostly in loops and appeared unlikely to interfere with molecular stability.</p> <p>Conclusions</p> <p>The improved toxicity of the Cry8Ka5 mutant obtained in this study will allow the generation of a transgenic cotton event with improved potential to control <it>A. grandis</it>.</p