Radial packing, order, and disorder in collagen fibrils.

Collagen fibrils resemble smectic, liquid crystals in being highly ordered axially but relatively disordered laterally. In some connective tissues, x-ray diffraction reveals three-dimensional crystallinity in the molecular packing within fibrils, although the continued presence of diffuse scatter indicates significant underlying disorder. In addition, several observations from electron microscopy suggest that the molecular packing is organized concentrically about the fibril core. In the present work, theoretical equatorial x-ray diffraction patterns for a number of models for collagen molecular packing are calculated and compared with the experimental data from tendon fibrils. None of the models suggested previously can account for both the crystalline Bragg peaks and the underlying diffuse scatter. In addition, models in which any of the nearest-neighbor, intermolecular vectors are perpendicular to the radial direction are inconsistent with the observed radial orientation of the principal approximately 4 nm Bragg spacing. Both multiple-start spiral and concentric ring models are devised in which one of the nearest-neighbor vectors is along the radial direction. These models are consistent with the radial orientation of the approximately 4 nm spacing, and energy minimization results in radially oriented crystalline domains separated by disordered grain boundaries. Theoretical x-ray diffraction patterns show a combination of sharp Bragg peaks and underlying diffuse scatter. Close agreement with the observed equatorial diffraction pattern is obtained. The concentric ring model is consistent with the observation that the diameters of collagen fibrils are restricted to discrete values.     

Does assignment of orientation to dot patterns reveal optimization processes in the visual system?

Sixty subjects were tested to assign orientation to ten dot patterns differing in their overall form and the number of dots in the pattern. The patterns were presented in four different positions in the visual field and their orientation was estimated in two ways. It was demonstrated that the assignment of orientation did not depend on the position of the pattern in the visual field as well as on the method of estimation used. A quantitative measure for the elongation of a dot pattern is proposed which correlates with the degree of ambiguity in orientation estimation. The greater the elongation the smaller the standard deviation of the estimates given. The distributions of the estimates for the ten patterns were analyzed. It was shown that they can be presented as superpositions of two or more groups of normally distributed estimates determined by some salient characteristics of the stimuli. Data are discussed from the point of view that assignment of orientation to dot patterns reveals the existence of optimization mechanisms in human brain that extract perceptual invariants from external stimulation.     

Laminar processing in the visual cortical column

Sensory regions of neocortex are organized as arrays of vertical columns composed of cells that share similar response properties, with the orientation columns of the cat's visual cortex being the best known example. Interest in how sensitivity to different stimulus features first emerges in the columns and how this selectivity is refined by subsequent processing has fueled decades of research. A natural starting point in approaching these issues is anatomy. Each column traverses the six cortical layers and each layer has a unique pattern of inputs, intrinsic connections and outputs. Thus, it makes sense to explore the possibility of corresponding laminar differences in sensory function, that is, to examine relationships between morphology and physiology. In addition, to help identify general patterns of cortical organization, it is useful to compare results obtained from different sensory systems and diverse species. The picture that emerges from such comparisons is that each cortical layer serves a distinct role in sensory function. Furthermore, different cortices appear to share some common strategies for processing information but also have specialized mechanisms adapted for the demands of specific sensory tasks.     

Elastic anisotropy of bone lamellae as a function of fibril orientation pattern

In this study, the homogenized anisotropic elastic properties of single bone lamellae are computed using a finite element unit cell method. The resulting stiffness tensor is utilized to calculate indentation moduli for multiple indentation directions in the lamella plane which are then related to nanoindentation experiments. The model accounts for different fibril orientation patterns in the lamellae—the twisted and orthogonal plywood pattern, a 5-sublayer pattern and an X-ray diffraction-based pattern. Three-dimensional sectional views of each pattern facilitate the comparison to transmission electron (TEM) images of real lamella cuts. The model results indicate, that the 5-sublayer- and the X-ray diffraction-based patterns cause the lamellae to have a stiffness maximum between 0° and 45° to the osteon axis. Their in-plane stiffness characteristics are qualitatively matching the experimental findings that report a higher stiffness in the osteon axis than in the circumferential direction. In contrast, lamellae owning the orthogonal or twisted plywood fibril orientation patterns have no preferred stiffness alignment. This work shows that the variety of fibril orientation patterns leads to qualitative and quantitative differences in the lamella elastic mechanical behavior. The study is a step toward a deeper understanding of the structure—mechanical function relationship of bone lamellae.     

