Generative models of the human connectome.

The human connectome represents a network map of the brain's wiring diagram and the pattern into which its connections are organized is thought to play an important role in cognitive function. The generative rules that shape the topology of the human connectome remain incompletely understood. Earlier work in model organisms has suggested that wiring rules based on geometric relationships (distance) can account for many but likely not all topological features. Here we systematically explore a family of generative models of the human connectome that yield synthetic networks designed according to different wiring rules combining geometric and a broad range of topological factors. We find that a combination of geometric constraints with a homophilic attachment mechanism can create synthetic networks that closely match many topological characteristics of individual human connectomes, including features that were not included in the optimization of the generative model itself. We use these models to investigate a lifespan dataset and show that, with age, the model parameters undergo progressive changes, suggesting a rebalancing of the generative factors underlying the connectome across the lifespan.

Phylogenomics Controlling for Base Compositional Bias Reveals a Single Origin of Eusociality in Corbiculate Bees.

As increasingly large molecular data sets are collected for phylogenomics, the conflicting phylogenetic signal among gene trees poses challenges to resolve some difficult nodes of the Tree of Life. Among these nodes, the phylogenetic position of the honey bees (Apini) within the corbiculate bee group remains controversial, despite its considerable importance for understanding the emergence and maintenance of eusociality. Here, we show that this controversy stems in part from pervasive phylogenetic conflicts among GC-rich gene trees. GC-rich genes typically have a high nucleotidic heterogeneity among species, which can induce topological conflicts among gene trees. When retaining only the most GC-homogeneous genes or using a nonhomogeneous model of sequence evolution, our analyses reveal a monophyletic group of the three lineages with a eusocial lifestyle (honey bees, bumble bees, and stingless bees). These phylogenetic relationships strongly suggest a single origin of eusociality in the corbiculate bees, with no reversal to solitary living in this group. To accurately reconstruct other important evolutionary steps across the Tree of Life, we suggest removing GC-rich and GC-heterogeneous genes from large phylogenomic data sets. Interpreted as a consequence of genome-wide variations in recombination rates, this GC effect can affect all taxa featuring GC-biased gene conversion, which is common in eukaryotes.

TOP - um programa de cálculo de descritores topológicos para uso em correlações entre estrutura e atividade

A computational interface, using sybyl format as an input file, was created in order to calculate connectivity indexes. After generation and classification of all substructures, which derive from the molecular structure, this interface calculates all possible orders from zero up to the maximun number of bonds in the molecule. Other topological indexes such as Wiener and Schultz indexes can also be calculated.

Estudo do coeficiente de partição octanol-água de bifenilas policloradas (PCBs) utilizando parâmetros topológicos

A model based on chemical structure was developed for the accurate prediction of octanol/water partition coefficient (K OW) of polychlorinated biphenyls (PCBs), which are molecules of environmental interest. Partial least squares (PLS) was used to build the regression model. Topological indices were used as molecular descriptors. Variable selection was performed by Hierarchical Cluster Analysis (HCA). In the modeling process, the experimental K OW measured for 30 PCBs by thin-layer chromatography - retention time (TLC-RT) has been used. The developed model (Q² = 0,990 and r² = 0,994) was used to estimate the log K OW values for the 179 PCB congeners whose K OW data have not yet been measured by TLC-RT method. The results showed that topological indices can be very useful to predict the K OW.

Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7

Nitrophorins represent a unique class of heme proteins that are able to perform the delicate transportation and release of the free-radical gaseous messenger nitric oxide (NO) in a pH-triggered manner. Besides its ability to bind to phospholipid membranes, the N-terminus contains an additional Leu-Pro-Gly stretch, which is a unique sequence trait, and the heme cavity is significantly altered with respect to other nitrophorins. These distinctive features encouraged us to solve the X-ray crystallographic structures of NP7 at low and high pH and bound with different heme ligands (nitric oxide, histamine, imidazole). The overall fold of the lipocalin motif is well preserved in the different X-ray structures and resembles the fold of other nitrophorins. However, a chain-like arrangement in the crystal lattice due to a number of head-to-tail electrostatic stabilizing interactions is found in NP7. Furthermore, the X-ray structures also reveal ligand-dependent changes in the orientation of the heme, as well as in specific interactions between the A-B and G-H loops, which are considered to be relevant for the biological function of nitrophorins. Fast and ultrafast laser triggered ligand rebinding experiments demonstrate the pH-dependent ligand migration within the cavities and the exit route. Finally, the topological distribution of pockets located around the heme as well as from inner cavities present at the rear of the protein provides a distinctive feature in NP7, so that while a loop gated exit mechanism to the solvent has been proposed for most nitrophorins, a more complex mechanism that involves several interconnected gas hosting cavities is proposed for NP7.

