Space-based Models Research Articles

Constraints on the expansion of paralogous protein families.

Duplication and divergence is a major mechanism by which new proteins and functions emerge in biology. Consequently, most organisms, in all domains of life, have genomes that encode large paralogous families of proteins. For recently duplicated pathways to acquire different, independent functions, the two paralogs must acquire mutations that effectively insulate them from one another. For instance, paralogous signaling proteins must acquire mutations that endow them with different interaction specificities such that they can participate in different signaling pathways without disruptive cross-talk. Although duplicated genes undoubtedly shape each other's evolution as they diverge and attain new functions, it is less clear how other paralogs impact or constrain gene duplication. Does the establishment of a new pathway by duplication and divergence require the system-wide optimization of all paralogs? The answer has profound implications for molecular evolution and our ability to engineer biological systems. Here, we discuss models, experiments, and approaches for tackling this question, and for understanding how new proteins and pathways are born.

Precuneus stimulation alters the neural dynamics of autobiographical memory retrieval

Autobiographical memory (AM) unfolds over time, but little is known about the dynamics of its retrieval. Space-based models of memory implicate the hippocampus, retrosplenial cortex, and precuneus in early memory computations. Here we used transcranial magnetic stimulation (TMS) and magnetoencephalography (MEG) to investigate the causal role of the precuneus in the dynamics of AM retrieval. During early memory search and construction, precuneus stimulation compared to vertex stimulation led to delayed evoked neural activity within 1000 ​ms after cue presentation. During later memory elaboration, stimulation led to decreased sustained positivity. We further identified a parietal late positive component during memory elaboration, the amplitude of which was associated with spatial perspective during recollection. This association was disrupted following precuneus stimulation, suggesting that this region plays an important role in the neural representation of spatial perspective during AM. These findings demonstrate a causal role for the precuneus in early AM retrieval, during memory search before a specific memory is accessed, and in spatial context reinstatement during the initial stages of memory elaboration and re-experiencing. By utilizing the high temporal resolution of MEG and the causality of TMS, this study helps clarify the neural correlates of early naturalistic memory retrieval.

Analysis and Comparison of Vector Space and Metric Space Representations in QSAR Modeling.

The performance of quantitative structure–activity relationship (QSAR) models largely depends on the relevance of the selected molecular representation used as input data matrices. This work presents a thorough comparative analysis of two main categories of molecular representations (vector space and metric space) for fitting robust machine learning models in QSAR problems. For the assessment of these methods, seven different molecular representations that included RDKit descriptors, five different fingerprints types (MACCS, PubChem, FP2-based, Atom Pair, and ECFP4), and a graph matching approach (non-contiguous atom matching structure similarity; NAMS) in both vector space and metric space, were subjected to state-of-art machine learning methods that included different dimensionality reduction methods (feature selection and linear dimensionality reduction). Five distinct QSAR data sets were used for direct assessment and analysis. Results show that, in general, metric-space and vector-space representations are able to produce equivalent models, but there are significant differences between individual approaches. The NAMS-based similarity approach consistently outperformed most fingerprint representations in model quality, closely followed by Atom Pair fingerprints. To further verify these findings, the metric space-based models were fitted to the same data sets with the closest neighbors removed. These latter results further strengthened the above conclusions. The metric space graph-based approach appeared significantly superior to the other representations, albeit at a significant computational cost.

A Survey of Visual Attention Models

The present paper surveys visual attention models, showing factors’ categorization. It also studies bottom-up models in comparison to top-to-down, spatial models compared to spatial-temporal ones, obvious attention against the hidden one, and space-based models against the object-based ones. It categorizes some challenging model issues, including biological calculations, correlation with the set of eye-movement data, as well as bottom-up and top-to-down topics, explaining each in details.