Measurement of visual channels by contrast adaptation.

Inspection of a high-contrast grating pattern affects our ability to detect patterns that are similar. This technique can be used to infer the underlying mechanisms of the visual system. By using this technique, measurements of the bandwidth of orientation channels are taken for different levels of adapting contrast and adapting duration. If the threshold elevation is plotted as the difference between the unadapted and adapted threshold in decibels, then the orientation bandwidth is invariant if taken at some fraction of the maximum elevation. This results from the fact that, as the orientation difference between the adapting and test patterns increases, the function relating threshold elevation to adapting contrast reduces in slope. These data contradict the often-used 'equivalent contrast transformation' (in which the fall off in the adaptation effect with respect to orientation is expressed in terms of an equivalent reduction in adapting contrast) as this would produce quite different bandwidths at different adapting contrasts. The data also address the issue of the neuronal mechanisms of adaptation.     

Trying to fit in: are patterns of orientation of a keystone grazer set by behavioural responses to ecosystem engineers or wave action?

The distribution of animals varies at different temporal and spatial scales. At the smallest scale, distribution may be orientated in regard to particular environmental variables or habitat features. For animals on the rocky intertidal, the processes which set and maintain patterns of distribution and abundance in wave-exposed areas are well studied, with explanatory models focused on wave action and, more recently, the role of biogenic habitats. In contrast, patterns of orientation by intertidal animals have received less attention, although having ecological and fitness consequences. Here, we report tests of competing models to explain the observation that limpets on steeply sloped surfaces orientate downwards. A greater proportion of downwards-facing limpets was found in sheltered sites and areas without barnacles and this pattern was consistent across many shores and sampling occasions. Additionally, the frequency at which limpets were dislodged after a storm was independent of orientation. To test whether orientation is a behavioural response to habitat-forming barnacles, barnacles were removed and/or killed from patches of substrata and the change in proportion of downwards-facing limpets measured. The proportion increased with barnacle removal and this behaviour was a response to the structure of the barnacles, not a biotic effect associated with the living organism. Our study suggests that biogenic habitat not wave action sets patterns of limpet orientation and barnacle shells, regardless of whether the barnacle is alive or not, limit the ability of limpets to adopt a downward orientation.     

Role of biomechanics and muscle activation strategy in the production of endpoint force patterns in the cat hindlimb

We used a musculoskeletal model of the cat hindlimb to compare the patterns of endpoint forces generated by all possible combination of 12 hindlimb muscles under three different muscle activation rules: homogeneous activation of muscles based on uniform activation levels, homogeneous activation of muscles based on uniform (normalized) force production, and activation based on the topography of spinal motoneuron pools. Force patterns were compared with the patterns obtained experimentally by microstimulation of the lumbar spinal cord in spinal intact cats. Magnitude and orientation of the force patterns were compared, as well as the proportion of the types found, and the proportions of patterns exhibiting points of zero force (equilibrium points). The force patterns obtained with the homogenous activation and motoneuron topography models were quite similar to those measured experimentally, with the differences being larger for the patterns from the normalized endpoint forces model. Differences in the proportions of types of force patterns between the three models and the experimental results were significant for each model. Both homogeneous activation and normalized endpoint force models produced similar proportions of equilibrium points as found experimentally. The results suggest that muscle biomechanics play an important role in limiting the number of endpoint force pattern types, and that muscle combinations activated at similar levels reproduced best the experimental results obtained with intraspinal microstimulation.     

