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PubMed1991

Analysis of lymphocyte shape by visual classification, calculated measures of shape or light scattering.

Direct visual assays, calculated measures of shape (Dunn and Brown, 1986) and light scattering were applied to detect shape changes and to identify human peripheral blood lymphocytes displaying different shapes (e.g., spherical cells, polarized cells, non-polar cells with surface projections). Spherical cells could be distinguished from polarized cells and from non-polar cells with surface projections by means of calculated measures of shape obtained from outline drawings, the dispersion parameter being more efficient than extension or elongation parameters. Median values for elongation and extension of polarized cells vs. non-polar cells with surface projections differed significantly provided the cell populations consisted entirely of one particular morphological class. However, if the proportion of cells changing shape is small, this may not be detectable by a significant change in the median values. Therefore, we attempted to apply calculated shape factors to identify individual cells showing a particular type of shape change. Spherical cells could be distinguished relatively easily from non-spherical cells on the basis of the dispersion values. However, it was not possible to distinguish unequivocally between polarized cells and non-polar cells with surface projections because the values overlap to a great extent. For this purpose the visual classification was found to be more reliable. Preliminary experiments with light scattering showed that median values for right angle scatter or forward angle scatter are not sensitive enough to permit the detection of a small proportion of cells changing shape.

Humans↗
PubMed2000

Automatic recognition of biological shapes with and without representations of shape.

In this work it is described how to use the curvature function, the Fourier descriptors, and the coordinate functions of a contour to achieve automatic recognition of biological shapes. Those representations of shape and the coordinate functions were applied to recognize human corneal endothelial cells embedded in a sample of tissue. We assume that when the coordinates of the points of contours are analyzed directly, no representation of shape is being used. We applied scale-space filtering to the coordinate functions, to compensate the effects of scaling and to minimize the error due to quantization. A technique for compensating the effects of rotation, with or without the use of a representation of shape, is proposed. Our results show that, for a wide range of biological shapes, no representation of shape is required to solve or avoid the problems caused by translation, scaling, and rotation. We conclude that for certain applications the use of a representation of shape can provide some advantages. However, the coordinate functions of contours, evolved in scale-space, can be efficiently used, yielding even better results in applications of robotics and computer vision related to the recognition of biological shapes.

Cell Biology↗
PubMed1999

Platelet shape change is mediated by both calcium-dependent and -independent signaling pathways. Role of p160 Rho-associated coiled-coil-containing protein kinase in platelet shape change.

Platelets undergo shape change upon activation with agonists. During shape change, disc-shaped platelets turn into spiculated spheres with protruding filopodia. When agonist-induced cytosolic Ca(2+) increases were prevented using the cytosolic Ca(2+) chelator, 5, 5'-dimethyl-bis-(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid (5, 5'-dimethyl-BAPTA), platelets still underwent shape change, although the onset was delayed and the initial rate was dramatically decreased. In the absence of cytosolic Ca(2+), agonist-stimulated myosin light chain phosphorylation was significantly inhibited. The myosin light chain was maximally phosphorylated at 2 s in control platelets compared with 30 s in 5,5'-dimethyl-BAPTA-treated platelets. ADP, thrombin, or U46619-induced Ca(2+)-independent platelet shape change was significantly reduced by staurosporine, a nonselective kinase inhibitor, by the selective p160 Rho-associated coiled-coil-containing protein kinase inhibitor Y-27632, or by HA 1077. Both Y-27632 and HA 1077 reduced peak levels of ADP-induced platelet shape change and myosin light chain phosphorylation in control platelets. In 5,5'-dimethyl-BAPTA-treated platelets, Y-27632 and HA 1077 completely abolished both ADP-induced platelet shape change and myosin light chain phosphorylation. Our results indicate that Ca(2+)/calmodulin-stimulated myosin light chain kinase and p160 Rho-associated coiled-coil-containing protein kinase independently contribute to myosin light chain phosphorylation and platelet shape change, through Ca(2+)-sensitive and Ca(2+)-insensitive pathways, respectively.

