The Ran/TC4 GTPase-binding domain: identification by expression cloning and characterization of a conserved sequence motif.

Ran/TC4 is an essential, nuclear GTPase implicated in the initiation of DNA replication, entry into and exit from mitosis, and in nuclear RNA and protein transport through the nuclear pore complex. This diversity of functions suggests that Ran interacts with a large number of down-stream targets. Using an overlay assay, we detected a family of putative target proteins that associate with GTP-bound Ran. The sequence of only one such protein, HTF9a/RanBP1, is known. We have now cloned two additional Ran-binding proteins, allowing identification of a distinctive, highly conserved sequence motif of approximately 150 residues. This motif represents a minimal Ran-binding domain that stabilizes the GTP-bound state of Ran. The isolated domain also functions as a coactivator of Ran-GTPase-activating protein. Mutation of a conserved residue within the Ran-binding domain of HTF9a protein drastically reduced Ran binding. Ran-binding proteins coimmunoprecipitated with epitope-tagged Ran from cell lysates, suggesting that these proteins may associate in vivo. A previously uncharacterized Caenorhabditis elegans gene could encode a protein (96 kDa) possessing two Ran-binding domains. This open reading frame also contains similarities to nucleoporins, suggesting a functional link between Ran and nuclear pore complexes.

A finite element model of perforated panel absorbers including viscothermal effects

Most of the analytical models devoted to determine the acoustic properties of a rigid perforated panel consider the acoustic impedance of a single hole and then use the porosity to determine the impedance for the whole panel. However, in the case of not homogeneous hole distribution or more complex configurations this approach is no longer valid. This work explores some of these limitations and proposes a finite element methodology that implements the linearized Navier Stokes equations in the frequency domain to analyse the acoustic performance under normal incidence of perforated panel absorbers. Some preliminary results for a homogenous perforated panel show that the sound absorption coefficient derived from the Maa analytical model does not match those from the simulations. These differences are mainly attributed to the finite geometry effect and to the spatial distribution of the perforations for the numerical case. In order to confirm these statements, the acoustic field in the vicinities of the perforations is analysed for a more complex configuration of perforated panel. Additionally, experimental studies are carried out in an impedance tube for the same configuration and then compared to previous methods. The proposed methodology is shown to be in better agreement with the laboratorial measurements than the analytical approach.

Experimental muscle pain changes feedforward postural responses of the trunk muscles

Many studies have identified changes in trunk muscle recruitment in clinical low back pain (LBP). However, due to the heterogeneity of the LBP population these changes have been variable and it has been impossible to identify a cause-effect relationship. Several studies have identified a consistent change in the feed-forward postural response of transversus abdominis (TrA), the deepest abdominal muscle, in association with arm movements in chronic LBP. This study aimed to determine whether the feedforward recruitment of the trunk muscles in a postural task could be altered by acute experimentally induced LBP. Electromyographic (EMG) recordings of the abdominal and paraspinal muscles were made during arm movements in a control trial, following the injection of isotonic (non-painful) and hypertonic (painful) saline into the longissimus muscle at L4, and during a 1-h follow-up. Movements included rapid arm flexion in response to a light and repetitive arm flexion-extension. Temporal and spatial EMG parameters were measured. The onset and amplitude of EMG of most muscles was changed in a variable manner during the period of experimentally induced pain. However, across movement trials and subjects the activation of TrA was consistently reduced in amplitude or delayed. Analyses in the time and frequency domain were used to confirm these findings. The results suggest that acute experimentally induced pain may affect feedforward postural activity of the trunk muscles. Although the response was variable, pain produced differential changes in the motor control of the trunk muscles, with consistent impairment of TrA activity.

Effects of the rate of formant-frequency variation on the grouping of formants in speech perception