Computational Modeling of Orientation Tuning Dynamics in Monkey Primary Visual Cortex

In the primate visual pathway, orientation tuning of neurons is first observed in the primary visual cortex. The LGN cells that comprise the thalamic input to V1 are not orientation tuned, but some V1 neurons are quite selective. Two main classes of theoretical models have been offered to explain orientation selectivity: feedforward models, in which inputs from spatially aligned LGN cells are summed together by one cortical neuron; and feedback models, in which an initial weak orientation bias due to convergent LGN input is sharpened and amplified by intracortical feedback. Recent data on the dynamics of orientation tuning, obtained by a cross-correlation technique, may help to distinguish between these classes of models. To test this possibility, we simulated the measurement of orientation tuning dynamics on various receptive field models, including a simple Hubel-Wiesel type feedforward model: a linear spatiotemporal filter followed by an integrate-and-fire spike generator. The computational study reveals that simple feedforward models may account for some aspects of the experimental data but fail to explain many salient features of orientation tuning dynamics in V1 cells. A simple feedback model of interacting cells is also considered. This model is successful in explaining the appearance of Mexican-hat orientation profiles, but other features of the data continue to be unexplained.     

Browsing gene banks for Fe2S2 ferredoxins and structural modeling of 88 plant-type sequences: an analysis of fold and function.

One-hundred-and-seventy-nine sequences of Fe2S2 ferredoxins and ferredoxin precursors were identified in and retrieved from currently available protein and cDNA databases. On the basis of their cluster-binding patterns, these sequences were divided into three groups: those containing the CX4CX2CXnC pattern (plant-type ferredoxins), those with the CX5CX2CXnC pattern (adrenodoxins), and those with a different pattern. These three groups contain, respectively, 139, 36, and 4 sequences. After excluding ferredoxin precursors in the first group, two subgroups were identified, again based on their cluster-binding patterns: 88 sequences had the CX4CX2CX29C pattern, and 29 had the CX4CX2CXmC (m not equal 29) pattern. The structures of the 88 ferredoxins with the CX4CX2CX29C pattern were modeled based on the available experimental structures of nine proteins within this same group. The modeling procedure was tested by building structural models for the ferredoxins with known structures. The models resulted, on average, in being within 1 A of the backbone root-mean-square deviation from the corresponding experimental structures. In addition, these structural models were shown to be of high quality by using assessment procedures based on energetic and stereochemical parameters. Thus, these models formed a reliable structural database for this group of ferredoxins, which is meaningful within the framework of current structural genomics efforts. From the analysis of the structural database generated it was observed that the secondary structural elements and the overall three-dimensional structures are maintained throughout the superfamily. In particular, the residues in the hydrophobic core of the protein were found to be either absolutely conserved or conservatively substituted. In addition, certain solvent-accessible charged groups, as well as hydrophobic groups, were found to be conserved to the same degree as the core residues. The patterns of conservation of exposed residues identified the regions of the protein that are critical for its function in electron transfer. An extensive analysis of protein-protein interactions is now possible. Some conserved interactions between residues have been identified and related to structural and/or functional features. All this information could not be obtained from the analyses of the primary sequences alone. Finally, the analysis of the sequences of the related subgroup featuring the CX4CX2CXmC (m not equal 29) cluster-binding pattern in the light of the structural and functional insights provided by the inspection of the mentioned structural database affords some hints on the functional features of ferredoxins belonging to this subgroup.     

