Modal contribution and state space order selection in operational modal analysis

The estimation of modal parameters of a structure from ambient measurements has attracted the attention of many researchers in the last years. The procedure is now well established and the use of state space models, stochastic system identification methods and stabilization diagrams allows to identify the modes of the structure. In this paper the contribution of each identified mode to the measured vibration is discussed. This modal contribution is computed using the Kalman filter and it is an indicator of the importance of the modes. Also the variation of the modal contribution with the order of the model is studied. This analysis suggests selecting the order for the state space model as the order that includes the modes with higher contribution. The order obtained using this method is compared to those obtained using other well known methods, like Akaike criteria for time series or the singular values of the weighted projection matrix in the Stochastic Subspace Identification method. Finally, both simulated and measured vibration data are used to show the practicability of the derived technique. Finally, it is important to remark that the method can be used with any identification method working in the state space model.

Análisis dinámico experimental de edificios esbeltos

Es conocido que la variación del comportamiento dinámico de las estructuras puede ser empleado dentro de un sistema de monitorización de su integridad estructural. Así, este estudio tiene como objetivo comprender el comportamiento dinámico de edificios esbeltos, frente a diferentes agentes ambientales como la temperatura y/o dirección y velocidad del viento. En el marco de esta investigación, se estudian dos edificios: la Torre de la ETSI (Escuela Técnica Superior de Ingenieros) de Caminos, Canales y Puertos de la UPM (Universidad Politécnica de Madrid) y un edificio de viviendas situado en la calle de Arturo Soria de Madrid. Los datos medioambientales antes mencionados, se registraron con sendas estacionales meteorológicas situadas en las azoteas de ambos edificios. Se realiza el análisis modal operacional de ambas estructuras. Este análisis se realiza a partir de las mediciones de las aceleraciones ante excitaciones ambientales, es un análisis basado sólo en la respuesta de la estructura. Por tanto, no es necesario interrumpir el funcionamiento en servicio de la instalación, obteniendo su comportamientos en este estado. A partir de este análisis, se obtienen las frecuencias naturales, los amortiguamientos modales y las formas modales. Así, en este trabajo se ha estudiado la relación existente entre la variación en la estimación de las frecuencias naturales y la variación de los agentes ambientales (fundamentalmente la temperatura). Los ensayos dinámicos en los dos edificios mencionados anteriormente, se han realizado utilizando acelerómetros de alta sensibilidad sincronizados inalámbricamente, lo cual ha simplificado el trabajo experimental si lo comparamos con los sistemas tradicionales. Como resultado del trabajo realizado se pueden destacar los siguientes puntos: (i) se ha visto que con el equipamiento disponible se pueden realizar análisis dinámicos de edificios, (ii) se ha mejorado el conocimiento dinámico de estas estructuras, y (iii) se ha visto la importancia que pueden tener los agentes ambientales dependiendo por un lado del tipo estructura del edificio. A partir del trabajo, se podrían actualizar modelos matemáticos que sirvan para la predicción de daños en las estructuras, y por otro, se podrán eliminar los efectos de los agentes ambientales, lo cual es un punto vital si se quiere emplear los parámetros modales para el cálculo de indices de daño. La aplicación de este tipo de investigación ayudará a tener una información mayor sobre el comportamiento de las estructuras y así, en el futuro, poder realizar distintos tipos de procesos, como la formulación de modelos matemáticos que reflejen con mayor fidelidad el comportamiento real. De esta forma, la monitorización de los agentes medioambientales permitirán valorar la influencia de estas variaciones sobre la estructura pudiéndose eliminar estos efectos. Con ello, se mejora la incertidumbre en la variación de frecuencias que puede ser utilizada como un sistema de activación de alarmas frente a la detección de daños estructurales. It is known that the variation of the dynamic behavior of structures can be used within a system to monitor structural integrity. So, this study aims to understand the dynamic behavior of slender buildings, against different environmental agents such as temperature and / or wind direction and velocity. As part of this investigation, two buildings are studied: the ETSI's (Escuela Técnica Superior de Ingenieros) main tower of Escuela de Caminos, Canales y Puertos of UPM (Universidad Politécnica de Madrid) and a residential building located in the streets Arturo Soria Madrid. The environmental data were recorded with weather stations located on the roof of both buildings. In both structures a modal operational analysis has been carried out. This analysis is performed from the measurements of the acceleration to the environmental excitation, this analysis is based only on the response of the structure. Therefore, it is not necessary to interrupt the operation of the structure, getting its behavior in this state. From this analysis, the natural frequencies, modal damping and mode shapes are obtained. So, in this work we have studied the existing relationship between the variation in the estimate of the natural frequencies and the variation of environmental agents (mainly temperature). The dynamic tests in the two buildings mentioned above, have been made using high-sensitivity accelerometers wirelessly synchronized, which has simplified the experimental work when compared to traditional systems. As a result of work performed can highlight the following points: (i) it has been found that with the available equipment can perform dynamic analysis of buildings, (ii) has improved dynamic knowledge of these structures, and, (iii) can be seen the potential importance of environmental agents depending on the type of building structure. From the work, mathematical models can be updated that serve to prediction of damage to structures, and on the other side, may eliminate the effects of environmental agents, which is a vital point if you want to use the modal parameters for calculating damage ratings. The application of this type of research will help to have more information about the behavior of structures and so, in the future, conduct various processes, as the formulation of mathematical models that reflect more accurately an actual behavior. In this way the monitoring of environmental agents will allow evaluate the influence of these variations on the structure being possible eliminate these effects. Thereby, improvement the uncertainty in the frequencies variation that can be used as an alarm activation system from detection of structural damage.