Highly eccentric hip-hop solutions of the 2N

We show the existence of families of hip-hop solutions in the equal-mass 2N-body problem which are close to highly eccentric planar elliptic homographic motions of 2N bodies plus small perpendicular non-harmonic oscillations. By introducing a parameter ϵ, the homographic motion and the small amplitude oscillations can be uncoupled into a purely Keplerian homographic motion of fixed period and a vertical oscillation described by a Hill type equation. Small changes in the eccentricity induce large variations in the period of the perpendicular oscillation and give rise, via a Bolzano argument, to resonant periodic solutions of the uncoupled system in a rotating frame. For small ϵ ≠ 0, the topological transversality persists and Brouwer's fixed point theorem shows the existence of this kind of solutions in the full system

Aromaticidade: evolução histórica do conceito e critérios quantitativos

In this paper the evolution of the concept of aromaticity is discussed. It considers not only historical aspects of the aromaticity concept but also the different criteria (theoretical and experimental) that have appeared to explain the properties of the aromatic compounds. The topics range from the isolation of benzene by Faraday (1825) until the modern criteria based on geometries, magnetic properties, resonance energy (RE), aromatic stabilization energy (ASE), topological analyses, and others. A chronological separation of issues concerning aromaticity was made, splitting the definitions before and after the appearance of the quantum chemistry. This work reviews the concept of aromaticity.

Estudos de QSAR 2D baseados em descritores topológicos e fragmentos moleculares para uma série de derivados azólicos ativos contra Candida albicans

Azole derivatives are the main therapeutical resource against Candida albicans infection in immunocompromised patients. Nevertheless, the widespread use of azoles has led to reduced effectiveness and selection of resistant strains. In order to guide the development of novel antifungal drugs, 2D-QSAR models based on topological descriptors or molecular fragments were developed for a dataset of 74 molecules. The optimal fragment-based model (r² = 0.88, q² = 0.73 and r²pred = 0.62 with 6PCs) and descriptor-based model (r² = 0.82, q² = 0.79 and r²pred = 0.70 with 2 PCs), when analysed synergically, suggested that the triazolone ring and lipophilic properties are both important to antifungal activity.

A FORMAÇÃO DE LIGAÇÕES DE HIDROGÊNIO π‧‧‧H, F‧‧‧H E C‧‧‧H NOS COMPLEXOS C2H2‧‧‧(HF), C2H2‧‧‧2(HF) E C2H2‧‧‧3(HF)

In this work, a theoretical study on the basis of structural, vibrational, electronic and topological parameters of the C2H2‧‧‧(HF), C2H2‧‧‧2(HF) and C2H2‧‧‧3(HF) complexes concerning the formation of π‧‧‧H, F‧‧‧H and C‧‧‧H hydrogen bonds is presented. The main difference among these complexes is not properly the interaction strength, but the hydrogen bond type whose benchmark is ruled justly by the structure. Meanwhile, the occurrence of π‧‧‧H hydrogen bonds was unveiled in both C2H2‧‧‧(HF) dimer and C2H2‧‧‧3(HF) tetramer, although in latter, this interaction is stronger than C‧‧‧H of the C2H2‧‧‧2(HF) trimer. However, the F‧‧‧H hydrogen bonds within the subunits of hydrofluoric acid are the strongest ones, reaching a partial covalent limit, and thereby contribute decisively to the stabilization of the tetramer structure. In line with this, the largest red-shifts were observed on the hydrofluoric acid trimer of the C2H2‧‧‧3(HF) complex.