How speech is separated perceptually from other speech remains poorly understood. Recent research suggests that the ability of an extraneous formant to impair intelligibility depends on the modulation of its frequency, but not its amplitude, contour. This study further examined the effect of formant-frequency variation on intelligibility by manipulating the rate of formant-frequency change. Target sentences were synthetic three-formant (F1?+?F2?+?F3) analogues of natural utterances. Perceptual organization was probed by presenting stimuli dichotically (F1?+?F2C?+?F3C; F2?+?F3), where F2C?+?F3C constitute a competitor for F2 and F3 that listeners must reject to optimize recognition. Competitors were derived using formant-frequency contours extracted from extended passages spoken by the same talker and processed to alter the rate of formant-frequency variation, such that rate scale factors relative to the target sentences were 0, 0.25, 0.5, 1, 2, and 4 (0?=?constant frequencies). Competitor amplitude contours were either constant, or time-reversed and rate-adjusted in parallel with the frequency contour. Adding a competitor typically reduced intelligibility; this reduction increased with competitor rate until the rate was at least twice that of the target sentences. Similarity in the results for the two amplitude conditions confirmed that formant amplitude contours do not influence across-formant grouping. The findings indicate that competitor efficacy is not tuned to the rate of the target sentences; most probably, it depends primarily on the overall rate of frequency variation in the competitor formants. This suggests that, when segregating the speech of concurrent talkers, differences in speech rate may not be a significant cue for across-frequency grouping of formants.

Cognition, ocular accommodation, and cardiovascular function in emmetropes and late-onset myopes

PURPOSE. To investigate objectively and noninvasively the role of cognitive demand on autonomic control of systemic cardiovascular and ocular accommodative responses in emmetropes and myopes of late-onset. METHODS. Sixteen subjects (10 men, 6 women) aged between 18 and 34 years (mean ± SD: 22.6 ± 4.4 years), eight emmetropes (EMMs; mean spherical equivalent [MSE] refractive error ± SD: 0.05 ± 0.24 D) and eight with late-onset myopia (LOMs; MSE ± SD: -3.66 ± 2.31 D) participated in the study. Subjects viewed stationary numerical digits monocularly within a Badal optical system (at both 0.0 and -3.0 D) while performing a two-alternative, forced-choice paradigm that matched cognitive loading across subjects. Five individually matched cognitive levels of increasing difficulty were used in random order for each subject. Five 20-second, continuous-objective recordings of the accommodative response measured with an open-view infrared autorefractor were obtained for each cognitive level, whereas simultaneous measurement of heart rate was continuously recorded with a finger-mounted piezoelectric pulse transducer for 5 minutes. Fast Fourier transformation of cardiovascular function allowed the relative power of the autonomic components to be assessed in the frequency domain, whereas heart period gave an indication of the time-domain response. RESULTS. Increasing the cognitive demand led to a significant reduction in the accommodative response in all subjects (0.0 D: by -0.35 ± 0.33 D; -3.0 D: by -0.31 ± 0.40 D, P < 0.001). The greater lag of LOMs compared with EMMs was not significant (P = 0.07) at both distance (0.38 ± 0.35 D) and near (0.14 ± 0.42 D). Mean heart period reduced with increasing levels of workload (P < 0.0005). LOMs exhibited a relative elevation in sympathetic system activity compared to EMMs. Within refractive groups, however, accommodative shifts with increasing cognition correlated with parasympathetic activity (r = 0.99, P < 0.001), more than with sympathetic activity (r = 0.62, P > 0.05). CONCLUSIONS. In an equivalent workload paradigm, increasing cognitive demand caused a reduction in accommodative response that was attributable principally to a concurrent reduction in the relative power of the parasympathetic component of the autonomic nervous system (ANS). The disparity in accommodative response between EMMs and LOMs, however, appears to be augmented by changes in the sympathetic nervous component of the systemic ANS. Copyright © Association for Research in Vision and Ophthalmology.

Signal Processing under Active Monitoring

This paper describes a method of signal preprocessing under active monitoring. Suppose we want to solve the inverse problem of getting the response of a medium to one powerful signal, which is equivalent to obtaining the transmission function of the medium, but do not have an opportunity to conduct such an experiment (it might be too expensive or harmful for the environment). Practically the problem can be reduced to obtaining the transmission function of the medium. In this case we can conduct a series of experiments of relatively low power and superpose the response signals. However, this method is conjugated with considerable loss of information (especially in the high frequency domain) due to fluctuations of the phase, the frequency and the starting time of each individual experiment. The preprocessing technique presented in this paper allows us to substantially restore the response of the medium and consequently to find a better estimate for the transmission function. This technique is based on expanding the initial signal into the system of orthogonal functions.

