Point mutations and sequence variability in proteins: Redistributions of preexisting populations

Here we study the effect of point mutations in proteins on the redistributions of the conformational substates. We show that regardless of the location of a mutation in the protein structure and of its type, the observed movements of the backbone recur largely at the same positions in the structures. Despite the different interactions that are disrupted and formed by the residue substitution, not only are the conformations very similar, but the regions that move are also the same, regardless of their sequential or spatial distance from the mutation. This observation leads us to conclude that, apart from some extreme cases, the details of the interactions are not critically important in determining the protein conformation or in specifying which parts of the protein would be more prone to take on different local conformations in response to changes in the sequence. This finding further illustrates why proteins manifest a robustness toward many mutational events. This nonuniform distribution of the conformer population is consistently observed in a variety of protein structural types. Topology is critically important in determining folding pathways, kinetics, building block cutting, and anatomy trees. Here we show that topology is also very important in determining which regions of the protein structure will respond to sequence changes, regardless of the sequential or spatial location of the mutation.

Rapidly induced auditory plasticity: The ventriloquism aftereffect

Cortical representational plasticity has been well documented after peripheral and central injuries or improvements in perceptual and motor abilities. This has led to inferences that the changes in cortical representations parallel and account for the improvement in performance during the period of skill acquisition. There have also been several examples of rapidly induced changes in cortical neuronal response properties, for example, by intracortical microstimulation or by classical conditioning paradigms. This report describes similar rapidly induced changes in a cortically mediated perception in human subjects, the ventriloquism aftereffect, which presumably reflects a corresponding change in the cortical representation of acoustic space. The ventriloquism aftereffect describes an enduring shift in the perception of the spatial location of acoustic stimuli after a period of exposure of spatially disparate and simultaneously presented acoustic and visual stimuli. Exposure of a mismatch of 8° for 20–30 min is sufficient to shift the perception of acoustic space by approximately the same amount across subjects and acoustic frequencies. Given that the cerebral cortex is necessary for the perception of acoustic space, it is likely that the ventriloquism aftereffect reflects a change in the cortical representation of acoustic space. Comparisons between the responses of single cortical neurons in the behaving macaque monkey and the stimulus parameters that give rise to the ventriloquism aftereffect suggest that the changes in the cortical representation of acoustic space may begin as early as the primary auditory cortex.

Mechanisms and streams for processing of “what” and “where” in auditory cortex

The functional specialization and hierarchical organization of multiple areas in rhesus monkey auditory cortex were examined with various types of complex sounds. Neurons in the lateral belt areas of the superior temporal gyrus were tuned to the best center frequency and bandwidth of band-passed noise bursts. They were also selective for the rate and direction of linear frequency modulated sweeps. Many neurons showed a preference for a limited number of species-specific vocalizations (“monkey calls”). These response selectivities can be explained by nonlinear spectral and temporal integration mechanisms. In a separate series of experiments, monkey calls were presented at different spatial locations, and the tuning of lateral belt neurons to monkey calls and spatial location was determined. Of the three belt areas the anterolateral area shows the highest degree of specificity for monkey calls, whereas neurons in the caudolateral area display the greatest spatial selectivity. We conclude that the cortical auditory system of primates is divided into at least two processing streams, a spatial stream that originates in the caudal part of the superior temporal gyrus and projects to the parietal cortex, and a pattern or object stream originating in the more anterior portions of the lateral belt. A similar division of labor can be seen in human auditory cortex by using functional neuroimaging.

Color and Shape: A Plea for Equal Treatment

Many philosophers, especially in the wake of the 17th century, have favored an inegalitarian view of shape and color, according to which shape is mind-independent while color is mind-dependent. In this essay, I advance a novel argument against inegalitarianism. The argument begins with an intuition about the modal dependence of color on shape, namely: it is impossible for something to have a color without having a shape (i.e. without having some sort of spatial extension, or at least spatial location). I then argue that, given reasonable assumptions, inegalitarianism contradicts this modal-dependence principle. Given the plausibility of the latter, I conclude that we should reject inegalitarianism in favor of some form of egalitarianism—either a subjective egalitarianism on which both shape and color are mind-dependent or an objective egalitarianism on which both shape and color are mind-independent.

