Effects of carpal tunnel syndrome on adaptation of multi-digit forces to object weight for whole-hand manipulation

The delicate tuning of digit forces to object properties can be disrupted by a number of neurological and musculoskeletal diseases. One such condition is Carpal Tunnel Syndrome (CTS), a compression neuropathy of the median nerve that causes sensory and motor deficits in a subset of digits in the hand. Whereas the effects of CTS on median nerve physiology are well understood, the extent to which it affects whole-hand manipulation remains to be addressed. CTS affects only the lateral three and a half digits, which raises the question of how the central nervous system integrates sensory feedback from affected and unaffected digits to plan and execute whole-hand object manipulation. We addressed this question by asking CTS patients and healthy controls to grasp, lift, and hold a grip device (445, 545, or 745 g) for several consecutive trials. We found that CTS patients were able to successfully adapt grip force to object weight. However, multi-digit force coordination in patients was characterized by lower discrimination of force modulation to lighter object weights, higher across-trial digit force variability, the consistent use of excessively large digit forces across consecutive trials, and a lower ability to minimize net moments on the object. Importantly, the mechanical requirement of attaining equilibrium of forces and torques caused CTS patients to exert excessive forces at both CTS-affected digits and digits with intact sensorimotor capabilities. These findings suggest that CTS-induced deficits in tactile sensitivity interfere with the formation of accurate sensorimotor memories of previous manipulations. Consequently, CTS patients use compensatory strategies to maximize grasp stability at the expense of exerting consistently larger multi-digit forces than controls. These behavioral deficits might be particularly detrimental for tasks that require fine regulation of fingertip forces for manipulating light or fragile objects.     

Effects of the inter-stimulus interval on visual evoked potentials to patterned stimuli

Visual evoked potentials to patterned stimulation of the upper and lower half of the visual field were investigated in nine adult Ss. The inter-stimulus interval varied between 350 and 2,600 msec. With patterned stimulation, no inter-stimulus interval effects were obtained for occipital components. In contrast for the vertex lead, on the other hand, as inter-stimulus interval increased, the N140-P200 amplitude increased. Because of the heterogeneity subjects' responses evoked by upper half-field stimulation, this effect was more pronounced in lower half-field stimulation.     

Flexible representations of dynamics are used in object manipulation

To manipulate an object skillfully, the brain must learn its dynamics, specifying the mapping between applied force and motion. A fundamental issue in sensorimotor control is whether such dynamics are represented in an extrinsic frame of reference tied to the object or an intrinsic frame of reference linked to the arm. Although previous studies have suggested that objects are represented in arm-centered coordinates [1-6], all of these studies have used objects with unusual and complex dynamics. Thus, it is not known how objects with natural dynamics are represented. Here we show that objects with simple (or familiar) dynamics and those with complex (or unfamiliar) dynamics are represented in object- and arm-centered coordinates, respectively. We also show that objects with simple dynamics are represented with an intermediate coordinate frame when vision of the object is removed. These results indicate that object dynamics can be flexibly represented in different coordinate frames by the brain. We suggest that with experience, the representation of the dynamics of a manipulated object may shift from a coordinate frame tied to the arm toward one that is linked to the object. The additional complexity required to represent dynamics in object-centered coordinates would be economical for familiar objects because such a representation allows object use regardless of the orientation of the object in hand.     

Conformation-opioid activity relationships of bicyclic guanidines from 3D similarity analysis

Conformation of bicyclic guanidines with kappa-opioid receptor activity derived in our laboratory from a positional scanning synthetic combinatorial library is presented in this work. We propose a common bioactive conformation and putative pharmacophoric features by means of 3D similarity methods. Our 'Y' shape molecular binding model explains structure-activity relationships and suggests that the guanidine functionality and a 4-methoxybenzyl group may be involved in key interactions with the receptor. Comparison of our model with known opiates suggest a similar binding mode showing that the bicyclic guanidines presented in this work are suitable scaffolds for further development of new opioid receptors ligands.     

