Efficient Optimization Algorithms for Nonlinear Data Analysis

Identification of low-dimensional structures and main sources of variation from multivariate data are fundamental tasks in data analysis. Many methods aimed at these tasks involve solution of an optimization problem. Thus, the objective of this thesis is to develop computationally efficient and theoretically justified methods for solving such problems. Most of the thesis is based on a statistical model, where ridges of the density estimated from the data are considered as relevant features. Finding ridges, that are generalized maxima, necessitates development of advanced optimization methods. An efficient and convergent trust region Newton method for projecting a point onto a ridge of the underlying density is developed for this purpose. The method is utilized in a differential equation-based approach for tracing ridges and computing projection coordinates along them. The density estimation is done nonparametrically by using Gaussian kernels. This allows application of ridge-based methods with only mild assumptions on the underlying structure of the data. The statistical model and the ridge finding methods are adapted to two different applications. The first one is extraction of curvilinear structures from noisy data mixed with background clutter. The second one is a novel nonlinear generalization of principal component analysis (PCA) and its extension to time series data. The methods have a wide range of potential applications, where most of the earlier approaches are inadequate. Examples include identification of faults from seismic data and identification of filaments from cosmological data. Applicability of the nonlinear PCA to climate analysis and reconstruction of periodic patterns from noisy time series data are also demonstrated. Other contributions of the thesis include development of an efficient semidefinite optimization method for embedding graphs into the Euclidean space. The method produces structure-preserving embeddings that maximize interpoint distances. It is primarily developed for dimensionality reduction, but has also potential applications in graph theory and various areas of physics, chemistry and engineering. Asymptotic behaviour of ridges and maxima of Gaussian kernel densities is also investigated when the kernel bandwidth approaches infinity. The results are applied to the nonlinear PCA and to finding significant maxima of such densities, which is a typical problem in visual object tracking.

Stiffness based trajectory planning and feedforward based vibration suppression control of parallel robot machines

The dissertation proposes two control strategies, which include the trajectory planning and vibration suppression, for a kinematic redundant serial-parallel robot machine, with the aim of attaining the satisfactory machining performance. For a given prescribed trajectory of the robot's end-effector in the Cartesian space, a set of trajectories in the robot's joint space are generated based on the best stiffness performance of the robot along the prescribed trajectory. To construct the required system-wide analytical stiffness model for the serial-parallel robot machine, a variant of the virtual joint method (VJM) is proposed in the dissertation. The modified method is an evolution of Gosselin's lumped model that can account for the deformations of a flexible link in more directions. The effectiveness of this VJM variant is validated by comparing the computed stiffness results of a flexible link with the those of a matrix structural analysis (MSA) method. The comparison shows that the numerical results from both methods on an individual flexible beam are almost identical, which, in some sense, provides mutual validation. The most prominent advantage of the presented VJM variant compared with the MSA method is that it can be applied in a flexible structure system with complicated kinematics formed in terms of flexible serial links and joints. Moreover, by combining the VJM variant and the virtual work principle, a systemwide analytical stiffness model can be easily obtained for mechanisms with both serial kinematics and parallel kinematics. In the dissertation, a system-wide stiffness model of a kinematic redundant serial-parallel robot machine is constructed based on integration of the VJM variant and the virtual work principle. Numerical results of its stiffness performance are reported. For a kinematic redundant robot, to generate a set of feasible joints' trajectories for a prescribed trajectory of its end-effector, its system-wide stiffness performance is taken as the constraint in the joints trajectory planning in the dissertation. For a prescribed location of the end-effector, the robot permits an infinite number of inverse solutions, which consequently yields infinite kinds of stiffness performance. Therefore, a differential evolution (DE) algorithm in which the positions of redundant joints in the kinematics are taken as input variables was employed to search for the best stiffness performance of the robot. Numerical results of the generated joint trajectories are given for a kinematic redundant serial-parallel robot machine, IWR (Intersector Welding/Cutting Robot), when a particular trajectory of its end-effector has been prescribed. The numerical results show that the joint trajectories generated based on the stiffness optimization are feasible for realization in the control system since they are acceptably smooth. The results imply that the stiffness performance of the robot machine deviates smoothly with respect to the kinematic configuration in the adjacent domain of its best stiffness performance. To suppress the vibration of the robot machine due to varying cutting force during the machining process, this dissertation proposed a feedforward control strategy, which is constructed based on the derived inverse dynamics model of target system. The effectiveness of applying such a feedforward control in the vibration suppression has been validated in a parallel manipulator in the software environment. The experimental study of such a feedforward control has also been included in the dissertation. The difficulties of modelling the actual system due to the unknown components in its dynamics is noticed. As a solution, a back propagation (BP) neural network is proposed for identification of the unknown components of the dynamics model of the target system. To train such a BP neural network, a modified Levenberg-Marquardt algorithm that can utilize an experimental input-output data set of the entire dynamic system is introduced in the dissertation. Validation of the BP neural network and the modified Levenberg- Marquardt algorithm is done, respectively, by a sinusoidal output approximation, a second order system parameters estimation, and a friction model estimation of a parallel manipulator, which represent three different application aspects of this method.

