Three-factor models versus time series models:quantifying time-dependencies of interactions between stimuli in cell biology and psychobiology for short longitudinal data

Signal integration determines cell fate on the cellular level, affects cognitive processes and affective responses on the behavioural level, and is likely to be involved in psychoneurobiological processes underlying mood disorders. Interactions between stimuli may subjected to time effects. Time-dependencies of interactions between stimuli typically lead to complex cell responses and complex responses on the behavioural level. We show that both three-factor models and time series models can be used to uncover such time-dependencies. However, we argue that for short longitudinal data the three factor modelling approach is more suitable. In order to illustrate both approaches, we re-analysed previously published short longitudinal data sets. We found that in human embryonic kidney 293 cells cells the interaction effect in the regulation of extracellular signal-regulated kinase (ERK) 1 signalling activation by insulin and epidermal growth factor is subjected to a time effect and dramatically decays at peak values of ERK activation. In contrast, we found that the interaction effect induced by hypoxia and tumour necrosis factor-alpha for the transcriptional activity of the human cyclo-oxygenase-2 promoter in HEK293 cells is time invariant at least in the first 12-h time window after stimulation. Furthermore, we applied the three-factor model to previously reported animal studies. In these studies, memory storage was found to be subjected to an interaction effect of the beta-adrenoceptor agonist clenbuterol and certain antagonists acting on the alpha-1-adrenoceptor / glucocorticoid-receptor system. Our model-based analysis suggests that only if the antagonist drug is administer in a critical time window, then the interaction effect is relevant.

A Bayesian state space modelling approach to probabilistic quantitative precipitation forecasting

The generation of very short range forecasts of precipitation in the 0-6 h time window is traditionally referred to as nowcasting. Most existing nowcasting systems essentially extrapolate radar observations in some manner, however, very few systems account for the uncertainties involved. Thus deterministic forecast are produced, which have a limited use when decisions must be made, since they have no measure of confidence or spread of the forecast. This paper develops a Bayesian state space modelling framework for quantitative precipitation nowcasting which is probabilistic from conception. The model treats the observations (radar) as noisy realisations of the underlying true precipitation process, recognising that this process can never be completely known, and thus must be represented probabilistically. In the model presented here the dynamics of the precipitation are dominated by advection, so this is a probabilistic extrapolation forecast. The model is designed in such a way as to minimise the computational burden, while maintaining a full, joint representation of the probability density function of the precipitation process. The update and evolution equations avoid the need to sample, thus only one model needs be run as opposed to the more traditional ensemble route. It is shown that the model works well on both simulated and real data, but that further work is required before the model can be used operationally. © 2004 Elsevier B.V. All rights reserved.

Investigation of neural correlates of faces and emotional expressions using magnetoencephalography

The recognition of faces and of facial expressions in an important evolutionary skill, and an integral part of social communication. It has been argued that the processing of faces is distinct from the processing of non-face stimuli and functional neuroimaging investigations have even found evidence of a distinction between the perception of faces and of emotional expressions. Structural and temporal correlates of face perception and facial affect have only been separately identified. Investigation neural dynamics of face perception per se as well as facial affect would allow the mapping of these in space, time and frequency specific domains. Participants were asked to perform face categorisation and emotional discrimination tasks and Magnetoencephalography (MEG) was used to measure the neurophysiology of face and facial emotion processing. SAM analysis techniques enable the investigation of spectral changes within specific time-windows and frequency bands, thus allowing the identification of stimulus specific regions of cortical power changes. Furthermore, MEG’s excellent temporal resolution allows for the detection of subtle changes associated with the processing of face and non-face stimuli and different emotional expressions. The data presented reveal that face perception is associated with spectral power changes within a distributed cortical network comprising occipito-temporal as well as parietal and frontal areas. For the perception of facial affect, spectral power changes were also observed within frontal and limbic areas including the parahippocampal gyrus and the amygdala. Analyses of temporal correlates also reveal a distinction between the processing of faces and facial affect. Face perception per se occurred at earlier latencies whereas the discrimination of facial expression occurred within a longer time-window. In addition, the processing of faces and facial affect was differentially associated with changes in cortical oscillatory power for alpha, beta and gamma frequencies. The perception of faces and facial affect is associated with distinct changes in cortical oscillatory activity that can be mapped to specific neural structures, specific time-windows and latencies as well as specific frequency bands. Therefore, the work presented in this thesis provides further insight into the sequential processing of faces and facial affect.