The role of oscillatory brain activity in object processing and figure-ground segmentation in human vision

The perception of an object as a single entity within a visual scene requires that its features are bound together and segregated from the background and/or other objects. Here, we used magnetoencephalography (MEG) to assess the hypothesis that coherent percepts may arise from the synchronized high frequency (gamma) activity between neurons that code features of the same object. We also assessed the role of low frequency (alpha, beta) activity in object processing. The target stimulus (i.e. object) was a small patch of a concentric grating of 3c/°, viewed eccentrically. The background stimulus was either a blank field or a concentric grating of 3c/° periodicity, viewed centrally. With patterned backgrounds, the target stimulus emerged--through rotation about its own centre--as a circular subsection of the background. Data were acquired using a 275-channel whole-head MEG system and analyzed using Synthetic Aperture Magnetometry (SAM), which allows one to generate images of task-related cortical oscillatory power changes within specific frequency bands. Significant oscillatory activity across a broad range of frequencies was evident at the V1/V2 border, and subsequent analyses were based on a virtual electrode at this location. When the target was presented in isolation, we observed that: (i) contralateral stimulation yielded a sustained power increase in gamma activity; and (ii) both contra- and ipsilateral stimulation yielded near identical transient power changes in alpha (and beta) activity. When the target was presented against a patterned background, we observed that: (i) contralateral stimulation yielded an increase in high-gamma (>55 Hz) power together with a decrease in low-gamma (40-55 Hz) power; and (ii) both contra- and ipsilateral stimulation yielded a transient decrease in alpha (and beta) activity, though the reduction tended to be greatest for contralateral stimulation. The opposing power changes across different regions of the gamma spectrum with 'figure/ground' stimulation suggest a possible dual role for gamma rhythms in visual object coding, and provide general support of the binding-by-synchronization hypothesis. As the power changes in alpha and beta activity were largely independent of the spatial location of the target, however, we conclude that their role in object processing may relate principally to changes in visual attention.

Rhythmic masking release:effects of asynchrony, temporal overlap, harmonic relations, and source separation on cross-spectral grouping

The rhythm created by spacing a series of brief tones in a regular pattern can be disguised by interleaving identical distractors at irregular intervals. The disguised rhythm can be unmasked if the distractors are allocated to a separate stream from the rhythm by integration with temporally overlapping captors. Listeners identified which of 2 rhythms was presented, and the accuracy and rated clarity of their judgment was used to estimate the fusion of the distractors and captors. The extent of fusion depended primarily on onset asynchrony and degree of temporal overlap. Harmonic relations had some influence, but only an extreme difference in spatial location was effective (dichotic presentation). Both preattentive and attentionally driven processes governed performance. (PsycINFO Database Record (c) 2012 APA, all rights reserved)

Representações discursivas sobre lampião e seu bando em notícias de jornais mossoroenses (1927): “O mais audaz e miserável de todos os bandidos” e o seu “grupo de asseclas”

In this doctoral thesis analyzed the discursive representations of the bandit Lampião, the Lantern and his bandits gang in news mossoroenses newspapers published in the twenties of the last century (1927), when the gang invasion of the city of Mossoro in the state of Rio Grande do Norte, on June 13 of that year. To this end, we take as basis the theoretical assumptions of linguistics Textual, especially the narrower context of what is known today as Textual Analysis of the Discourses (ADT), theoretical and descriptive approach to linguistic studies of the text proposed by the French linguist Jean-Michel Adam. In this approach, we are interested in, specifically, the semantic level of the text, highlighting the notion of discursive representation, studied based on benchmarking operations, predication, modification, spatial location and temporal connection and analogy (ADAM, 2011; CASTILHO, 2010; KOCH, 2002, 2006; MARCUSCHI, 1998, 2008; NEVES, 2007; RODRIGUES, PASSEGGI & SILVA NETO, 2010). The corpus of this research consists of three reports in the twenties of the last century in newspapers The Mossoroense, Correio do Povo and the Northeast, and reconstituted through the collection held in the Municipal Museum Lauro Scotland files, Memorial Resistance Mossoro, both located in Natal, and in the news collection of Lampião newspapers in Natal, north of Rio Grande Raimundo Nonato historian. The discursive representations are built from the use of semantic analysis operations. Lampião to, the following representations are built: bandit, head of bandits, briber, defeated, Captain and Lord. To the outlaws of Lampião bunch of the following discursive representations were built: group, gang, gangsters, mates, bloodthirsty pack, brigands, bandits, criminals, burglar horde, and wild beasts. These representations reveal mainly the views of the newspapers of that time, which represented mainly the interests of traders, politicians, the government itself and generally Mossoró population.