Clustering basado en redes bayesianas con predictoras continuas: aplicaciones en neurociencia

Desentrañar el funcionamiento del cerebro es uno de los principales desafíos a los que se enfrenta la ciencia actual. Un área de estudio que ha despertado muchas expectativas e interés es el análisis de la estructura cortical desde el punto de vista morfológico, de manera que se cree una simulación del cerebro a nivel molecular. Con ello se espera poder profundizar en el estudio de numerosas enfermedades neurológicas y patológicas. Con el desarrollo de este proyecto se persigue el estudio del soma y de las espinas desde el punto de vista de la neuromorfología teórica. Es común en el estado del arte que en el análisis de las características morfológicas de una neurona en tres dimensiones el soma sea ignorado o, en el mejor de los casos, que sea sustituido por una simple esfera. De hecho, el concepto de soma resulta abstracto porque no se dispone de una dfinición estricta y robusta que especifique exactamente donde finaliza y comienzan las dendritas. En este proyecto se alcanza por primera vez una definición matemática de soma para determinar qué es el soma. Con el fin de simular somas se ahonda en los atributos utilizados en el estado del arte. Estas propiedades, de índole genérica, no especifican una morfología única. Es por ello que se propone un método que agrupe propiedades locales y globales de la morfología. En disposición de las características se procede con la categorización del cuerpo celular en distintas clases a partir de un nuevo subtipo de red bayesiana dinámica adaptada al espacio. Con ello se discute la existencia de distintas clases de somas y se descubren las diferencias entre los somas piramidales de distintas capas del cerebro. A partir del modelo matemático se simulan por primera vez somas virtuales. Algunas morfologías de espinas han sido atribuidas a ciertos comportamientos cognitivos. Por ello resulta de interés dictaminar las clases existentes y relacionarlas con funciones de la actividad cerebral. La clasificación más extendida (Peters y Kaiserman-Abramof, 1970) presenta una definición ambigua y subjetiva dependiente de la interpretación de cada individuo y por tanto discutible. Este estudio se sustenta en un conjunto de descriptores extraídos mediante una técnica de análisis topológico local para representaciones 3D. Sobre estos datos se trata de alcanzar el conjunto de clases más adecuado en el que agrupar las espinas así como de describir cada grupo mediante reglas unívocas. A partir de los resultados, se discute la existencia de un continuo de espinas y las propiedades que caracterizan a cada subtipo de espina. ---ABSTRACT---Unravel how the brain works is one of the main challenges faced by current science. A field of study which has aroused great expectations and interest is the analysis of the cortical structure from a morphological point of view, so that a molecular level simulation of the brain is achieved. This is expected to deepen the study of many neurological and pathological diseases. This project seeks the study of the soma and spines from the theoretical neuromorphology point of view. In the state of the art it is common that when it comes to analyze the morphological characteristics of a three dimension neuron the soma is ignored or, in the best case, it is replaced by a simple sphere. In fact, the concept of soma is abstract because there is not a robust and strict definition on exactly where it ends and dendrites begin. In this project a mathematical definition is reached for the first time to determine what a soma is. With the aim to simulate somas the atributes applied in the state of the art are studied. These properties, generic in nature, do not specify a unique morphology. It is why it was proposed a method to group local and global morphology properties. In arrangement of the characteristics it was proceed with the categorization of the celular body into diferent classes by using a new subtype of dynamic Bayesian network adapted to space. From the result the existance of different classes of somas and diferences among pyramidal somas from distinct brain layers are discovered. From the mathematical model virtual somas were simulated for the first time. Some morphologies of spines have been attributed to certain cognitive behaviours. For this reason it is interesting to rule the existent classes and to relate them with their functions in the brain activity. The most extended classification (Peters y Kaiserman-Abramof, 1970) presents an ambiguous and subjective definition that relies on the interpretation of each individual and consequently it is arguable. This study was based on the set of descriptors extracted from a local topological analysis technique for 3D representations. On these data it was tried to reach the most suitable set of classes to group the spines as well as to describe each cluster by unambiguous rules. From these results, the existance of a continuum of spines and the properties that characterize each spine subtype were discussed .