You can detect the trees as well as the forest when adding the leaves: Evidence from visual search tasks containing three-level hierarchical stimuli

The present study investigated how multiple levels of hierarchical stimuli (i.e., global, intermediate and local) are processed during a visual search task. Healthy adults participated in a visual search task in which a target was either present or not at one of the three levels of hierarchical stimuli (global geometrical form made by intermediate forms themselves constituted by local forms). By varying the number of distractors, the results showed that targets presented at global and intermediate levels were detected efficiently (i.e., the detection times did not vary with the number of distractors) whereas local targets were processed less efficiently (i.e., the detection times increased with the number of distractors). Additional experiments confirmed that these results were not due to the size of the target elements or to the spatial proximity among the structural levels. Taken together, these results show that the most local level is always processed less efficiently, suggesting that it is disadvantaged during the competition for attentional resources compared to higher structural levels. The present study thus supports the view that the processing occurring in visual search acts dichotomously rather than continuously. Given that pure structuralist and pure space-based models of attention cannot account for the pattern of our findings, we discuss the implication for perception, attentional selection and executive control of target position on hierarchical stimuli.

Re-placing sport migrants: Moving beyond the institutional structures informing international sport migration

Interest in international sport migration has been burgeoning recently. This article considers the dominant theoretical models used to explore these movements and suggests that it is time to rethink some of our theoretical presumptions. Recent permutations of these theoretical models, shifting from globalization to network theoretical models, make this reconsideration of migration-related theories necessary. Drawing on the groundbreaking work done in the 1990s and on Rafaelle Poli’s rapidly expanding body of work, it becomes apparent that a more flexible, open-ended theoretical model is necessary. This article reviews these theoretical models before making a suggestion of how international sport migration might be better framed for understanding how migration is structured and experienced in multiple locations around the world. Considering that migrants are bodies moving through space, it seems crucial to return migrants to space-based models of movement thereby advocating a theoretical model that takes into account the complexly dynamic relationships between migrants, institutions, and places.

Feature integration across space, time, and orientation.

The perception of a visual target can be strongly influenced by flanking stimuli. In static displays, performance on the target improves when the distance to the flanking elements increases-presumably because feature pooling and integration vanishes with distance. Here, we studied feature integration with dynamic stimuli. We show that features of single elements presented within a continuous motion stream are integrated largely independent of spatial distance (and orientation). Hence, space-based models of feature integration cannot be extended to dynamic stimuli. We suggest that feature integration is guided by perceptual grouping operations that maintain the identity of perceptual objects over space and time.

Precise Point Positioning Using IGS Orbit and Clock Products

The contribution details a post-processing approach that used undifferentiated dual-frequency pseudorange and carrier phase observations along with IGS procise orbit products, for stand-alone precise geodetic point positioning (static or kinematic) with cm precision. This is possible if one takes advantage of the satellite clock estimates available with the satellite coordinates in the IGS precise orbit products and models systematic effects that cause cm variations in the satelite to user range. This paper will describe the approach, summarize the adjustment procedure, and specify the earth- and space-based models that must be implementetd to achieve cm-level positioning in static mode. Furthermore, station tropospheric zenth path delays with cm precision and GPS receiver clock estimates procise to 0.1 ns are also obtained. © 2001 John Wiley & Sons, Inc.

Global empirical wind model for the upper mesosphere/lower thermosphere. I. Prevailing wind

Abstract. An updated empirical climatic zonally averaged prevailing wind model for the upper mesosphere/lower thermosphere (70-110 km), extending from 80°N to 80°S is presented. The model is constructed from the fitting of monthly mean winds from meteor radar and MF radar measurements at more than 40 stations, well distributed over the globe. The height-latitude contour plots of monthly mean zonal and meridional winds for all months of the year, and of annual mean wind, amplitudes and phases of annual and semiannual harmonics of wind variations are analyzed to reveal the main features of the seasonal variation of the global wind structures in the Northern and Southern Hemispheres. Some results of comparison between the ground-based wind models and the space-based models are presented. It is shown that, with the exception of annual mean systematic bias between the zonal winds provided by the ground-based and space-based models, a good agreement between the models is observed. The possible origin of this bias is discussed.Key words: Meteorology and Atmospheric dynamics (general circulation; middle atmosphere dynamics; thermospheric dynamics)

Object-based attentional selection and aging.