Quasi-separation of the biharmonic partial differential equation

In this paper, we consider analytical and numerical solutions to the Dirichlet boundary-value problem for the biharmonic partial differential equation on a disc of finite radius in the plane. The physical interpretation of these solutions is that of the harmonic oscillations of a thin, clamped plate. For the linear, fourth-order, biharmonic partial differential equation in the plane, it is well known that the solution method of separation in polar coordinates is not possible, in general. However, in this paper, for circular domains in the plane, it is shown that a method, here called quasi-separation of variables, does lead to solutions of the partial differential equation. These solutions are products of solutions of two ordinary linear differential equations: a fourth-order radial equation and a second-order angular differential equation. To be expected, without complete separation of the polar variables, there is some restriction on the range of these solutions in comparison with the corresponding separated solutions of the second-order harmonic differential equation in the plane. Notwithstanding these restrictions, the quasi-separation method leads to solutions of the Dirichlet boundary-value problem on a disc with centre at the origin, with boundary conditions determined by the solution and its inward drawn normal taking the value 0 on the edge of the disc. One significant feature for these biharmonic boundary-value problems, in general, follows from the form of the biharmonic differential expression when represented in polar coordinates. In this form, the differential expression has a singularity at the origin, in the radial variable. This singularity translates to a singularity at the origin of the fourth-order radial separated equation; this singularity necessitates the application of a third boundary condition in order to determine a self-adjoint solution to the Dirichlet boundary-value problem. The penultimate section of the paper reports on numerical solutions to the Dirichlet boundary-value problem; these results are also presented graphically. Two specific cases are studied in detail and numerical values of the eigenvalues are compared with the results obtained in earlier studies.

Modulation of long-range neural synchrony reflects temporal limitations of visual attention in humans

Because of attentional limitations, the human visual system can process for awareness and response only a fraction of the input received. Lesion and functional imaging studies have identified frontal, temporal, and parietal areas as playing a major role in the attentional control of visual processing, but very little is known about how these areas interact to form a dynamic attentional network. We hypothesized that the network communicates by means of neural phase synchronization, and we used magnetoencephalography to study transient long-range interarea phase coupling in a well studied attentionally taxing dual-target task (attentional blink). Our results reveal that communication within the fronto-parieto-temporal attentional network proceeds via transient long-range phase synchronization in the beta band. Changes in synchronization reflect changes in the attentional demands of the task and are directly related to behavioral performance. Thus, we show how attentional limitations arise from the way in which the subsystems of the attentional network interact. The human brain faces an inestimable task of reducing a potentially overloading amount of input into a manageable flow of information that reflects both the current needs of the organism and the external demands placed on it. This task is accomplished via a ubiquitous construct known as “attention,” whose mechanism, although well characterized behaviorally, is far from understood at the neurophysiological level. Whereas attempts to identify particular neural structures involved in the operation of attention have met with considerable success (1-5) and have resulted in the identification of frontal, parietal, and temporal regions, far less is known about the interaction among these structures in a way that can account for the task-dependent successes and failures of attention. The goal of the present research was, thus, to unravel the means by which the subsystems making up the human attentional network communicate and to relate the temporal dynamics of their communication to observed attentional limitations in humans. A prime candidate for communication among distributed systems in the human brain is neural synchronization (for review, see ref. 6). Indeed, a number of studies provide converging evidence that long-range interarea communication is related to synchronized oscillatory activity (refs. 7-14; for review, see ref. 15). To determine whether neural synchronization plays a role in attentional control, we placed humans in an attentionally demanding task and used magnetoencephalography (MEG) to track interarea communication by means of neural synchronization. In particular, we presented 10 healthy subjects with two visual target letters embedded in streams of 13 distractor letters, appearing at a rate of seven per second. The targets were separated in time by a single distractor. This condition leads to the “attentional blink” (AB), a well studied dual-task phenomenon showing the reduced ability to report the second of two targets when an interval <500 ms separates them (16-18). Importantly, the AB does not prevent perceptual processing of missed target stimuli but only their conscious report (19), demonstrating the attentional nature of this effect and making it a good candidate for the purpose of our investigation. Although numerous studies have investigated factors, e.g., stimulus and timing parameters, that manipulate the magnitude of a particular AB outcome, few have sought to characterize the neural state under which “standard” AB parameters produce an inability to report the second target on some trials but not others. We hypothesized that the different attentional states leading to different behavioral outcomes (second target reported correctly or not) are characterized by specific patterns of transient long-range synchronization between brain areas involved in target processing. Showing the hypothesized correspondence between states of neural synchronization and human behavior in an attentional task entails two demonstrations. First, it needs to be demonstrated that cortical areas that are suspected to be involved in visual-attention tasks, and the AB in particular, interact by means of neural synchronization. This demonstration is particularly important because previous brain-imaging studies (e.g., ref. 5) only showed that the respective areas are active within a rather large time window in the same task and not that they are concurrently active and actually create an interactive network. Second, it needs to be demonstrated that the pattern of neural synchronization is sensitive to the behavioral outcome; specifically, the ability to correctly identify the second of two rapidly succeeding visual targets