Linear latent force models using Gaussian Processes

Purely data-driven approaches for machine learning present difficulties when data are scarce relative to the complexity of the model or when the model is forced to extrapolate. On the other hand, purely mechanistic approaches need to identify and specify all the interactions in the problem at hand (which may not be feasible) and still leave the issue of how to parameterize the system. In this paper, we present a hybrid approach using Gaussian processes and differential equations to combine data-driven modeling with a physical model of the system. We show how different, physically inspired, kernel functions can be developed through sensible, simple, mechanistic assumptions about the underlying system. The versatility of our approach is illustrated with three case studies from motion capture, computational biology, and geostatistics.

Detection of Transient In Vivo Interactions between Substrate and Transporter during Protein Translocation into the Endoplasmic Reticulum

The split-ubiquitin technique was used to detect transient protein interactions in living cells. Nub, the N-terminal half of ubiquitin (Ub), was fused to Sec62p, a component of the protein translocation machinery in the endoplasmic reticulum of Saccharomyces cerevisiae. Cub, the C-terminal half of Ub, was fused to the C terminus of a signal sequence. The reconstitution of a quasi-native Ub structure from the two halves of Ub, and the resulting cleavage by Ub-specific proteases at the C terminus of Cub, serve as a gauge of proximity between the two test proteins linked to Nub and Cub. Using this assay, we show that Sec62p is spatially close to the signal sequence of the prepro-α-factor in vivo. This proximity is confined to the nascent polypeptide chain immediately following the signal sequence. In addition, the extent of proximity depends on the nature of the signal sequence. Cub fusions that bore the signal sequence of invertase resulted in a much lower Ub reconstitution with Nub-Sec62p than otherwise identical test proteins bearing the signal sequence of prepro-α-factor. An inactive derivative of Sec62p failed to interact with signal sequences in this assay. These in vivo findings are consistent with Sec62p being part of a signal sequence-binding complex.

Differentiation of Chromatin during DNA Elimination in Euplotes crassus

In Euplotes crassus, most of the micronuclear genome is eliminated during formation of a transcriptionally active macronucleus. To understand how this is mediated throughout the genome, we have examined the chromatin structure of the macronucleus-destined sequences and Tec transposons, which are dispersed in 15,000 copies in the micronuclear genome and completely eliminated during formation of the macronuclear genome. Whereas the macronucleus-destined sequences show a typical pattern of nucleosomal repeats in micrococcal nuclease digests, the Tec element chromatin structure digests to a nucleosome-like repeat pattern that is not typical: the minimum digestion products are ∼300–600 base pairs, or “subnucleosomal,” in size. In addition, the excised, circular forms of the Tec elements are exceedingly resistant to nucleases. Nevertheless, an underlying nucleosomal structure of the Tec elements can be demonstrated from the size differences between repeats in partial micrococcal nuclease digests and by trypsin treatment of nuclei, which results in mononucleosome-sized products. Characterization of the most micrococcal nuclease–resistant DNA indicates that micronuclear telomeres are organized into a chromatin structure with digestion properties identical to those of the Tec elements in the developing macronucleus. Thus, these major repetitive sequence components of the micronuclear genome differ in their chromatin structure from the macronuclear-destined sequences during DNA elimination. The potential role of developmental stage–specific histone variants in this chromatin differentiation is discussed.