An efficient, approximate path-following algorithm for elastic net based nonlinear spike enhancement

Unwanted spike noise in a digital signal is a common problem in digital filtering. However, sometimes the spikes are wanted and other, superimposed, signals are unwanted, and linear, time invariant (LTI) filtering is ineffective because the spikes are wideband - overlapping with independent noise in the frequency domain. So, no LTI filter can separate them, necessitating nonlinear filtering. However, there are applications in which the noise includes drift or smooth signals for which LTI filters are ideal. We describe a nonlinear filter formulated as the solution to an elastic net regularization problem, which attenuates band-limited signals and independent noise, while enhancing superimposed spikes. Making use of known analytic solutions a novel, approximate path-following algorithm is given that provides a good, filtered output with reduced computational effort by comparison to standard convex optimization methods. Accurate performance is shown on real, noisy electrophysiological recordings of neural spikes.

Multicolour nonlinearly bound chirped dissipative solitons

The dissipative soliton regime is one of the most advanced ways to generate high-energy femtosecond pulses in mode-locked lasers. On the other hand, the stimulated Raman scattering in a fibre laser may convert the excess energy out of the coherent dissipative soliton to a noisy Raman pulse, thus limiting its energy. Here we demonstrate that intracavity feedback provided by re-injection of a Raman pulse into the laser cavity leads to formation of a coherent Raman dissipative soliton. Together, a dissipative soliton and a Raman dissipative soliton (of the first and second orders) form a two (three)-colour stable complex with higher total energy and broader spectrum than those of the dissipative soliton alone. Numerous applications can benefit from this approach, including frequency comb spectroscopy, transmission lines, seeding femtosecond parametric amplifiers, enhancement cavities and multiphoton fluorescence microscopy.

Resonance properties of domain boundaries in quasi-two dimensional antiferromagnets

The so-called "internal modes" localized near the domain boundaries in quasi-two dimensional antiferromagnets are investigated. The possible localized states are classified and their frequency dependences on the system discreteness parameter λ=J/β, which describes the ratio of the magnitudes of the exchange interplane interaction and the magnetic anisotropy, are found. A sudden change in the spectrum of the local internal modes is observed at a critical value of this parameter, λ=λb=3/4, where the domain wall shifts from a collinear to a canted shape. When λ<λb there are one symmetric and two antisymmetric local modes, and when λ>λb the modes are two symmetric, one antisymmetric, and one shear. For discreteness parameters close to the critical value, the frequencies of some of the local modes lie deep inside the gap for the linear AFM magnon spectrum and can be observed experimentally. © 2010 American Institute of Physics.

Seizure detection in subdural recordings using nonlinear decision functions

This dissertation proposed a new approach to seizure detection in intracranial EEG recordings using nonlinear decision functions. It implemented well-established features that were designed to deal with complex signals such as brain recordings, and proposed a 2-D domain of analysis. Since the features considered assume both the time and frequency domains, the analysis was carried out both temporally and as a function of different frequency ranges in order to ascertain those measures that were most suitable for seizure detection. In retrospect, this study established a generalized approach to seizure detection that works across several features and across patients. ^ Clinical experiments involved 8 patients with intractable seizures that were evaluated for potential surgical interventions. A total of 35 iEEG data files collected were used in a training phase to ascertain the reliability of the formulated features. The remaining 69 iEEG data files were then used in the testing phase. ^ The testing phase revealed that the correlation sum is the feature that performed best across all patients with a sensitivity of 92% and an accuracy of 99%. The second best feature was the gamma power with a sensitivity of 92% and an accuracy of 96%. In the frequency domain, all of the 5 other spectral bands considered, revealed mixed results in terms of low sensitivity in some frequency bands and low accuracy in other frequency bands, which is expected given that the dominant frequencies in iEEG are those of the gamma band. In the time domain, other features which included mobility, complexity, and activity, all performed very well with an average a sensitivity of 80.3% and an accuracy of 95%. ^ The computational requirement needed for these nonlinear decision functions to be generated in the training phase was extremely long. It was determined that when the duration dimension was rescaled, the results improved and the convergence rates of the nonlinear decision functions were reduced dramatically by more than a 100 fold. Through this rescaling, the sensitivity of the correlation sum improved to 100% and the sensitivity of the gamma power to 97%, which meant that there were even less false negatives and false positives detected. ^

Localized surface plasmon resonance biosensors for real-time biomolecular binding study