Optimal time following fluorescein instillation to evaluate rigid gas permeable contact lens fit

PURPOSE: To examine the optimum time at which fluorescein patterns of gas permeable lenses (GPs) should be evaluated. METHODS: Aligned, 0.2mm steep and 0.2mm flat GPs were fitted to 17 patients (aged 20.6±1.1 years, 10 male). Fluorescein was applied to their upper temporal bulbar conjunctiva with a moistened fluorescein strip. Digital slit lamp images (CSO, Italy) at 10× magnification of the fluorescein pattern viewed with blue light through a yellow filter were captured every 15s. Fluorescein intensity in central, mid peripheral and edge regions of the superior, inferior, temporal and nasal quadrants of the lens were graded subjectively using a +2 to -2 scale and using ImageJ software on the simultaneously captured images. RESULTS: Subjectively graded and objectively image analysed fluorescein intensity changed with time (p<0.001), lens region (centre, mid-periphery and edge: p<0.05) and there was interaction between lens region with lens fit (p<0.001). For edge band width, there was a significant effect of time (F=118.503, p<0.001) and lens fit (F=5.1249, p=0.012). The expected alignment, flat and steep fitting patterns could be seen from approximately after 30 to 180s subjectively and 15 to 105s in captured images. CONCLUSION: Although the stability of fluorescein intensity can start to decline in as little as 45s post fluorescein instillation, the diagnostic pattern of alignment, steep or flat fit is seen in each meridian by subjective observation from about 30s to 3min indicating this is the most appropriate time window to evaluate GP lenses in clinical practice.

Use of time-resolved spectroscopy as a method to monitor carotenoids present in tomato extract obtained using ultrasound treatment