CKAAPs DB: a conserved key amino acid positions database

The Conserved Key Amino Acid Positions DataBase (CKAAPs DB) provides access to an analysis of structurally similar proteins with dissimilar sequences where key residues within a common fold are identified. The derivation and significance of CKAAPs starting from pairwise structure alignments is described fully in Reddy et al. [Reddy,B.V.B., Li,W.W., Shindyalov,I.N. and Bourne,P.E. (2000) Proteins, in press]. The CKAAPs identified from this theoretical analysis are provided to experimentalists and theoreticians for potential use in protein engineering and modeling. It has been suggested that CKAAPs may be crucial features for protein folding, structural stability and function. Over 170 substructures, as defined by the Combinatorial Extension (CE) database, which are found in approximately 3000 representative polypeptide chains have been analyzed and are available in the CKAAPs DB. CKAAPs DB also provides CKAAPs of the representative set of proteins derived from the CE and FSSP databases. Thus the database contains over 5000 representative poly­peptide chains, covering all known structures in the PDB. A web interface to a relational database permits fast retrieval of structure-sequence alignments, CKAAPs and associated statistics. Users may query by PDB ID, protein name, function and Enzyme Classification number. Users may also submit protein alignments of their own to obtain CKAAPs. An interface to display CKAAPs on each structure from a web browser is also being implemented. CKAAPs DB is maintained by the San Diego Supercomputer Center and accessible at the URL http://ckaaps.sdsc.edu.

The structures of anthranilate synthase of Serratia marcescens crystallized in the presence of (i) its substrates, chorismate and glutamine, and a product, glutamate, and (ii) its end-product inhibitor, l-tryptophan

The crystal structure of anthranilate synthase (AS) from Serratia marcescens, a mesophilic bacterium, has been solved in the presence of its substrates, chorismate and glutamine, and one product, glutamate, at 1.95 Å, and with its bound feedback inhibitor, tryptophan, at 2.4 Å. In comparison with the AS structure from the hyperthermophile Sulfolobus solfataricus, the S. marcescens structure shows similar subunit structures but a markedly different oligomeric organization. One crystal form of the S. marcescens enzyme displays a bound pyruvate as well as a putative anthranilate (the nitrogen group is ambiguous) in the TrpE subunit. It also confirms the presence of a covalently bound glutamyl thioester intermediate in the TrpG subunit. The tryptophan-bound form reveals that the inhibitor binds at a site distinct from that of the substrate, chorismate. Bound tryptophan appears to prevent chorismate binding by a demonstrable conformational effect, and the structure reveals how occupancy of only one of the two feedback inhibition sites can immobilize the catalytic activity of both TrpE subunits. The presence of effectors in the structure provides a view of the locations of some of the amino acid residues in the active sites. Our findings are discussed in terms of the previously described AS structure of S. solfataricus, mutational data obtained from enteric bacteria, and the enzyme's mechanism of action.

Identification of four acidic amino acids that constitute the catalytic center of the RuvC Holliday junction resolvase.