Surface Plasmon Resonance (SPR) and localized surface plasmon resonance (LSPR) biosensors have brought a revolutionary change to in vitro study of biological and biochemical processes due to its ability to measure extremely small changes in surface refractive index (RI), binding equilibrium and kinetics. Strategies based on LSPR have been employed to enhance the sensitivity for a variety of applications, such as diagnosis of diseases, environmental analysis, food safety, and chemical threat detection. In LSPR spectroscopy, absorption and scattering of light are greatly enhanced at frequencies that excite the LSPR, resulting in a characteristic extinction spectrum that depends on the RI of the surrounding medium. Compositional and conformational change within the surrounding medium near the sensing surface could therefore be detected as shifts in the extinction spectrum. This dissertation specifically focuses on the development and evaluation of highly sensitive LSPR biosensors for in situ study of biomolecular binding process by incorporating nanotechnology. Compared to traditional methods for biomolecular binding studies, LSPR-based biosensors offer real-time, label free detection. First, we modified the gold sensing surface of LSPR-based biosensors using nanomaterials such as gold nanoparticles (AuNPs) and polymer to enhance surface absorption and sensitivity. The performance of this type of biosensors was evaluated on the application of small heavy metal molecule binding affinity study. This biosensor exhibited ∼7 fold sensitivity enhancement and binding kinetics measurement capability comparing to traditional biosensors. Second, a miniaturized cell culture system was integrated into the LSPR-based biosensor system for the purpose of real-time biomarker signaling pathway studies and drug efficacy studies with living cells. To the best of our knowledge, this is the first LSPR-based sensing platform with the capability of living cell studies. We demonstrated the living cell measurement ability by studying the VEGF signaling pathway in living SKOV-3 cells. Results have shown that the VEGF secretion level from SKOV-3 cells is 0.0137 ± 0.0012 pg per cell. Moreover, we have demonstrated bevacizumab drug regulation to the VEGF signaling pathway using this biosensor. This sensing platform could potentially help studying biomolecular binding kinetics which elucidates the underlying mechanisms of biotransportation and drug delivery.

Infrared image enhancement based on hybrid-domain consideration and data fusion methods

Au cours des dernières décennies, l’effort sur les applications de capteurs infrarouges a largement progressé dans le monde. Mais, une certaine difficulté demeure, en ce qui concerne le fait que les objets ne sont pas assez clairs ou ne peuvent pas toujours être distingués facilement dans l’image obtenue pour la scène observée. L’amélioration de l’image infrarouge a joué un rôle important dans le développement de technologies de la vision infrarouge de l’ordinateur, le traitement de l’image et les essais non destructifs, etc. Cette thèse traite de la question des techniques d’amélioration de l’image infrarouge en deux aspects, y compris le traitement d’une seule image infrarouge dans le domaine hybride espacefréquence, et la fusion d’images infrarouges et visibles employant la technique du nonsubsampled Contourlet transformer (NSCT). La fusion d’images peut être considérée comme étant la poursuite de l’exploration du modèle d’amélioration de l’image unique infrarouge, alors qu’il combine les images infrarouges et visibles en une seule image pour représenter et améliorer toutes les informations utiles et les caractéristiques des images sources, car une seule image ne pouvait contenir tous les renseignements pertinents ou disponibles en raison de restrictions découlant de tout capteur unique de l’imagerie. Nous examinons et faisons une enquête concernant le développement de techniques d’amélioration d’images infrarouges, et ensuite nous nous consacrons à l’amélioration de l’image unique infrarouge, et nous proposons un schéma d’amélioration de domaine hybride avec une méthode d’évaluation floue de seuil amélioré, qui permet d’obtenir une qualité d’image supérieure et améliore la perception visuelle humaine. Les techniques de fusion d’images infrarouges et visibles sont établies à l’aide de la mise en oeuvre d’une mise en registre précise des images sources acquises par différents capteurs. L’algorithme SURF-RANSAC est appliqué pour la mise en registre tout au long des travaux de recherche, ce qui conduit à des images mises en registre de façon très précise et des bénéfices accrus pour le traitement de fusion. Pour les questions de fusion d’images infrarouges et visibles, une série d’approches avancées et efficaces sont proposés. Une méthode standard de fusion à base de NSCT multi-canal est présente comme référence pour les approches de fusion proposées suivantes. Une approche conjointe de fusion, impliquant l’Adaptive-Gaussian NSCT et la transformée en ondelettes (Wavelet Transform, WT) est propose, ce qui conduit à des résultats de fusion qui sont meilleurs que ceux obtenus avec les méthodes non-adaptatives générales. Une approche de fusion basée sur le NSCT employant la détection comprime (CS, compressed sensing) et de la variation totale (TV) à des coefficients d’échantillons clairsemés et effectuant la reconstruction de coefficients fusionnés de façon précise est proposée, qui obtient de bien meilleurs résultats de fusion par le biais d’une pré-amélioration de l’image infrarouge et en diminuant les informations redondantes des coefficients de fusion. Une procédure de fusion basée sur le NSCT utilisant une technique de détection rapide de rétrécissement itératif comprimé (fast iterative-shrinking compressed sensing, FISCS) est proposée pour compresser les coefficients décomposés et reconstruire les coefficients fusionnés dans le processus de fusion, qui conduit à de meilleurs résultats plus rapidement et d’une manière efficace.