Comparison of object manipulation among 74 species of non-human primates

Seventy-four primates species (24 genera of six families) were presented with a nylon rope and a wooden cube, and their subsequent manipulations were recorded in detail. Five hundreds and six manipulation patterns were distinguished on the basis of the actions performed, body-parts used and relations to other objects. Inter-specific comparisons revealed three groups: (1) lemurs, marmosets, spider monkeys and leaf-eaters; (2) Old World monkeys except leaf-eaters; and (3) cebus monkeys and apes. The first group had the smallest repertoire of manipulations, in which only a few types of actions and body-parts were involved. The second and third groups had more varied modes of manipulation. Actions such as Roll, Rub and Slide, and use of fingers characterized these groups. Except for the lesser ape, their manipulations were frequently related with other objects. Moreover, actions such as Drape, Drop, Strike, Swing and Throw were typical of the third group. The factors producing such inter-specific differences in manipulations and the relations to tool use are discussed.     

Perspectives on object manipulation and action grammar for percussive actions in primates

The skill of object manipulation is a common feature of primates including humans, although there are species-typical patterns of manipulation. Object manipulation can be used as a comparative scale of cognitive development, focusing on its complexity. Nut cracking in chimpanzees has the highest hierarchical complexity of tool use reported in non-human primates. An analysis of the patterns of object manipulation in naive chimpanzees after nut-cracking demonstrations revealed the cause of difficulties in learning nut-cracking behaviour. Various types of behaviours exhibited within a nut-cracking context can be examined in terms of the application of problem-solving strategies, focusing on their basis in causal understanding or insightful intentionality. Captive chimpanzees also exhibit complex forms of combinatory manipulation, which is the precursor of tool use. A new notation system of object manipulation was invented to assess grammatical rules in manipulative actions. The notation system of action grammar enabled direct comparisons to be made between primates including humans in a variety of object-manipulation tasks, including percussive-tool use.     

Class similarity and viewpoint invariance in the recognition of 3D objects

 In human vision, the processes and the representations involved in identifying specific individuals are frequently assumed to be different from those used for basic level classification, because classification is largely viewpoint-invariant, but identification is not. This assumption was tested in psychophysical experiments, in which objective similarity between stimuli (and, consequently, the level of their distinction) varied in a controlled fashion. Subjects were trained to discriminate between two classes of computer-generated three-dimensional objects, one resembling monkeys and the other, dogs. Both classes were defined by the same set of 56 parameters, which encoded sizes, shapes, and placement of the limbs, ears, snout, etc. Interpolation between parameter vectors of the class prototypes yielded shapes that changed smoothly between monkey and dog. Within-class variation was induced in each trial by randomly perturbing all the parameters. After the subjects reached 90% correct performance on a fixed canonical view of each object, discrimination performance was tested for novel views that differed by up to 60° from the training view. In experiment 1 (in which the distribution of parameters in each class was unimodal) and in experiment 2 (bimodal classes), the stimuli differed only parametrically and consisted of the same geons (parts), yet were recognized virtually independently of viewpoint in the low-similarity condition. In experiment 3, the prototypes differed in their arrangement of geons, yet the subjects’ performance depended significantly on viewpoint in the high-similarity condition. In all three experiments, higher interstimulus similarity was associated with an increase in the mean error rate and, for misorientation of up to 45°, with an increase in the degree of viewpoint dependence. These results suggest that a geon-level difference between stimuli is neither strictly necessary nor always sufficient for viewpoint-invariant performance. Thus, basic and subordinate-level processes in visual recognition may be more closely related than previously thought. Received: 15 November 1993/Accepted in revised form: 14 July 1994     

Effects of stimulus manipulations on visual categorization in pigeons

Four pigeons were previously trained [Lazareva, O.F., Freiburger, K.L., Wasserman, E.A., 2004. Pigeons concurrently categorize photographs at both basic and superordinate levels. Psychon. Bull. Rev. 11, 1111-1117] to classify color photographs into either their proper basic-level category (cars, chairs, flowers, or people) or a superordinate-level category (nominally natural or artificial). In Experiment 1, the same pigeons were shown either reflected or inverted versions of the training stimuli. Reflection had no effect on pigeons' classification behavior, whereas inversion impaired discrimination of all stimulus categories, except flowers, on the basic-level and superordinate-level tasks. Pixel matching analysis revealed that pattern matching played at most a minor role in the birds' categorization behavior. In Experiment 2, the pigeons were shown test stimuli that were either blurred or quartered and scrambled. Blurring impaired discrimination of cars, but had no effect on discrimination of people and flowers; scrambling impaired discrimination of people and flowers leaving discrimination of cars and chairs unaffected. These results suggest that categorization of flowers and people may be controlled primarily by the overall shape of the object rather than by local features, whereas categorization of cars and chairs may rely primarily on local features rather than the overall shape of the object.     

Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity

Background  

Virtual screening methods are now well established as effective to identify hit and lead candidates and are fully integrated in most drug discovery programs. Ligand-based approaches make use of physico-chemical, structural and energetics properties of known active compounds to search large chemical libraries for related and novel chemotypes. While 2D-similarity search tools are known to be fast and efficient, the use of 3D-similarity search methods can be very valuable to many research projects as integration of 3D knowledge can facilitate the identification of not only related molecules but also of chemicals possessing distant scaffolds as compared to the query and therefore be more inclined to scaffolds hopping. To date, very few methods performing this task are easily available to the scientific community.     

Effects of trophic similarity on community composition

Understanding how ecological processes determine patterns among species coexisting within ecosystems is central to ecology. Here, we explore relationships between species’ local coexistence and their trophic niches in terms of their feeding relationships both as consumers and as resources. We build on recent concepts and methods from community phylogenetics to develop a framework for analysing mechanisms responsible for community composition using trophic similarity among species and null models of community assembly. We apply this framework to 50 food webs found in 50 Adirondack lakes and find that species composition in these communities appears to be driven by both bottom‐up effects by which the presence of prey species selects for predators of those prey, and top‐down effects by which prey more tolerant of predation out‐compete less tolerant prey of the same predators. This approach to community food webs is broadly applicable and shows how species interaction networks can inform an increasingly large array of theory central to community ecology.     

Evaluation of a 3D object registration method for analysis of humeral kinematics

In 3D image-based studies of joint kinematics, 3D registration methods should be automatic, insensitive to segmentation inconsistencies and use coordinate systems that have clinically relevant orientations and locations because this is important for analyzing rotation angles and translation directions. We developed and evaluated a registration method, which is based on the cylindrical geometry of the humerus shaft and an analysis of the inertia moments of the humerus head, in order to consistently and automatically orient the humerus coordinate system according to its anatomy. Registration techniques must be thoroughly evaluated. In this study we used a well-detectable marker as reference, from which coordinate system determination errors of a 3D object could be measured. This allowed us to quantify by means of unique error analysis the translational and rotational errors in terms of how much and about/along which humeral axis errors occurred. The evaluation experiments were performed using virtual rotations of 3D humeral binary image, a humerus model and a 3D image of a volunteer's shoulder. They indicated that the humeral coordinate system determination errors primarily originated from segmentation inconsistencies, which influenced mostly the humeral transverse axes orientation. The error analysis revealed that the developed registration method reduced the effect of manual segmentation inconsistencies on the orientation of the humeral transverse axes up to 37%, in comparison to the commonly used inertia registration.     

Fast similarity search for protein 3D structures using topological pattern matching based on spatial relations

Similarity search for protein 3D structures become complex and computationally expensive due to the fact that the size of protein structure databases continues to grow tremendously. Recently, fast structural similarity search systems have been required to put them into practical use in protein structure classification whilst existing comparison systems do not provide comparison results on time. Our approach uses multi-step processing that composes of a preprocessing step to represent geometry of protein structures with spatial objects, a filter step to generate a small candidate set using approximate topological string matching, and a refinement step to compute a structural alignment. This paper describes the preprocessing and filtering for fast similarity search using the discovery of topological patterns of secondary structure elements based on spatial relations. Our system is fully implemented by using Oracle 8i spatial. We have previously shown that our approach has the advantage of speed of performance compared with other approach such as DALI. This work shows that the discovery of topological relations of secondary structure elements in protein structures by using spatial relations of spatial databases is practical for fast structural similarity search for proteins.     