Development of an HTR-10 model in the Serpent reactor physics code

The use of exact coordinates of pebbles and fuel particles of pebble bed reactor modelling becoming possible in Monte Carlo reactor physics calculations is an important development step. This allows exact modelling of pebble bed reactors with realistic pebble beds without the placing of pebbles in regular lattices. In this study the multiplication coefficient of the HTR-10 pebble bed reactor is calculated with the Serpent reactor physics code and, using this multiplication coefficient, the amount of pebbles required for the critical load of the reactor. The multiplication coefficient is calculated using pebble beds produced with the discrete element method and three different material libraries in order to compare the results. The received results are lower than those from measured at the experimental reactor and somewhat lower than those gained with other codes in earlier studies.

Contrast sensitivity to radial frequencies modulated by Jn and j n Bessel profiles

We measured human contrast sensitivity to radial frequencies modulated by cylindrical (Jo) and spherical (j o) Bessel profiles. We also measured responses to profiles of j o, j1, j2, j4, j8, and j16. Functions were measured three times by at least three of eight observers using a forced-choice method. The results conform to our expectations that sensitivity would be higher for cylindrical profiles. We also observed that contrast sensitivity is increased with the j n order for n greater than zero, having distinct orderly effects at the low and high frequency ends. For n = 0, 1, 2, and 4 sensitivity tended to occur around 0.8-1.0 cpd while for n = 8 and 16 it seemed to shift gradually to 0.8-3.0 cpd. We interpret these results as being consistent with the possibility that spatial frequency processing by the human visual system can be defined a priori in terms of polar coordinates and discuss its application to study face perception.

Palvelutuotteiden strateginen johtaminen suunnitteluliiketoiminnassa

Tutkimuksen tarkoituksena oli löytää suunnitteluliiketoiminnan palvelutuotteiden strategisen johdon käyttöön soveltuva menetelmä, tai työkalu, jonka avulla palvelutuotteiden kilpailukykyä ja kehitystarpeita voidaan helposti arvioida. Diplomityö pitää sisällään kolme tutkimuskysymystä. Ensimmäisellä tutkimuskysymyksellä pyritään keräämään tietoa suunnitteluorganisaation taustalla vaikuttavista menestystekijöistä. Toisen tutkimuskysymyksen avulla pyrittiin löytämään työkalu, tai menetelmä, palvelutuotteiden strategisen johdon käyttöön, tai sellaisen muodostamisen pohjaksi. Kolmas tutkimuskysymys liittyi suunnittelupalveluiden strategisen johtamisen työkalun muodostamiseen. Tutkimuksen tuloksena tuotettiin suunnitteluorganisaation palvelutuotteiden johtamisen viitekehys. Viitekehyksessä palvelutuotteet lajitellaan havainnolliselle luokittelutaululle, jossa pystykoordinaattina käytetään palvelutuotteen markkinoiden houkuttelevuutta ja vaakakoordinaattina palvelutuotteen vahvuutta organisaatiossa. Tutkimuksessa on esitetty suunnitteluliiketoiminnan strategisen johtamisen onnistumisessa vaikuttavat taustatekijät, markkinoiden houkuttelevuuden keskeisimmät mittarit, sekä suunnittelupalveluiden vahvuutta kuvaavat tekijät.