Spatial point pattern analysis of available and exploited resources

A patchy spatial distribution of resources underpins many models of population regulation and species coexistence, so ecologists require methods to analyse spatially‐explicit data of resource distribution and use. We describe a method for analysing maps of resources and testing hypotheses about species' distributions and selectivity. The method uses point pattern analysis based on the L‐function, the linearised form of Ripley's K‐function. Monte Carlo permutations are used for statistical tests. We estimate the difference between observed and expected values of L(t), an approach with several advantages: 1) The results are easy to interpret ecologically. 2) It obviates the need for edge correction, which has largely precluded the use of L‐functions where plot boundaries are “real”. Including edge corrections may lead to erroneous conclusions if the underlying assumptions are invalid. 3) The null expectation can take many forms, we illustrate two models: complete spatial randomness (to describe the spatial pattern of resources in the landscape) and the underlying pattern of resource patches in the landscape (akin to a neutral landscape approach). The second null is particularly useful to test whether spatial patterns of exploited resource points simply reflect the spatial patterns of all resource points. We tested this method using over 100 simulated point patterns encompassing a range of patterns that might occur in ecological systems, and some very extreme patterns. The approach is generally robust, but Type II decision errors might arise where spatial patterns are weak and when trying to detect a clumped pattern of exploited points against a clumped pattern of all points. An empirical example of an intertidal lichen growing on barnacle shells illustrates how this technique might be used to test hypotheses about dispersal mechanisms. This approach can increase the value of survey data, by permitting quantification of natural resource patch distribution in the landscape as well as patterns of resource use by species.     

Comparative squamation of the lateral line canal pores in sharks

The current study collected the first quantitative data on lateral line pore squamation patterns in sharks and assessed whether divergent squamation patterns are similar to experimental models that cause reduction in boundary layer turbulence. In addition, the hypothesis that divergent orientation angles are exclusively found in fast‐swimming shark species was tested. The posterior lateral line and supraorbital lateral line pore squamation of the fast‐swimming pelagic shortfin mako shark Isurus oxyrinchus and the slow‐swimming epi‐benthic spiny dogfish shark Squalus acanthias was examined. Pore scale morphology and pore coverage were qualitatively analysed and compared. In addition, pore squamation orientation patterns were quantified for four regions along the posterior lateral line and compared for both species. Isurus oxyrinchus possessed consistent pore scale coverage among sampled regions and had a divergent squamation pattern with multiple scale rows directed dorsally and ventrally away from the anterior margin of the pore with an average divergent angle of 13° for the first row of scales. Squalus acanthias possessed variable amounts of scale coverage among the sampled regions and had a divergent squamation pattern with multiple scale rows directed ventrally away from the anterior margin of the pore with an average angle of 19° for the first row of scales. Overall, the squamation pattern measured in I. oxyrinchus fell within the parameters used in the fluid flow analysis, which suggests that this pattern may reduce boundary layer turbulence and affect lateral line sensitivity. The exclusively ventral oriented scale pattern seen in S. acanthias possessed a high degree of divergence but the pattern did not match that of the fluid flow models. Given current knowledge, it is unclear how this would affect boundary layer flow. By studying the relationship between squamation patterns and the lateral line, new insights are provided into sensory biology that warrant future investigation due to the implications for the ecology, morphology and sensory evolution of sharks.     

Formation and deformation of patterns through diffusion

Simulating various patterns exhibited on biological forms with mathematical models has become an important supplement to theoretical biology. Models based on a certain mechanism are intended to provide explanations to the formation of a basic pattern. However, in real phenomena, among a basic pattern there always exist some difference between any two individuals. Such differences are consequences of environmental factors posed during the developmental processes. These factors, such as temperature, affect the diffusion rates of corresponding morphogenes which, in turn, alter a basic pattern to certain extent. We provide, in this paper, a quantitative characterization of this effect for a class of reaction-diffusion models.Mathematically, we study the emergence of stationary patterns and their dependence on diffusion rates for this class of models (RD-equations) with no-flux boundary conditions. The results are generalized to systems with homogeneous Dirichlet boundary conditions when the kinetic terms are odd functions. Through an analysis of the phase dynamics, we show that the deformation of stationary patterns, as the diffusion rates change, is governed by the variation of certain plane curves in the phase space. A constructive proof is given which shows explicitly how to obtain such curves.Applications of this study are illustrated with three model examples. We use these models to explain the biological implications of the mathematical features we investigated. Results from computer simulations are presented and compared with physical patterns.     