Escherichia coli RuvC protein is a specific endonuclease that resolves Holliday junctions during homologous recombination. Since the endonucleolytic activity of RuvC requires a divalent cation and since 3 or 4 acidic residues constitute the catalytic centers of several nucleases that require a divalent cation for the catalytic activity, we examined whether any of the acidic residues of RuvC were required for the nucleolytic activity. By site-directed mutagenesis, we constructed a series of ruvC mutant genes with similar amino acid replacements in 1 of the 13 acidic residues. Among them, the mutant genes with an alteration at Asp-7, Glu-66, Asp-138, or Asp-141 could not complement UV sensitivity of a ruvC deletion strain, and the multicopy mutant genes showed a dominant negative phenotype when introduced into a wild-type strain. The products of these mutant genes were purified and their biochemical properties were studied. All of them retained the ability to form a dimer and to bind specifically to a synthetic Holliday junction. However, they showed no, or extremely reduced, endonuclease activity specific for the junction. These 4 acidic residues, which are dispersed in the primary sequence, are located in close proximity at the bottom of the putative DNA binding cleft in the three-dimensional structure. From these results, we propose that these 4 acidic residues constitute the catalytic center for the Holliday junction resolvase and that some of them play a role in coordinating a divalent metal ion in the active center.

Regulation of Sticholysin II-Induced Pore Formation by Lipid Bilayer Composition, Phase State, and Interfacial Properties

Sticholysin II (StnII) is a pore-forming toxin that uses sphingomyelin (SM) as the recognition molecule in targeting membranes.After StnII monomers bind to SM, several toxin monomers act in concert to oligomerize into a functional pore. The regulation of StnII binding to SM, and the subsequent pore-formation process, is not fully understood. In this study, we examined how the biophysical properties of bilayers, originating from variations in the SM structure, from the presence of sterol species, or from the presence of increasingly polyunsaturated glycerophospholipids,affected StnII-induced pore formation. StnII-induced pore formation, as determined from calcein permeabilization, was fastest in the pure unsaturated SM bilayers. In 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/saturated SM bilayers (4:1 molar ratio), pore formation became slower as the chain length of the saturated SMs increased from 14 up to 24 carbons. In the POPC/palmitoyl-SM (16:0-SM) 4:1 bilayers, SM could not support pore formation by StnII if dimyristoyl-PC was included at 1:1 stoichiometry with 16:0-SM, suggesting that free clusters of SM were required for toxin binding and/or pore formation. Cholesterol and other sterols facilitated StnII-induced pore formation markedly, but the efficiency did not appear to correlate with the sterol structure. Benzyl alcohol was more efficient than sterols in enhancing the pore-formation process, suggesting that the effect on pore formation originated from alcohol-induced alteration of the hydrogen-bonding network in the SM-containing bilayers. Finally, we observed that pore formation by StnII was enhanced in the PC/16:0-SM 4:1 bilayers, in which the PC was increasingly unsaturated. We conclude that the physical state of bilayer lipids greatly affected pore formation by StnII. Phase boundaries were not required for pore formation, although SM in a gel state attenuated pore formation.

Strength of the Iberian intraplate lithosphere: Cenozoic deformations and seismicity

Previous studies about the strength of the lithosphere in the center of Iberia fail to resolve the depth of earthquakes because of the rheological uncertainties. Therefore, new contributions are considered (the crustal structure from a density model) and several parameters (tectonic regime, mantle rheology, strain rate) are checked in this paper to properly examine the role of lithospheric strength in the intraplate seismicity and the Cenozoic evolution. The strength distribution with depth, the integrated strength, the effective elastic thickness and the seismogenic thickness have been calculated by a finite element modelling of the lithosphere across the Central System mountain range and the bordering Duero and Madrid sedimentary basins. Only a dry mantle under strike-slip/extension and a strain rate of 10-15 s-1, or under extension and 10-16 s-1, causes a strong lithosphere. The integrated strength and the elastic thickness are lower in the mountain chain than in the basins. This heterogeneity has been maintained since the Cenozoic and determine the mountain uplift and the biharmonic folding of the Iberian lithosphere during the Alpine deformations. The seismogenic thickness bounds the seismic activity in the upper–middle crust, and the decreasing crustal strength from the Duero Basin towards the Madrid Basin is related to a parallel increase in Plio–Quaternary deformations and seismicity. However, elasto–plastic modelling shows that current African–Eurasian convergence is resolved elastically or ductilely, which accounts for the low seismicity recorded in this region.