The authors conducted 2 studies to examine potential age-related differences in object-based attentional selection. Participants were briefly presented with pairs of wrenches and were asked to make 1 response if both target properties (i.e., an open end and a hexagonal end) were present and another response if only a single target property was present in the display. The critical manipulation was whether the target properties were present on 1 wrench or distributed between 2 wrenches. Space-based models of selective attention predict no difference in performance between these conditions. However, object-based attentional selection models predict better performance when both target properties appear on a single object. The results from both of the studies were consistent with object-based models of attentional selection. Furthermore, both young and old adults showed similar performance effects, suggesting the object-based attentional selection is insensitive to normal aging.

What's in a location? Comparing object-based and space-based models of feature integration in visual search.

What's in a location? Comparing object-based and space-based models of feature integration in visual search.

What's in a location? Comparing object-based and space-based models of feature integration in visual search.

What's in a location? Comparing object-based and space-based models of feature integration in visual search.

Object versus space-based models of visual attention: Implications for the design of head-up displays.

Object versus space-based models of visual attention: Implications for the design of head-up displays.

Object versus space-based models of visual attention: Implications for the design of head-up displays.

Object versus space-based models of visual attention: Implications for the design of head-up displays.

Space-based visual attention models and object selection: Constraints, problems, and possible solutions

One of the functions of visual attention is the selection of object information. This seems to be in line with an influential group of attentional models that assume that attentional selection is space based. These models assume that the selection of an object in vision is realized by selection of the location of that object. Whether this relatively simple idea of space-based attention and the corresponding, more elaborated space-based models are sufficient to handle selected constraints and problems of object selection is the main issue of this article. The first step toward an answer is to describe the common computational structure of space-based attentional models. Two model classes will be distinguished: capacity-limited models (e.g., Treisman, 1988; LaBerge & Brown, 1989) and models that do not assume a capacity limitation (e.g., Van der Heijden, 1992). Next, three kinds of task and data on object selection are introduced that are especially challenging for space-based models. The first type of data refers to experiments that require selection between overlapping objects. The second type of data concerns the influence of early perceptual grouping--a strong object-defining factor--on late response competition, and the third type consists of a selection task in which a high-level (semantic) attribute defines an object and controls selection. In all three cases, problems of space-based models are analyzed and possible solutions are sketched. Finally, a brief evaluative summary is given.

Movement and focused attention: A failure to replicate

Our original goal was to explore the nature of the grouping-by-movement phenomenon reported by Driver and Baylis (1989). In their studies, distractors that moved in common with a centrally located target had a larger influence on focused-attention performance than did more proximate but stationary distractors. These results seemed particularly important since they suggested, contrary to the predictions of space-based models of attention, that attention could be allocated to noncontiguous regions of the visual field. Their results also suggested mandatory processing of stimuli with common motion. Unfortunately, we were unable to replicate this grouping-by-movement effect. In the conditions of Experiment 1 in which we replicated Driver and Baylis's methodology, stationary distractors produced a larger response-compatibility effect than did the more distant distractors that moved in common with the target. In Experiment 2, we redundantly coded the centrally located target and the far distractors with common movement and color. However, the results were identical to those obtained in Experiment 1. The stationary near distractors that appeared in a different color from the target and the far distractors produced the largest response-compatibility effect. In a final experiment, we attempted to compensate for the reduced acuity of the moving distractors by adjusting their size by a cortical magnification factor. However, even with this manipulation, we found a larger response-compatibility effect for the stationary near distractors than for the moving distant distractors. Our results suggest that subjects are capable of selectively processing a target item that moves in common with distractors.

A comparison of Space-Based and Object-Based Models of Visual Attention

In the present study we examined the degree to which contour and color could be used to minimize focused attention costs. Twelve subjects performed a task in which they were instructed to respond to a centrally located stimulus and ignore flanking items. The flankers could be either compatible or incompatible with the response of the target. Additionally, the flankers could be embedded in the same object as the target or embedded in different objects. When the target and flankers were embedded in the same object, performance was poorer when the target was surrounded by response incompatible items than when it was surrounded by compatible items. However, the response compatibility effect was eliminated when the target and flankers were embedded in different objects. The results are interpreted within a Hybrid Space/Object-based model of visual attention.