Estratégia de navegação com planejamento dinâmico e algoritmo genético aplicada a robôs móveis terrestres

This work proposes a new autonomous navigation strategy assisted by genetic algorithm with dynamic planning for terrestrial mobile robots, called DPNA-GA (Dynamic Planning Navigation Algorithm optimized with Genetic Algorithm). The strategy was applied in environments - both static and dynamic - in which the location and shape of the obstacles is not known in advance. In each shift event, a control algorithm minimizes the distance between the robot and the object and maximizes the distance from the obstacles, rescheduling the route. Using a spatial location sensor and a set of distance sensors, the proposed navigation strategy is able to dynamically plan optimal collision-free paths. Simulations performed in different environments demonstrated that the technique provides a high degree of flexibility and robustness. For this, there were applied several variations of genetic parameters such as: crossing rate, population size, among others. Finally, the simulation results successfully demonstrate the effectiveness and robustness of DPNA-GA technique, validating it for real applications in terrestrial mobile robots.

Estratégia de navegação com planejamento dinâmico e algoritmo genético aplicada a robôs móveis terrestres

This work proposes a new autonomous navigation strategy assisted by genetic algorithm with dynamic planning for terrestrial mobile robots, called DPNA-GA (Dynamic Planning Navigation Algorithm optimized with Genetic Algorithm). The strategy was applied in environments - both static and dynamic - in which the location and shape of the obstacles is not known in advance. In each shift event, a control algorithm minimizes the distance between the robot and the object and maximizes the distance from the obstacles, rescheduling the route. Using a spatial location sensor and a set of distance sensors, the proposed navigation strategy is able to dynamically plan optimal collision-free paths. Simulations performed in different environments demonstrated that the technique provides a high degree of flexibility and robustness. For this, there were applied several variations of genetic parameters such as: crossing rate, population size, among others. Finally, the simulation results successfully demonstrate the effectiveness and robustness of DPNA-GA technique, validating it for real applications in terrestrial mobile robots.

The VLT-FLAMES tarantula survey:XII. Rotational velocities of the single O-type stars

Context. The 30 Doradus (30 Dor) region of the Large Magellanic Cloud, also known as the Tarantula nebula, is the nearest starburst region. It contains the richest population of massive stars in the Local Group, and it is thus the best possible laboratory to investigate open questions on the formation and evolution of massive stars. Aims. Using ground-based multi-object optical spectroscopy obtained in the framework of the VLT-FLAMES Tarantula Survey (VFTS), we aim to establish the (projected) rotational velocity distribution for a sample of 216 presumably single O-type stars in 30 Dor. The sample is large enough to obtain statistically significant information and to search for variations among subpopulations - in terms of spectral type, luminosity class, and spatial location - in the field of view. Methods. We measured projected rotational velocities, 3e sin i, by means of a Fourier transform method and a profile fitting method applied to a set of isolated spectral lines. We also used an iterative deconvolution procedure to infer the probability density, P(3e), of the equatorial rotational velocity, 3e. Results. The distribution of 3e sin i shows a two-component structure: a peak around 80 km s1 and a high-velocity tail extending up to 600 km s^-1 This structure is also present in the inferred distribution P(3e) with around 80% of the sample having 0 <3e ≤ 300 km s^-1 and the other 20% distributed in the high-velocity region. The presence of the low-velocity peak is consistent with what has been found in other studies for late O- and early B-type stars. Conclusions. Most of the stars in our sample rotate with a rate less than 20% of their break-up velocity. For the bulk of the sample, mass loss in a stellar wind and/or envelope expansion is not efficient enough to significantly spin down these stars within the first few Myr of evolution. If massive-star formation results in stars rotating at birth with a large portion of their break-up velocities, an alternative braking mechanism, possibly magnetic fields, is thus required to explain the present-day rotational properties of the O-type stars in 30 Dor. The presence of a sizeable population of fast rotators is compatible with recent population synthesis computations that investigate the influence of binary evolution on the rotation rate of massive stars. Even though we have excluded stars that show significant radial velocity variations, our sample may have remained contaminated by post-interaction binary products. That the highvelocity tail may be populated primarily (and perhaps exclusively) by post-binary interaction products has important implications for the evolutionary origin of systems that produce gamma-ray bursts. © 2013 Author(s).

On Pauli pairs

The state of a system in classical mechanics can be uniquely reconstructed if we know the positions and the momenta of all its parts. In 1958 Pauli has conjectured that the same holds for quantum mechanical systems. The conjecture turned out to be wrong. In this paper we provide a new set of examples of Pauli pairs, being the pairs of quantum states indistinguishable by measuring the spatial location and momentum. In particular, we construct a new set of spatially localized Pauli pairs.