1-(5-Isoquinolinesulfonyl)-2-Methylpiperazine↗
PubMed2005

A method for aligning trans-tibial residual limb shapes so as to identify regions of shape change.

Quantification of the change in shape of a residual limb over time is relevant to the fitting of an external prosthesis. Three algorithms were developed and evaluated to align residual limb shapes: iterative closest points (ICP), mean absolute difference, and weighted surface normals/mean absolute difference. Evaluations were conducted by aligning residual limb shapes with known deformations and transformations with their original shapes. Results showed that ICP did not perform well in that it tended to favor a global distribution of local shape difference rather than localization of the error. The mean absolute difference algorithm performed well as long as the shape difference was localized to one region. Weighted mean surface normals/absolute difference provided the best alignment results, performing well both if shape changes were localized and if they were globally distributed. Mean alignment errors for this method were less than 0.285 mm for each of the three translation directions and less than 0.357 degrees for each of the three rotation directions. This algorithm could be helpful to patients, prosthetists, and researchers developing treatments to overcome the detrimental fitting effects of residual limb shape change.

Algorithms↗
PubMed2004

Analysis of planar shapes using geodesic paths on shape spaces.

For analyzing shapes of planar, closed curves, we propose differential geometric representations of curves using their direction functions and curvature functions. Shapes are represented as elements of infinite-dimensional spaces and their pairwise differences are quantified using the lengths of geodesics connecting them on these spaces. We use a Fourier basis to represent tangents to the shape spaces and then use a gradient-based shooting method to solve for the tangent that connects any two shapes via a geodesic. Using the Surrey fish database, we demonstrate some applications of this approach: 1) interpolation and extrapolations of shape changes, 2) clustering of objects according to their shapes, 3) statistics on shape spaces, and 4) Bayesian extraction of shapes in low-quality images.

Algorithms↗
PubMed2006

Modulation of V1 activity by shape: image-statistics or shape-based perception?

It is current dogma that neurons in primary visual cortex extract local edges from the scene from which later visual areas reconstruct more meaningful shapes. Recent neuroimaging studies, however, have shown V1 modulations by the degree of structure in the image (shape). These V1 modulations due to the level of shape coherence have been explained in one of two possible ways: due to changes in image statistics or shape-based perceptual influences from higher visual areas. Here we compare both hypotheses using stimuli composed of Gabor arrays constructed to form circular shapes that can be successively degraded by manipulating the orientations of individual Gabors while maintaining local and global statistics. In a first experiment, we confirm that V1 responses are inversely correlated with the degree of structure in the image. In a second experiment, stimulus predictions are compared based on the degree of circular shape or change in the image statistic varied (orientation variance) in the image. We find that these V1 modulations to shape change are correlated with low-level changes in orientation contrast rather than shape perception per se.

Adult↗
PubMed2006

Comparing view sensitivity in shape discrimination with shape sensitivity in view discrimination.

In three picture-picture matching experiments, the effects of a view change on our ability to detect a shape change (Experiments 1 and 2) were contrasted with the effects of a shape change on our ability to detect a view change (Experiment 3). In each experiment, both view changes and shape changes influenced performance. However, shape changes had more influence than did view changes in the shape change detection task Conversely, view changes were more influential when the task was to detect view changes. Thus, the participants could often discriminate between the effects of shape changes and the effects of view changes. The disruptive effect of task-irrelevant changes (view changes in the first two experiments; shape changes in the final experiment) does not support Stankiewicz's (2002) claim that information about viewpoint and about shape can be estimated independently by human observers. However, the greater effect of variation in the task-relevant than in the task-irrelevant dimension indicates that the observers were moderately successful at disregarding irrelevant changes.

Attention↗
PubMed1995

Computer simulation of the directional displacement of rod-shaped, arc-shaped, and circular objects in an array of obstacles, representing a simple model for the gel electrophoresis of small DNA.