First- and second-order stimulus length selectivity in New World monkey striate cortex

Motion is a powerful cue for figure-ground segregation, allowing the recognition of shapes even if the luminance and texture characteristics of the stimulus and background are matched. In order to investigate the neural processes underlying early stages of the cue-invariant processing of form, we compared the responses of neurons in the striate cortex (V1) of anaesthetized marmosets to two types of moving stimuli: bars defined by differences in luminance, and bars defined solely by the coherent motion of random patterns that matched the texture and temporal modulation of the background. A population of form-cue-invariant (FCI) neurons was identified, which demonstrated similar tuning to the length of contours defined by first- and second-order cues. FCI neurons were relatively common in the supragranular layers (where they corresponded to 28% of the recorded units), but were absent from layer 4. Most had complex receptive fields, which were significantly larger than those of other V1 neurons. The majority of FCI neurons demonstrated end-inhibition in response to long first- and second-order bars, and were strongly direction selective, Thus, even at the level of V1 there are cells whose variations in response level appear to be determined by the shape and motion of the entire second-order object, rather than by its parts (i.e. the individual textural components). These results are compatible with the existence of an output channel from V1 to the ventral stream of extrastriate areas, which already encodes the basic building blocks of the image in an invariant manner.

Predicting residue-wise contact orders in proteins by support vector regression

Background: The residue-wise contact order (RWCO) describes the sequence separations between the residues of interest and its contacting residues in a protein sequence. It is a new kind of one-dimensional protein structure that represents the extent of long-range contacts and is considered as a generalization of contact order. Together with secondary structure, accessible surface area, the B factor, and contact number, RWCO provides comprehensive and indispensable important information to reconstructing the protein three-dimensional structure from a set of one-dimensional structural properties. Accurately predicting RWCO values could have many important applications in protein three-dimensional structure prediction and protein folding rate prediction, and give deep insights into protein sequence-structure relationships. Results: We developed a novel approach to predict residue-wise contact order values in proteins based on support vector regression (SVR), starting from primary amino acid sequences. We explored seven different sequence encoding schemes to examine their effects on the prediction performance, including local sequence in the form of PSI-BLAST profiles, local sequence plus amino acid composition, local sequence plus molecular weight, local sequence plus secondary structure predicted by PSIPRED, local sequence plus molecular weight and amino acid composition, local sequence plus molecular weight and predicted secondary structure, and local sequence plus molecular weight, amino acid composition and predicted secondary structure. When using local sequences with multiple sequence alignments in the form of PSI-BLAST profiles, we could predict the RWCO distribution with a Pearson correlation coefficient (CC) between the predicted and observed RWCO values of 0.55, and root mean square error (RMSE) of 0.82, based on a well-defined dataset with 680 protein sequences. Moreover, by incorporating global features such as molecular weight and amino acid composition we could further improve the prediction performance with the CC to 0.57 and an RMSE of 0.79. In addition, combining the predicted secondary structure by PSIPRED was found to significantly improve the prediction performance and could yield the best prediction accuracy with a CC of 0.60 and RMSE of 0.78, which provided at least comparable performance compared with the other existing methods. Conclusion: The SVR method shows a prediction performance competitive with or at least comparable to the previously developed linear regression-based methods for predicting RWCO values. In contrast to support vector classification (SVC), SVR is very good at estimating the raw value profiles of the samples. The successful application of the SVR approach in this study reinforces the fact that support vector regression is a powerful tool in extracting the protein sequence-structure relationship and in estimating the protein structural profiles from amino acid sequences.

Spatially localized distortions of event time

A fundamental question about the perception of time is whether the neural mechanisms underlying temporal judgements are universal and centralized in the brain or modality specific and distributed []. Time perception has traditionally been thought to be entirely dissociated from spatial vision. Here we show that the apparent duration of a dynamic stimulus can be manipulated in a local region of visual space by adapting to oscillatory motion or flicker. This implicates spatially localized temporal mechanisms in duration perception. We do not see concomitant changes in the time of onset or offset of the test patterns, demonstrating a direct local effect on duration perception rather than an indirect effect on the time course of neural processing. The effects of adaptation on duration perception can also be dissociated from motion or flicker perception per se. Although 20 Hz adaptation reduces both the apparent temporal frequency and duration of a 10 Hz test stimulus, 5 Hz adaptation increases apparent temporal frequency but has little effect on duration perception. We conclude that there is a peripheral, spatially localized, essentially visual component involved in sensing the duration of visual events.