The invasion risk in the Pacific Northwest of two closely related grass species in the Genus Cortaderia

Thesis (Master's)--University of Washington, 2016-08

Environmental impacts of freshwater use and suspended solids in life cycle assessment

Perturbation of natural ecosystems, namely by increasing freshwater use and its degradative use, as well as topsoil erosion by water of land-use production systems, have been emerging as topics of high environmental concern. Freshwater use has become a focus of attention in the last few years for all stakeholders involved in the production of goods, mainly agro-industrial and forest-based products, which are freshwater-intensive consumers, requiring large inputs of green and blue water. This thesis presents a global review on the available Water Footprint Assessment and Life Cycle Assessment (LCA)-based methods for measuring and assessing the environmental relevance of freshwater resources use, based on a life cycle perspective. Using some of the available midpoint LCA-based methods, the freshwater use-related impacts of a Portuguese wine (white ‘vinho verde’) were assessed. However, the relevance of environmental green water has been neglected because of the absence of a comprehensive impact assessment method associated with green water flows. To overcome this constraint, this thesis helps to improve and enhance the LCA-based methods by providing a midpoint and spatially explicit Life Cycle Impact Assessment (LCIA) method for assessing impacts on terrestrial green water flow and addressing reductions in surface blue water production caused by reductions in surface runoff due to land-use production systems. The applicability of the proposed method is illustrated by a case study on Eucalyptus globulus conducted in Portugal, as the growth of short rotation forestry is largely dependent on local precipitation. Topsoil erosion by water has been characterised as one of the most upsetting problems for rivers. Because of this, this thesis also focuses on the ecosystem impacts caused by suspended solids (SS) from topsoil erosion that reach freshwater systems. A framework to conduct a spatially distributed SS delivery to freshwater streams and a fate and effect LCIA method to derive site-specific characterisation factors (CFs) for endpoint damage on aquatic ecosystem diversity, namely on algae, macrophyte, and macroinvertebrates organisms, were developed. The applicability of this framework, combined with the derived site-specific CFs, is shown by conducting a case study on E. globulus stands located in Portugal as an example of a land use based system. A spatially explicit LCA assessment was shown to be necessary, since the impacts associated with both green water flows and SS vary greatly as a function of spatial location.

Which way is up? Grounded mental representations of space

Processing language is postulated to involve a mental simulation, or re-enactment of perceptual, motor, and introspective states that were acquired experientially (Barsalou, 1999, 2008). One such aspect that is mentally simulated during processing of certain concepts is spatial location. For example, upon processing the word “moon” the prominent spatial location of the concept (e.g. ‘upward’) is mentally simulated. In six eye-tracking experiments, we investigate how mental simulations of spatial location affect processing. We first address a conflict in previous literature whereby processing is shown to be impacted in both a facilitatory and inhibitory way. Two of our experiments showed that mental simulations of spatial association facilitate saccades launched toward compatible locations; however, a third experiment showed an inhibitory effect on saccades launched towards incompatible locations. We investigated these differences with further experiments, which led us to conclude that the nature of the effect (facilitatory or inhibitory) is dependent on the demands of the task and, in fitting with the theory of Grounded Cognition (Barsalou, 2008), that mental simulations impact processing in a dynamic way. Three further experiments explored the nature of verticality – specifically, whether ‘up’ is perceived as away from gravity, or above our head. Using similar eye-tracking methods, and by manipulating the position of participants, we were able to dissociate these two possible standpoints. The results showed that mental simulations of spatial location facilitated saccades to compatible locations, but only when verticality was dissociated from gravity (i.e. ‘up’ was above the participant’s head). We conclude that this is not due to an ‘embodied’ mental simulation, but rather a result of heavily ingrained visuo-motor association between vertical space and eye movements.

Mode locking in a spatially extended neuron model: active soma and compartmental tree

Understanding the mode-locked response of excitable systems to periodic forcing has important applications in neuroscience. For example it is known that spatially extended place cells in the hippocampus are driven by the theta rhythm to generate a code conveying information about spatial location. Thus it is important to explore the role of neuronal dendrites in generating the response to periodic current injection. In this paper we pursue this using a compartmental model, with linear dynamics for each compartment, coupled to an active soma model that generates action potentials. By working with the piece-wise linear McKean model for the soma we show how the response of the whole neuron model (soma and dendrites) can be written in closed form. We exploit this to construct a stroboscopic map describing the response of the spatially extended model to periodic forcing. A linear stability analysis of this map, together with a careful treatment of the non-differentiability of the soma model, allows us to construct the Arnol'd tongue structure for 1:q states (one action potential for q cycles of forcing). Importantly we show how the presence of quasi-active membrane in the dendrites can influence the shape of tongues. Direct numerical simulations confirm our theory and further indicate that resonant dendritic membrane can enlarge the windows in parameter space for chaotic behavior. These simulations also show that the spatially extended neuron model responds differently to global as opposed to point forcing. In the former case spatio-temporal patterns of activity within an Arnol'd tongue are standing waves, whilst in the latter they are traveling waves.