Lesions of the commissural subnucleus of the nucleus of the solitary tract increase isoproterenol-induced water intake

The nucleus of the solitary tract (NTS) is the primary site of the cardiovascular afferent information about arterial blood pressure and volume. The NTS projects to areas in the central nervous system involved in cardiovascular regulation and hydroelectrolyte balance, such as the anteroventral third ventricle region and the lateral parabrachial nucleus. The aim of the present study was to investigate the effects of electrolytic lesion of the commissural NTS on water and 0.3 M NaCl intake and the cardiovascular responses to subcutaneous injection of isoproterenol. Male Holtzman rats weighing 280 to 320 g were submitted to sham lesion or electrolytic lesion of the commissural NTS (N = 6-15/group). The sham-lesioned rats had the electrode placed along the same coordinates, except that no current was passed. Water intake induced by subcutaneous isoproterenol (30 µg/kg body weight) significantly increased in chronic (15 days) commissural NTS-lesioned rats (to 2.4 ± 0.2 vs sham: 1.9 ± 0.2 mL 100 g body weight-1 60 min-1). Isoproterenol did not induce any sodium intake in sham or in commissural NTS-lesioned rats. The isoproterenol-induced hypotension (sham: -27 ± 4 vs commissural NTS-lesioned rats: -22 ± 4 mmHg/20 min) and tachycardia (sham: 168 ± 10 vs commissural NTS: 144 ± 24 bpm/20 min) were not different between groups. The present results suggest that the commissural NTS is part of an inhibitory neural pathway involved in the control of water intake induced by subcutaneous isoproterenol, and that the overdrinking observed in lesioned rats is not the result of a cardiovascular imbalance in these animals.

Nuclear calcium signaling: a cell within a cell

Calcium (Ca2+) is a versatile second messenger that regulates a wide range of cellular functions. Although it is not established how a single second messenger coordinates diverse effects within a cell, there is increasing evidence that the spatial patterns of Ca2+ signals may determine their specificity. Ca2+ signaling patterns can vary in different regions of the cell and Ca2+ signals in nuclear and cytoplasmic compartments have been reported to occur independently. No general paradigm has been established yet to explain whether, how, or when Ca2+ signals are initiated within the nucleus or their function. Here we highlight that receptor tyrosine kinases rapidly translocate to the nucleus. Ca2+ signals that are induced by growth factors result from phosphatidylinositol 4,5-bisphosphate hydrolysis and inositol 1,4,5-trisphosphate formation within the nucleus rather than within the cytoplasm. This novel signaling mechanism may be responsible for growth factor effects on cell proliferation.

The Streptococcus mutans GlnR protein exhibits an increased affinity for the glnRA operon promoter when bound to GlnK

The control of nitrogen metabolism in pathogenic Gram-positive bacteria has been studied in a variety of species and is involved with the expression of virulence factors. To date, no data have been reported regarding nitrogen metabolism in the odontopathogenic species Streptococcus mutans. GlnR, which controls nitrogen assimilation in the related bacterial species, Bacillus subtilis, was assessed in S. mutans for its DNA and protein binding activity. Electrophoretic mobility shift assay of the S. mutans GlnR protein indicated that GlnR binds to promoter regions of the glnRA and amtB-glnK operons. Cross-linking and pull-down assays demonstrated that GlnR interacts with GlnK, a signal transduction protein that coordinates the regulation of nitrogen metabolism. Upon formation of this stable complex, GlnK enhances the affinity of GlnR for the glnRA operon promoter. These results support an involvement of GlnR in transcriptional regulation of nitrogen metabolism-related genes and indicate that GlnK relays information regarding ammonium availability to GlnR.