Symmetries,non-Euclidean metrics,and patterns in a Swift–Hohenberg model of the visual cortex

The aim of this work is to investigate the effect of the shift-twist symmetry on pattern formation processes in the visual cortex. First, we describe a generic set of Riemannian metrics of the feature space of orientation preference that obeys properties of the shift-twist, translation, and reflection symmetries. Second, these metrics are embedded in a modified Swift-Hohenberg model. As a result we get a pattern formation process that resembles the pattern formation process in the visual cortex. We focus on the final stable patterns that are regular and periodic. In a third step we analyze the influences on pattern formation using weakly nonlinear theory and mode analysis. We compare the results of the present approach with earlier models.     

基于不同零模型的点格局分析

在种群空间格局研究中,定量分析格局及其形成过程已成为生态学家的主要目标。在量化分析的众多方法中,点格局分析是最常用的方法,而在选择零模型时,完全空间随机模型以外的复杂零模型很少使用,实际上,这些零模型可能有助于认识格局的内在特征。为此,我们在研究实例中,选择完全空间随机模型(complete spatial randomness)、泊松聚块模型(Poisson cluster process)和嵌套双聚块模型(nested double-cluster process)对典型草原处于不同恢复演替阶段的羊草(Leymus chinensis)种群空间格局进行了分析。结果发现:完全空间随机模型仅能检测种群在不同尺度下的格局类型;而通过泊松聚块模型和嵌套双聚块模型检验表明,在恢复演替的初期阶段,羊草种群在小尺度范围内偏离泊松聚块模型,而在整个取样范围内完全符合嵌套双聚块模型;随着恢复演替时间的推移,在恢复演替的后期,在整个取样尺度上,羊草种群与泊松聚块模型相吻合。这是很有意义的生态学现象。这一实例表明在应用点格局分析种群空间格局时,仅通过完全空间随机模型的检验来分析格局特征,或许很难论证复杂的生态过程,而选择一些完全空间随机模型以外的较复杂的零模型,可能发现一些有价值的生态学现象,对揭示格局掩盖下的内在机制有所裨益。     

Shoulder and elbow muscle activity during fully supported trajectory tracking in neurologically intact older people

An inability to perform tasks involving reaching is a common problem for stroke patients. Knowledge of normal muscle activation patterns during these tasks is essential to the identification of abnormal patterns in post-stroke hemiplegia. Findings will provide insight into changes in muscle activation patterns associated with recovery of upper limb function.In this study with neurologically intact participants the co-ordination of shoulder and elbow muscle activity during two dimensional reaching tasks is explored. Eight participants undertook nine tracking tasks in which trajectory (orientation and length), duration, speed and resistance to movement were varied. The participants’ forearm was supported using a hinged arm-holder, which constrained their hand to move in a two dimensional plane. EMG signals were recorded from triceps, biceps, anterior deltoid, upper, middle and lower trapezius and pectoralis major.A wide variation in muscle activation patterns, in terms of timing and amplitude, was observed between participants performing the same task. EMG amplitude increased significantly with length, duration and resistance of the task for all muscles except anterior deltoid. Co-activation between biceps and triceps was significantly dependent on both task and trajectory orientation. Activation pattern of pectoralis major was dependent on trajectory. Neither trajectory orientation nor task condition affected the activation pattern of anterior deltoid. Normal ranges of timing of muscle activity during the tasks were identified.     