Introduction Compounds exhibiting antioxidant activity have received much interest in the food industry because of their potential health benefits. Carotenoids such as lycopene, which in the human diet mainly derives from tomatoes (Solanum lycopersicum), have attracted much attention in this aspect and the study of their extraction, processing and storage procedures is of importance. Optical techniques potentially offer advantageous non-invasive and specific methods to monitor them. Objectives To obtain both fluorescence and Raman information to ascertain if ultrasound assisted extraction from tomato pulp has a detrimental effect on lycopene. Method Use of time-resolved fluorescence spectroscopy to monitor carotenoids in a hexane extract obtained from tomato pulp with application of ultrasound treatment (583 kHz). The resultant spectra were a combination of scattering and fluorescence. Because of their different timescales, decay associated spectra could be used to separate fluorescence and Raman information. This simultaneous acquisition of two complementary techniques was coupled with a very high time-resolution fluorescence lifetime measurement of the lycopene. Results Spectroscopic data showed the presence of phytofluene and chlorophyll in addition to lycopene in the tomato extract. The time-resolved spectral measurement containing both fluorescence and Raman data, coupled with high resolution time-resolved measurements, where a lifetime of ~5 ps was attributed to lycopene, indicated lycopene appeared unaltered by ultrasound treatment. Detrimental changes were, however, observed in both chlorophyll and phytofluene contributions. Conclusion Extracted lycopene appeared unaffected by ultrasound treatment, while other constituents (chlorophyll and phytofluene) were degraded.

COLLABORATIVE TESTING ACROSS SHARED SOFTWARE COMPONENTS

Large component-based systems are often built from many of the same components. As individual component-based software systems are developed, tested and maintained, these shared components are repeatedly manipulated. As a result there are often significant overlaps and synergies across and among the different test efforts of different component-based systems. However, in practice, testers of different systems rarely collaborate, taking a test-all-by-yourself approach. As a result, redundant effort is spent testing common components, and important information that could be used to improve testing quality is lost. The goal of this research is to demonstrate that, if done properly, testers of shared software components can save effort by avoiding redundant work, and can improve the test effectiveness for each component as well as for each component-based software system by using information obtained when testing across multiple components. To achieve this goal I have developed collaborative testing techniques and tools for developers and testers of component-based systems with shared components, applied the techniques to subject systems, and evaluated the cost and effectiveness of applying the techniques. The dissertation research is organized in three parts. First, I investigated current testing practices for component-based software systems to find the testing overlap and synergy we conjectured exists. Second, I designed and implemented infrastructure and related tools to facilitate communication and data sharing between testers. Third, I designed two testing processes to implement different collaborative testing algorithms and applied them to large actively developed software systems. This dissertation has shown the benefits of collaborative testing across component developers who share their components. With collaborative testing, researchers can design algorithms and tools to support collaboration processes, achieve better efficiency in testing configurations, and discover inter-component compatibility faults within a minimal time window after they are introduced.

Time-of-use electricity tariffs with smart meters

This paper proposes a method for scheduling tariff time periods for electricity consumers. Europe will see a broader use of modern smart meters for electricity at residential consumers which must be used for enabling demand response. A heuristic-based method for tariff time period scheduling and pricing is proposed which considers different consumer groups with parameters studied a priori, taking advantage of demand response potential for each group and the fairness of electricity pricing for all consumers. This tool was applied to the case of Portugal, considering the actual network and generation costs, specific consumption profiles and overall electricity low voltage demand diagram. The proposed method achieves valid results. Its use will provide justification for the setting of tariff time periods by energy regulators, network operators and suppliers. It is also useful to estimate the consumer and electric sector benefits from changes in tariff time periods.

Electron theoretical investigation of the stability of the B2-TiFe compound

The metastable phase diagram of the BCC-based ordering equilibria in the Ti-Fe system has been calculated using a truncated cluster expansion, through the combination of FP-LAPW and cluster variation method (CVM) in the irregular tetrahedron cluster approximation. The results are compared with phenomenological CVM assessments of the system and suggest that the value for the experimental formation enthalpy of the B2-TiFe compound should be significantly more negative than the currently assessed value. (C) 2008 Elsevier B.V. All rights reserved.