The gel electrophoresis of DNA of identical length but various static conformations was simulated using a two-dimensional model of the movement of rod-shaped, arc-shaped, and circular objects through random arrays of disk-shaped obstacles. At low obstacle density, the displacement rate of these objects decreases from the rod-shaped to the circular to the arc-shaped objects. At high obstacle densities, the displacement rate of circular objects approaches zero. The alignment of the arc-shaped objects along the axis of the directional movement of the objects were retarded in their movement by collisions with the obstacles; the number of collisions of the former, in view of their greater ability to align, was less than that of the latter. Circular objects were exclusively retarded by collisions, while the arc-shaped objects exhibited an additional retarding mechanism, viz. the suspension ("hanging") on the obstacles. When the rigid objects were made flexible, their displacement increased. The increase was most pronounced with the circular objects, allowing them to penetrate at obstacle densities from which the rigid objects were excluded.

Computer Simulation↗
PubMed2003

Attentional selection of overlapped shapes: a study using brief shape aftereffects.

Prior studies using brief stimulus sequences revealed "opponent shape aftereffects", indicative of direct opponent coding of global shape attributes such as aspect ratio, skew, taper, curvature, and convexity (perhaps in IT). Further, aftereffects from overlapped opponent pairs of adaptor shapes (e.g., concave and convex shapes) were substantially modulated by attention [Vision Res. 41 (2001) 3883]. Hypothetically, (1) attention might weight the attended and ignored contours at early stages of processing, or (2) it might sway opposing neural activity (e.g., of convex- vs. concave-tuned units) at the stage of opponent shape coding. Attentional modulation was equivalent for opponent pairs (producing opposite aftereffects) and non-opponent pairs (producing orthogonal aftereffects) of overlapped adaptor shapes, whether convexity or aspect-ratio aftereffects were measured. Further, the degree of attentional modulation obtained for these aftereffects (approximately 60%) was comparable to that obtained for V4 cells [J. Neurosci. 19 (1999) 1736]. Taken together, differential contour weighting appears to be the primary mechanism of attentional modulation of brief shape aftereffects.

Attention↗
PubMed2000

Does face recognition rely on encoding of 3-D surface? Examining the role of shape-from-shading and shape-from-stereo.

It is now well known that processing of shading information in face recognition is susceptible to bottom lighting and contrast reversal, an effect that may be due to a disruption of 3-D shape processing. The question then is whether the disruption can be rectified by other sources of 3-D information, such as shape-from-stereo. We examined this issue by comparing identification performance either with or without stereo information using top-lit and bottom-lit face stimuli in both photographic positive and negative conditions. The results show that none of the shading effects was reduced by the presence of stereo information. This finding supports the notion that shape-from-shading overrides shape-from-stereo in face perception. Although shape-from-stereo did produce some signs of facilitation for face identification, this effect was negligible. Together, our results support the view that 3-D shape processing plays only a minor role in face recognition. Our data are best accounted for by a weighted function of 2-D processing of shading pattern and 3-D processing of shapes, with a much greater weight assigned to 2-D pattern processing.

Adolescent↗
PubMed2003

Human sperm maintain their shape following decondensation and denaturation for fluorescent in situ hybridization: shape analysis and objective morphometry.

The relationship between abnormal sperm morphology and chromosomal aberrations has been of interest. Thus far, however, studies have focused on frequencies of sperm with either abnormal morphology or aneuploidies in semen samples, not on detection of individual spermatozoa exhibiting both abnormal morphology and aneuploidy. To assess the feasibility of simultaneous evaluation of both attributes in an individual sperm cell, we investigated whether sperm shape is preserved after decondensation and denaturation, procedures that are required for fluorescent in situ hybridization (FISH). On 21 slides, 395 sperm were fixed, photographed, and then digitized by the computer-assisted Metamorph morphometry program for individual evaluation before decondensation. To establish whether sperm of various shapes would behave in similar manners, the cells were also classified, according to their head shapes, into symmetrical (n = 115), asymmetrical (n = 115), irregular (n = 115), and amorphous (n = 50) categories. Following decondensation and subsequent denaturation, sperm that had been photographed initially were relocalized and digitized for morphometry. Head area, perimeter, long axis, short axis, shape factor, and tail length were evaluated in each of the 395 sperm in both the native and decondensed states. After the decondensation and denaturation protocol of the FISH procedure, the sperm exhibited a proportional increase in dimensions as compared to their original sizes. Their initial shapes were preserved with high fidelity whether the sperm were in the symmetrical, asymmetrical, irregular, or amorphous categories. Hybridization with the chromosome probes had no further effect on sperm shape or size. We provide images to demonstrate how these findings facilitate studies about the relationship between sperm shape and chromosomal content or aberrations in individual spermatozoa.