Orientation variance as a quantifier of structure in texture

I consider how structure is derived from texture containing changes in orientation over space, and propose that multi-local orientation variance (the average orientation variance across a series of discrete images locales) is an estimate of the degree of organization that is useful both for spatial scale selection and for discriminating structure from noise. The oriented textures used in this paper are Glass patterns, which contain structure at a narrow range of scales. The effect of adding noise to Glass patterns, on a structure versus noise task (Maloney et al., 1987), is compared to discrimination based on orientation variance and template matching (i.e. having prior knowledge of the target's orientation structure). At all but very low densities, the variance model accounts well for human data. Next, both models' estimates of tolerable orientation variance are shown to be broadly consistent with human discrimination of texture from noise. However, neither model can account for subjects' lower tolerance to noise for translational patterns than other (e.g. rotational) patterns. Finally, to investigate how well these structural measures preserve local orientation discontinuities, I show that the presence of a patch of unstructured dots embedded in a Glass pattern produces a change in multi-local orientation variance that is sufficient to account for human detection (Hel Or and Zucker, 1989). Together, these data suggest that simple orientation statistics could drive a range of 'texture tasks', although the dependency of noise resistance on the pattern type (rotation, translation, etc.) remains to be accounted for.     

Statistics and geometry of orientation selectivity in primary visual cortex

Orientation maps are a prominent feature of the primary visual cortex of higher mammals. In macaques and cats, for example, preferred orientations of neurons are organized in a specific pattern, where cells with similar selectivity are clustered in iso-orientation domains. However, the map is not always continuous, and there are pinwheel-like singularities around which all orientations are arranged in an orderly fashion. Although subject of intense investigation for half a century now, it is still not entirely clear how these maps emerge and what function they might serve. Here, we suggest a new model of orientation selectivity that combines the geometry and statistics of clustered thalamocortical afferents to explain the emergence of orientation maps. We show that the model can generate spatial patterns of orientation selectivity closely resembling the maps found in cats or monkeys. Without any additional assumptions, we further show that the pattern of ocular dominance columns is inherently connected to the spatial pattern of orientation.     

On visual orientation of dot patterns

Two-dimensional normally distributed random dot patterns were used in two experiments on visual orientation estimation. In the first experiment the patterns differed in their sample correlation and in dot number. In the second one the number of dots was maintained constant but the patterns were generated as a superposition of two normally distributed orthogonal sets composed of different number of dots. In both experiments the estimated orientation depended on stimuli correlation-with increasing correlation the estimated orientation gets closer to the orientation of the least square distance axis of the pattern. Even at very low unsignificant correlations there still remained a hint about stimulus orientation which was not estimated at random. Equalizing consecutively the number of dots in the two orthogonal dot patterns during the second experiment did not result in chance performance either. The bimodal angular distributions of the obtained responses permitted to approach the problem of orientation ambiguity. The results are discussed in terms of optimization processes taking place in the visual system.     

THE INCIDENCE AND ORIGIN OF SPOTTED PATTERNS IN THE ESTRILDIDAE

The plumage of the Estrildidae was examined in order to determine the incidence and origin of the spotted patterns.
In the Australian grassfinches a series of feathers showing the derivation of spotted patterns from transverse barring was found in two species. In most species such patterns consisted of single broad spots, but in two species paired spots were present.
The mannikins show three types of spotted pattern. One is derived from transverse barring, another from a rachial streak, and the third from a combination of both bars and streaks. The last one is not a true spotted pattern, the effect being due to overlapping feathers.
The waxbills show spotted patterns derived from transverse barring, the development of which exactly parallels that shown by the grassfinches, but differs in that almost all patterns show paired spots.
The spotted patterns appear to have been derived from a basic barred pattern in most cases, and to represent an increasing complexity of pattern rather than a gradual loss.
It is considered that similar patterns in widely separated species are due to parallel evolution of patterns and not to phylogenetically close relationship.
Where various species show different successive stages in the evolution of a pattern, this does not indicate that one is ancestral to another. Since the species concerned have a common family relationship, the potential for such a pattern may be present throughout the family.
Since the patterns have a function in specific recognition, it is suggested that similar patterns are likely to recur in widely separated localities and that the patterns of sympatric species are likely to differ. If similar patterns are present in one area they will probably indicate close relationship.
The inference of this in relation to plumage pattern problems in some other orders is briefly discussed.