Frequency Domain Connectivity Identification: An Application of Partial Directed Coherence in fMRI

Functional magnetic resonance imaging (fMRI) has become an important tool in Neuroscience due to its noninvasive and high spatial resolution properties compared to other methods like PET or EEG. Characterization of the neural connectivity has been the aim of several cognitive researches, as the interactions among cortical areas lie at the heart of many brain dysfunctions and mental disorders. Several methods like correlation analysis, structural equation modeling, and dynamic causal models have been proposed to quantify connectivity strength. An important concept related to connectivity modeling is Granger causality, which is one of the most popular definitions for the measure of directional dependence between time series. In this article, we propose the application of the partial directed coherence (PDC) for the connectivity analysis of multisubject fMRI data using multivariate bootstrap. PDC is a frequency domain counterpart of Granger causality and has become a very prominent tool in EEG studies. The achieved frequency decomposition of connectivity is useful in separating interactions from neural modules from those originating in scanner noise, breath, and heart beating. Real fMRI dataset of six subjects executing a language processing protocol was used for the analysis of connectivity. Hum Brain Mapp 30:452-461, 2009. (C) 2007 Wiley-Liss, Inc.

Preparation, characterization and in vitro cytotoxicity of BSA-based nanospheres containing nanosized magnetic particles and/or photosensitizer

This study reports on the preparation, characterization and in vitro toxicity test of a new nano-drug delivery system (NDDS) based on bovine serum albumin (BSA) nanospheres which incorporates surface-functionalized magnetic nanoparticles (MNP) and/or the silicon(IV) phthalocyanine (NzPc). The new NDDS was engineered for use in photodynamic therapy (PDT) combined with hyperthermia (HPT) to address cancer treatment. The BSA-based nanospheres, hosting NzPc, MNP or both (NzPc and MNP), present spherical shape with hydrodynamic average diameter values ranging from 170 to 450 nm and zeta potential of around -23 mV. No difference on the fluorescence spectrum of the encapsulated NzPc was found regardless of the presence of MNP. Time-dependent fluorescence measurements of the encapsulated NzPc revealed a bi-exponential decay for samples incorporating only NzPc and NzPc plus MNP, in the time window ranging from 1.70 to 5.20 ns. The in vitro assay, using human fibroblasts, revealed no cytotoxic effect in all samples investigated, demonstrating the potential of the tested system as a synergistic NDDS. (C) 2009 Elsevier B.V. All rights reserved.

Discrete and continuous models for dry masonry columns

The dynamic response of dry masonry columns can be approximated with finite-difference equations. Continuum models follow by replacing the difference quotients of the discrete model by corresponding differential expressions. The mathematically simplest of these models is a one-dimensional Cosserat theory. Within the presented homogenization context, the Cosserat theory is obtained by making ad hoc assumptions regarding the relative importance of certain terms in the differential expansions. The quality of approximation of the various theories is tested by comparison of the dispersion relations for bending waves with the dispersion relation of the discrete theory. All theories coincide with differences of less than 1% for wave-length-block-height (L/h) ratios bigger than 2 pi. The theory based on systematic differential approximation remains accurate up to L/h = 3 and then diverges rapidly. The Cosserat model becomes increasingly inaccurate for L/h < 2 pi. However, in contrast to the systematic approximation, the wave speed remains finite. In conclusion, considering its relative simplicity, the Cosserat model appears to be the natural starting point for the development of continuum models for blocky structures.

Spatio-temporal alignment of pedobarographic image sequences

O documento em anexo encontra-se na versão post-print (versão corrigida pelo editor).

Dynamical analysis of compositions

This paper analyzes musical opus from the point of view of two mathematical tools, namely the entropy and the multidimensional scaling (MDS). The Fourier analysis reveals a fractional dynamics, but the time rhythm variations are diluted along the spectrum. The combination of time-window entropy and MDS copes with the time characteristics and is well suited to treat a large volume of data. The experiments focus on a large number of compositions classified along three sets of musical styles, namely “Classical”, “Jazz”, and “Pop & Rock” compositions. Without lack of generality, the present study describes the application of the tools and the sets of musical compositions in a methodology leading to clear conclusions, but extensions to other possibilities are straightforward. The results reveal significant differences in the musical styles, demonstrating the feasibility of the proposed strategy and motivating further developments toward a dynamical analysis of musical compositions.