Thermal modelling of semiconductor switches in three-level Neutral Point Clamped Medium Voltage DTC-inverter

The aim of this thesis is to investigate the thermal loading of medium voltage three-level NPC inverter’s semiconductor IGCT switches in different operation points. The objective is to reach both a fairly accurate off-line simulation program and also so simple a simulation model that its implementation into an embedded system could be reasonable in practice and a real time use should become feasible. Active loading limitation of the inverter can be realized with a thermal model which is practical in a real time use. Determining of the component heating has been divided into two parts; defining of component losses and establishing the structure of a thermal network. Basics of both parts are clarified. The simulation environment is Matlab-Simulink. Two different models are constructed – a more accurate one and a simplified one. Potential simplifications are clarified with the help of the first one. Simplifications are included in the latter model and the functionalities of both models are compared. When increasing the calculation time step a decreased number of considered components and time constants of the thermal network can be used in the simplified model. Heating of a switching component is dependent on its topological position and inverter’s operation point. The output frequency of the converter defines mainly which one of the switching components is – because of its losses and heating – the performance limiting component of the converter. Comparison of results given by different thermal models demonstrates that with larger time steps, describing of fast occurring switching losses becomes difficult. Generally articles and papers dealing with this subject are written for two-level inverters. Also inverters which apply direct torque control (DTC) are investigated rarely from the heating point of view. Hence, this thesis completes the former material.

Photoinhibition of Photosystem II. Kinetics, Photoprotection and Mechanism

Photosystem II (PSII) is susceptible to light-induced damage defined as photoinhibition. In natural conditions, plants are capable of repairing the photoinhibited PSII by on-going degradation and re-synthesis of the D1 reaction centre protein of PSII. Photoinhibition is induced by both visible and ultraviolet light and photoinhibition occurs under all light intensities with the same efficiency per photon. In my thesis work, I studied the reaction kinetics and mechanism of photoinhibition of PSII, as well as photoprotection in leaves of higher plants. Action spectroscopy was used to identify photoreceptors of photoinhibition. I found that the action spectrum of photoinhibition in vivo shows resemblance to the absorption spectra of manganese model compounds of the oxygen evolving complex (OEC) suggesting a role for manganese as a photoreceptor of photoinhibition under UV and visible light. In order to study the protective effect of non-photochemical quenching, the action spectrum was measured from leaves of wild type Arabidopsis thaliana and two mutants impaired in nonphotochemical quenching of chlorophyll a excitations. The findings of action spectroscopy and simulations of chlorophyll-based photoinhibition mechanisms suggested that quenching of antenna excitations protects less efficiently than would be expected if antenna chlorophylls were the only photoreceptors of photoinhibition. The reaction kinetics of prolonged photoinhibition was studied in leaves of Cucurbita maxima and Capsicum annuum. The results indicated that photoinhibitory decrease in both the oxygen evolution activity and ratio of variable to maximum fluorescence follows firstorder kinetics in vivo. The persistence of first-order kinetics suggests that already photoinhibited reaction centres do not protect against photoinhibition and that the mechanism of photoinhibition does not have a reversible intermediate. When Cucurbita maxima leaves were photoinhibited with saturating single-turnover flashes and continuous light, the light response curve of photoinhibition was found to be essentially a straight line with both types of illumination, suggesting that similar photoinhibition mechanisms might function during illumination with continuous light and during illumination with short flashes.

On Undecidable Dynamical Properties of Reversible One-Dimensional Cellular Automata

Cellular automata are models for massively parallel computation. A cellular automaton consists of cells which are arranged in some kind of regular lattice and a local update rule which updates the state of each cell according to the states of the cell's neighbors on each step of the computation. This work focuses on reversible one-dimensional cellular automata in which the cells are arranged in a two-way in_nite line and the computation is reversible, that is, the previous states of the cells can be derived from the current ones. In this work it is shown that several properties of reversible one-dimensional cellular automata are algorithmically undecidable, that is, there exists no algorithm that would tell whether a given cellular automaton has the property or not. It is shown that the tiling problem of Wang tiles remains undecidable even in some very restricted special cases. It follows that it is undecidable whether some given states will always appear in computations by the given cellular automaton. It also follows that a weaker form of expansivity, which is a concept of dynamical systems, is an undecidable property for reversible one-dimensional cellular automata. It is shown that several properties of dynamical systems are undecidable for reversible one-dimensional cellular automata. It shown that sensitivity to initial conditions and topological mixing are undecidable properties. Furthermore, non-sensitive and mixing cellular automata are recursively inseparable. It follows that also chaotic behavior is an undecidable property for reversible one-dimensional cellular automata.