Cell Size↗
PubMed2006

Do rats use shape to solve "shape discriminations"?

Visual discrimination tasks are increasingly used to explore the neurobiology of vision in rodents, but it remains unclear how the animals solve these tasks: Do they process shapes holistically, or by using low-level features such as luminance and angle acuity? In the present study we found that when discriminating triangles from squares, rats did not use shape but instead relied on local luminance differences in the lower hemifield. A second experiment prevented this strategy by using stimuli-squares and rectangles-that varied in size and location, and for which the only constant predictor of reward was aspect ratio (ratio of height to width: a simple descriptor of "shape"). Rats eventually learned to use aspect ratio but only when no other discriminand was available, and performance remained very poor even at asymptote. These results suggest that although rats can process both dimensions simultaneously, they do not naturally solve shape discrimination tasks this way. This may reflect either a failure to visually process global shape information or a failure to discover shape as the discriminative stimulus in a simultaneous discrimination. Either way, our results suggest that simultaneous shape discrimination is not a good task for studies of visual perception in rodents.

Animals↗
PubMed2005

Efficient shape matching using shape contexts.

We demonstrate that shape contexts can be used to quickly prune a search for similar shapes. We present two algorithms for rapid shape retrieval: representative shape contexts, performing comparisons based on a small number of shape contexts, and shapemes, using vector quantization in the space of shape contexts to obtain prototypical shape pieces.

Algorithms↗
PubMed2005

Reproducibility of the bladder shape and bladder shape changes during filling.

The feasibility of high precision radiotherapy to the bladder region is limited by bladder motion and volume changes. In the near future, we plan to begin treatment delivery of bladder cancer patients with the acquisition of a cone beam CT image on which the complete bladder will be semi-automatically localized. Subsequently, a bladder shape model that was developed in a previous study will be used for bladder localization and for the prediction of shape changes in the time interval between acquisition and beam delivery. For such predictions, knowledge about urinary inflow rate is required. Therefore, a series of MR images was acquired over 1 h with time intervals of 10 min for 18 healthy volunteers. To gain insight in the reproducibility of the bladder shape over longer periods of time, two additional MRI series were recorded for 10 of the volunteers. To a good approximation, the bladder volume increased linearly in time for all individuals. Despite receiving drinking instructions, we found a large variation in the inflow rate between individuals, ranging from 2.1 to 15 cc/min (mean value: 9 +/- 3 cc/min). In contrast, the intravolunteer variation was much smaller, with a mean standard deviation (SD) of 0.4 cc/min. The inflow rate was linearly correlated with age (negative slope). To study the reproducibility of the bladder shape, we compared bladder shapes of equal volume. For all individuals, the caudal part of the bladder was the most reproducible (variations<0.3 cm in all cases). The cranial and posterior parts of the bladder was much less reproducible, with local SD values up to approximately 1.2 cm for bladders with a volume of 200 cc. These large long-term variations were primarily caused by changes in position and filling of the small bowel and rectum. However, for short time intervals, the rectal filling was (nearly) constant. Therefore, the reproducibility of urinary inflow, combined with the previously developed shape model gives us an excellent tool to predict short-term shape changes. We intend to use this tool for further improvement of image-guided radiotherapy for bladder cancer patients.

Adult↗
PubMed1990

Bacterial cell shape regulation: testing of additional predictions unique to the two-competing-sites model for peptidoglycan assembly and isolation of conditional rod-shaped mutants from some wild-type cocci.