Effects of manipulation of food supply on estuarine meiobenthos

A comparative mesocosm experiment was carried out to determine the effects of natural foods of different quality and quantity on the structure of natural meiobenthic communities collected in undisturbed sediment from the polluted Westerschelde and the comparatively undisturbed Gironde estuaries. Nematode communities are more diverse and species rich in the latter estuary. The organic matter or foods used were phytoplankton, green alga, salt marsh plant detritus and leaf litter detritus which were added at three dose rates including a high dose. There was no change in community structure in response to the treatments in either of the estuarine meiobenthic communities. Analysis of all the results from this experiment indicate that the food quantity manipulations had almost no effect on the deposit feeding meiofauna. It may be that the reserves of organic matter within the sediment were sufficient to satisfy their dietary requirements for the duration of the experiment. The abundance of diatom/epigrowth feeding nematodes which were initially dominant in the Gironde, declined substantially suggesting that they may have been food limited since diatoms were not among the sources of organic matter added to the mesocosm. There was no specific response to the five different types of organic matter added to the mesocosm     

Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA

Searching for similar 3D protein structures is one of the primary processes employed in the field of structural bioinformatics. However, the computational complexity of this process means that it is constantly necessary to search for new methods that can perform such a process faster and more efficiently. Finding molecular substructures that complex protein structures have in common is still a challenging task, especially when entire databases containing tens or even hundreds of thousands of protein structures must be scanned. Graphics processing units (GPUs) and general purpose graphics processing units (GPGPUs) can perform many time-consuming and computationally demanding processes much more quickly than a classical CPU can. In this paper, we describe the GPU-based implementation of the CASSERT algorithm for 3D protein structure similarity searching. This algorithm is based on the two-phase alignment of protein structures when matching fragments of the compared proteins. The GPU (GeForce GTX 560Ti: 384 cores, 2GB RAM) implementation of CASSERT (“GPU-CASSERT”) parallelizes both alignment phases and yields an average 180-fold increase in speed over its CPU-based, single-core implementation on an Intel Xeon E5620 (2.40GHz, 4 cores). In this paper, we show that massive parallelization of the 3D structure similarity search process on many-core GPU devices can reduce the execution time of the process, allowing it to be performed in real time. GPU-CASSERT is available at: http://zti.polsl.pl/dmrozek/science/gpucassert/cassert.htm.     

The calculation of molecular similarity: alternative formulas,data manipulation and graphical display

The use of electrostatic potential comparisons between molecules for the elucidation of structure activity relationships is now a well-established modeling technique. The Carbo and Hodgkin similarity indices are used extensively to make quantitative comparisons of this nature; yet their roots are found in the overlap of electron density distribution, with both formulas utilizing a product-based numerator.Two new similarity indices are suggested that calculate the electrostatic potential similarity using a difference-based numerator. The form of the new indices allows the creation of additional software functions that enhance the flexibility of similarity calculations and permit the creation of similarity maps.The general properties of these software functions and all indices are discussed and applied to a series of dopamine D2 receptor agonists.     

Further report on object manipulation in non-human primates: A comparison within 13 species of the genusMacaca

Thirteen captive species of the genusMacaca were presented with certain non-edible objects and the subsequent manipulation was observed. The following results were obtained: (1) Thefascicularis group species displayed a great variety in rolling the manipulandum, which has been reported to be one of the actions characterizing cercopithecine species; (2) manipulating the object with one finger was typical of thesilenus-sylvanus andsinica groups, whereas use of the fingers moving opposably was common to all species ofMacaca; (3) secondary manipulations in relation to the wire-mesh were observed only inM. silenus, M. sinica, andM. nemestrina, whereas those in relation to water were common to allMacaca species; and (4) within-subgroup differences were great in thesilenus-sylvanus andsinica groups as compared to thefascicularis group.     

Effects of 25-hydroxyvitamin D3 and 1,25-dihydroxyvitamin D3 on embryonic chick bone in organ culture

The ability of embryonic chick bone to respond to 25 hydroxyvitamin D3 and 1,25 dihydroxyvitamin D3 was assessed in organ culture. These metabolites were added to prelabeled chick embryo long-bone explants, and the amount of calcium-45 released into the medium after 24 or 48 h of hormone exposure was measured. For each time period a significant release of calcium-45 from hormone-treated bones was observed. The response to 25 hydroxyvitamin D3 and 1,25 dihydroxyvitamin D3 was always greater at 48 h and a clear dose-dependency was established at this time as well. 1,25 dihydroxyvitamin D3 was the more potent resorbing agent at all concentrations tested. The results from this study suggest that vitamin D metabolites may be involved in bone regulation in the chick embryo.