Neural regulation of the stress response: glucocorticoid feedback mechanisms

The mammalian stress response is an integrated physiological and psychological reaction to real or perceived adversity. Glucocorticoids are an important component of this response, acting to redistribute energy resources to both optimize survival in the face of challenge and to restore homeostasis after the immediate challenge has subsided. Release of glucocorticoids is mediated by the hypothalamo-pituitary-adrenal (HPA) axis, driven by a neural signal originating in the paraventricular nucleus (PVN). Stress levels of glucocorticoids bind to glucocorticoid receptors in multiple body compartments, including the brain, and consequently have wide-reaching actions. For this reason, glucocorticoids serve a vital function in negative feedback inhibition of their own secretion. Negative feedback inhibition is mediated by a diverse collection of mechanisms, including fast, non-genomic feedback at the level of the PVN, stress-shut-off at the level of the limbic system, and attenuation of ascending excitatory input through destabilization of mRNAs encoding neuropeptide drivers of the HPA axis. In addition, there is evidence that glucocorticoids participate in stress activation via feed-forward mechanisms at the level of the amygdala. Feedback deficits are associated with numerous disease states, underscoring the necessity for adequate control of glucocorticoid homeostasis. Thus, rather than having a single, defined feedback ‘switch’, control of the stress response requires a wide-reaching feedback ‘network’ that coordinates HPA activity to suit the overall needs of multiple body systems.

Differential effects of aging on spatial contrast sensitivity to linear and polar sine-wave gratings

Changes in visual function beyond high-contrast acuity are known to take place during normal aging. We determined whether sensitivity to linear sine-wave gratings and to an elementary stimulus preferentially processed in extrastriate areas could be distinctively affected by aging. We measured spatial contrast sensitivity twice for concentric polar (Bessel) and vertical linear gratings of 0.6, 2.5, 5, and 20 cycles per degree (cpd) in two age groups (20-30 and 60-70 years). All participants were free of identifiable ocular disease and had normal or corrected-to-normal visual acuity. Participants were more sensitive to Cartesian than to polar gratings in all frequencies tested, and the younger adult group was more sensitive to all stimuli tested. Significant differences between sensitivities of the two groups were found for linear (only 20 cpd; P<0.01) and polar gratings (all frequencies tested; P<0.01). The young adult group was significantly more sensitive to linear than to circular gratings in the 20 cpd frequency. The older adult group was significantly more sensitive to linear than to circular gratings in all spatial frequencies, except in the 20 cpd frequency. The results suggest that sensitivity to the two kinds of stimuli is affected differently by aging. We suggest that neural changes in the aging brain are important determinants of this difference and discuss the results according to current models of human aging.

Instrumental color and sensory acceptance of soy-based emulsions: a response surface approach

Response Surface Methodology (RSM) was applied to evaluate the chromatic features and sensory acceptance of emulsions that combine Soy Protein (SP) and red Guava Juice (GJ). The parameters analyzed were: instrumental color based on the coordinates a* (redness), b* (yellowness), L* (lightness), C* (chromaticity), h* (hue angle), visual color, acceptance, and appearance. The analyses of the results showed that GJ was responsible for the high measured values of red color, hue angle, chromaticity, acceptance, and visual color, whereas SP was the variable that increased the yellowness intensity of the assays. The redness (R²adj = 74.86%, p < 0.01) and hue angle (R²adj = 80.96%, p < 0.01) were related to the independent variables by linear models, while the sensory data (color and acceptance) could not be modeled due to a high variability. The models of yellowness, lightness, and chromaticity did not present lack of fit but presented adjusted determination coefficients bellow 70%. Notwithstanding, the linear correlations between sensory and instrumental data were not significant (p > 0.05) and low Pearson coefficients were obtained. The results showed that RSM is a useful tool to develop soy-based emulsions and model some chromatic features of guava-based emulsions through RSM.