Understanding near Fermi-level electronic structure through x-ray emission spectroscopy

Thesis (Ph.D.)--University of Washington, 2016-08

L’implication de SHP-1 en condition élevée de glucose inhibe la signalisation de l’insuline et du PDGF-BB dans les cellules musculaires lisses vasculaires hypoxiques

Résumé : Bien que l’hypoxie soit un puissant inducteur de l’angiogenèse, l’activation des facteurs de croissance est perturbée en hyperglycémie au niveau du pied et du cœur. Cette perturbation entraîne la perte de prolifération et de migration chez les cellules endothéliales, musculaires lisses vasculaires et péricytes empêchant la formation de nouveaux vaisseaux qui mènera à l’amputation des membres inférieurs chez les patients diabétiques. Une étude a démontré qu’une augmentation de la protéine tyrosine phosphatase Src homology-2 domain-containing phosphatase-1 (SHP-1) en condition hyperglycémique chez les péricytes entraînait l’inhibition de la signalisation du PDGF-BB, ce qui résultait en le développement d’une rétinopathie diabétique. Nous avons alors soulevé l’hypothèse que l’expression de SHP-1 dans les cellules musculaires lisses vasculaires affecte la prolifération et la migration cellulaire par l’inhibition de la signalisation de l’insuline et du PDGF-BB en condition diabétique. Nos expérimentations ont été effectuées principalement à l’aide d’une culture primaire de cellules musculaires lisses primaires provenant d’aortes bovines. Comparativement aux concentrations normales de glucose (NG : 5,6 mM), l’exposition à des concentrations élevées de glucose (HG : 25 mM) pendant 48 h a résulté en l’inhibition de la prolifération cellulaire par l’insuline et le PDGF-BB autant en normoxie (20% O2) qu’en hypoxie (24 dernières heures à 1% O2). Lors des essais de migration cellulaire, aucun effet de l’insuline n’a été observé alors que la migration par le PDGF-BB fut inhibée en HG autant en normoxie qu’en hypoxie. L’exposition en HG à mener à l’inhibition de la signalisation de la voie PI3K/Akt de l’insuline et du PDGF-BB en hypoxie. Aucune variation de l’expression de SHP-1 n’a été observée mais son activité phosphatase en hypoxie était fortement inhibée en NG contrairement en HG où on observait une augmentation de cette activité. Finalement, une association a été constatée entre SHP-1 et la sous-unité bêta du récepteur au PDGF. En conclusion, nous avons démontré que l’augmentation de l’activité phosphatase de SHP-1 en hypoxie cause l’inhibition des voies de l’insuline et du PDGF-BB réduisant les processus angiogéniques des cellules musculaires lisses vasculaires dans la maladie des artères périphériques.

Simulación de un enlace óptico WDM (Wavelength Division Multiplexing) utilizando POFs (Polymer Optical Fiber) en el espectro de luz visible

En este proyecto se analizaron las características y el modo de operación de las fibras ópticas plásticas en un enlace óptico WDM (Wavelenght Division Multiplexing) operando en el espectro visible. Se estudiaron los componentes activos y pasivos necesarios para el enlace, como son las fuentes LED, multiplexores, filtros y acopladores. Se analizaron los efectos no lineales que se pueden presentar en la fibra óptica, y que son importantes de considerar al transmitir señales WDM. Para respaldar el análisis se simuló en MATLAB un enlace óptico en el dominio de la frecuencia utilizando fuentes LED que emiten en el espectro visible, junto con multiplexores WDM, filtros de absorción, acopladores y como medio de transmisión la Fibra Óptica Plástica (POF -Plastic Optical Fiber).