Lärande som text : en dramapedagogiskt förankrad läsning av det kroppsliga, rumsliga och retoriska i kunskapsbildande processer

My presupposition, that learning at some level deals with life praxis, is expressed in four metaphors: space, time, fable and figure. Relations between learning,knowledge building and meaning making are linked to the concept of personal knowledge. I present a two part study of learning as text in a drama pedagogical rooted reading where learning is framed as the ongoing event, and knowledge, as the product of previous processes, is framed as culturally formed utterances. A frame analysis model is constructed as a topological guide for relations between the two concepts learning and knowledge. It visualises an aesthetic understanding, rooted in drama pedagogical comprehension. Insight and perception are linked in an inner relationship that is neither external nor identical. This understanding expresses the movement "in between" connecting asymmetrical and nonlinear features of human endeavour and societal issues. The performability of bodily and oral participation in the learning event in a socio-cultural setting is analysed as a dialogised text. In an ethnographical case study I have gathered material with an interest for the particular. The empirical material is based on three problem based learning situations in a Polytechnic setting. The act of transformation in the polyphony of the event is considered as a turning point in the narrative employment. Negotiation and figuration in the situation form patterns of the space for improvisation (flow) and tensions at the boundaries (thresholds) which imply the logical structure of transformation. Learning as a dialogised text of "yes" and "no", of structure and play for the improvised, interrelate in that movement. It is related to both the syntagmic and the paradigmatic forms of thinking. In the philosophical study, forms of understanding are linked to the logical structure of transformation as a cultural issue. The classical rhetorical concepts of Logos, Pathos, Ethos and Mythos are connected to the multidimensional rationality of the human being. In the Aristotelian form of knowledge, phronesis,a logic structure of inquiry is recognised. The shifting of perspectives between approaches, the construction of knowledge as context and the human project of meaning making as a subtext, illuminates multiple layers of the learning text. In an argumentation that post-modern apprehension of knowledge, emphasising contextual and situational values, has an empowering impact on learning, I find pedagogical benefits. The dialogical perspective has opened lenses that manage to hold in aesthetic doubling the individual action of inquiry and the stage with its cultural tools in a three dimensional reading.

Broadband excitation in the system identification of active magnetic bearing rotor systems

One of the targets of the climate and energy package of the European Union is to increase the energy efficiency in order to achieve a 20 percent reduction in primary energy use compared with the projected level by 2020. The energy efficiency can be improved for example by increasing the rotational speed of large electrical drives, because this enables the elimination of gearboxes leading to a compact design with lower losses. The rotational speeds of traditional bearings, such as roller bearings, are limited by mechanical friction. Active magnetic bearings (AMBs), on the other hand, allow very high rotational speeds. Consequently, their use in large medium- and high-speed machines has rapidly increased. An active magnetic bearing rotor system is an inherently unstable, nonlinear multiple-input, multiple-output system. Model-based controller design of AMBs requires an accurate system model. Finite element modeling (FEM) together with the experimental modal analysis provides a very accurate model for the rotor, and a linearized model of the magneticactuators has proven to work well in normal conditions. However, the overall system may suffer from unmodeled dynamics, such as dynamics of foundation or shrink fits. This dynamics can be modeled by system identification. System identification can also be used for on-line diagnostics. In this study, broadband excitation signals are adopted to the identification of an active magnetic bearing rotor system. The broadband excitation enables faster frequency response function measurements when compared with the widely used stepped sine and swept sine excitations. Different broadband excitations are reviewed, and the random phase multisine excitation is chosen for further study. The measurement times using the multisine excitation and the stepped sine excitation are compared. An excitation signal design with an analysis of the harmonics produced by the nonlinear system is presented. The suitability of different frequency response function estimators for an AMB rotor system are also compared. Additionally, analytical modeling of an AMB rotor system, obtaining a parametric model from the nonparametric frequency response functions, and model updating are discussed in brief, as they are key elements in the modeling for a control design. Theoretical methods are tested with a laboratory test rig. The results conclude that an appropriately designed random phase multisine excitation is suitable for the identification of AMB rotor systems.

Chaos and Unpredictability in the Vibration of an Elasto-Plastic Beam

This contribution discusses the nonlinear dynamics of a pin-ended elasto-plastic beam with both kinematic and isotropic hardening. An iterative numerical procedure based on the operator split technique is developed in order to deal with the nonlinearities in the equations of motion. Free and forced responses for harmonic sinusoidal and square wave excitations are investigated. Numerical simulations present many interesting behaviors such as jump phenomena, sensitivity to initial conditions, chaos and transient chaos. These results indicate that there are practical problems in predicting the response of the beam even when periodic steady state response is expected.