Sensory stability of whole mango juice: influence of temperature and storage time

This study investigated the degradation kinetics of the sensory attributes of commercial whole mango (cv. Ubá) juice and evaluated its sensory acceptability during storage. Samples of the product were stored in a BOD incubator at 25, 35, and 45 ºC under 24 hours light (650 lux) for 120 days. Sensory analyses (Quantitative Descriptive Analysis - QDA) were conducted with trained panel and consumers. The correlations between sensory and physicochemical characteristics (instrumental color and vitamin C content) were also assessed. Flavor, aroma, and color vary with temperature and time of storage. Aroma and flavor were most affected by temperature with values of Q10 and Ea equal to 4.16 and 25.31 kcal.mol-1; and 3.61 and 22.80 kcal.mol-1, respectively. The sensory changes observed by the trained panel are related to the degradation of vitamin C and changes in the color coordinates (L* and ΔE*) of mango juice. However, consumers were unable to detect changes in the overall quality of the juices. It was observed that the QDA can be a useful tool to assess shelf-life.

Stability of frozen marolo pulp during storage

Marolo, also known as araticum or head-to-black, is a globular berry, a species native to the Brazilian savannah. The aim of this study was to evaluate the physical, chemical, and microbiological stability of frozen marolo pulp during 12 months of frozen storage. It was observed that the levels of ash (0.28-0.22%), protein (0.77-0.71%), lipids (1.75-1.73%), carbohydrates (12.1-10.15%), calorie (67.23-59.01 kcal), sucrose (2.50-1.29%), citric acid (435.63-197.5 µg.g-1), tartaric acid (4.38-1.88 µg.g-1) , acetic acid (470.38-279.25 µg.g-1), ascorbic acid (3.00-0.00 µg.g-1), total pectin (0.67-0.39%), pH (3.88-3.83), and b* chromaticity coordinates (24.85-20.53) decreased reduced during storage, whereas the levels of moisture (85.10-87.19%), color parameters (L* 58.89-62.62 and a* 5.37-7.86), reducing sugars (4.53-5.62%), total soluble sugars (7.1-7.36%), soluble solids (7.0-8.4 ºBrix), total acidity (0.9-1.0%), malic acid (514.13-781.25 µg.g-1), soluble pectin (0.16-0.24%), and antioxidant (6.85-37.35% of DPPH discoloration) increased over the one-year of storage period. According to the physical, chemical, and microbiological parameters assessed, the product can be stored for 12 months without loss of quality with addition of citric acid as a preservative.

Stability of astaxanthin in yogurt used to simulate apricot color, under refrigeration

The aim of this study was to incorporate astaxanthin to yogurts with different fat content to match apricot (Prunus armeniaca L.) color. The samples containing astaxanthin were stored at 5 ± 3 °C, and color stability and astaxanthin content were determined by colorimetry and high performance liquid chromatography (HPLC), respectively. Yogurt samples were analyzed in triplicate every 24 hours for one week and subsequently every week for 3 more weeks There were no significant differences (p < 0.05) between astaxanthin concentration values at 0 and 28 days for both samples; therefore, it can be said that the fat content in the yogurt had not effect on the stability of pigment. The low dispersion of the data showed uniformity in the three chromaticity coordinates L*, a*, b* throughout the storage period for both types of yogurt. Values of ∆E ≥ 5.0 were not obtained at any time during storage, indicating high stability of the pigment.

A complexidade e o construtivismo na economia

Complexity and constructivism in economics. This paper attempts to show and summarize the concept of rules, order and complexity introduced around the mid-twentieth century by Friedrich August von Hayek. It also attempts to create a current parallel between those concepts and the field of complexity economics. At the time of his writings, the author sought to present arguments against the Cartesian rationality. Nowadays, the concepts presented by him could also serve as arguments against the way of thought used in mainstream microeconomics. A debate can now be seen between the mainstream microeconomics and the authors of the complexity theory applied to the economy, which can be understood as explanations guided by generic assumptions versus natural explanations guided in a computational approach.