The two-competing-sites model for peptidoglycan assembly for bacterial cell shape regulation suggests that in rods, bacterial cell shape depends on the balance between two reactions (sites), one responsible for lateral wall elongation and the other responsible for septum formation. The two reactions compete with each other so that no lateral wall can be formed during septum formation and vice versa. When the site for lateral wall elongation overcomes that for septum formation, long rods or filaments are formed and cell division may be blocked. When the reaction leading to septum formation is hyperactive compared with the other, coccobacilli or cocci are formed. Other bacteria carry only one site for peptidoglycan assembly and can grow only as cocci. The two-competing-sites model predicts that two different types of cocci exist (among both morphology mutants and wild-type strains); one carries only the site for septum formation, whereas the other also carries the site for lateral wall elongation, the former site predominating over the latter. As a consequence of the inhibition (by antibiotics or by mutations) of septum formation in wild-type cocci of various species and in coccoid morphology mutants, some cocci are expected to undergo transition to rod shape and others are not. We have evaluated these predictions and show that they are in agreement. In fact, we found that among wild-type cocci belonging to 13 species, those of 6 species formed rods, whereas the remaining organisms maintained their coccal shape when septa were inhibited by antibiotics. Some coccoid morphology mutants of rod-shaped bacteria underwent coccus-to-rod transition after septum inhibition by antibiotics, whereas others maintained their coccal shape. When a mutation that causes septum inhibition was expressed in a morphology mutant of Klebsiella pneumoniae grown as a coccus, transition to rod shape was observed. A total of 914 mutants unable to form colonies at 42 degrees C were isolated from the coccoid species mentioned above. Between 75 and 95% of the mutants isolated from the species that formed rods when septum formation was inhibited by antibiotics but none of those isolated from the others underwent coccus-to-rod transition upon incubation at the nonpermissive temperature.

Anti-Bacterial Agents↗
PubMed1992

Reinnervation of muscles in rats after repair of transsected sciatic nerves with Y-shaped and X-shaped silicone tubes. Muscle reinnervation after nerve repair.

Reinnervation of the gastrocnemius and anterior tibial muscles was assessed by measurements of tetanic force after repair of sciatic nerves with Y-shaped or X-shaped silicone tubes in rats. The transsected proximal stump of either the tibial or the peroneal fascicle was introduced into the opening of a Y-shaped silicone tube, or both fascicles were introduced into an X-shaped tube. The distal tibial and peroneal fascicles were inserted into the distal outlets of the tubes leaving a gap of 4 mm between proximal and distal stumps. In the X-shaped tubes the proximal inserts were placed opposite or adjacent to their respective distal parts. Sixteen weeks later reinnervation was evaluated by measurements of tetanic force of the gastrocnemius and anterior tibial muscles after electrical stimulation of the fascicles. There was preferential reinnervation in both types of tubes. In Y-shaped tubes about 90% of the tetanic force could be recorded from both muscles after stimulation of the peroneal and tibial fascicles, respectively. Recovery was lower in the X-shaped tubes, amounting to about 75%. Contractions evoked by misrouted fibres were similar (roughly 40%) in both models. We conclude that motor axons preferentially, but not exclusively, selected a path to reinnervate their original target muscle.

Animals↗
PubMed2001

Heritability of teat-end shape and the relationship of teat-end shape with somatic cell score for an experimental herd of cows.

Teat-end shapes were categorized for 1443 Holstein cows with 3582 lactations, in the Iowa State University herd at Ankeny, approximately 40 d postpartum between 1970 and 1995. Frequencies of teat-end shapes were as follows: round, 52.2%; prolapsed, 0.8%; flat, 14.2%; plate, 3.4%; funnel, 8.9%; and mixed, 20.5%. Cows were coded as mixed if all four teat-end shapes were not the same. Heritability estimates were obtained with an animal model with pedigrees traced back to registration numbers roughly conforming to birth year 1955. The heritability estimates for first, second, and third and later lactations were 34, 21, and 13%, respectively. Lactation averages for linear somatic cell scores were adjusted for days in milk, and month and age at calving, and were available for 255 cows with 431 lactations categorized from 1992 to 1995. Frequencies of teat-end shape on the 255 cows were as follows: round, 58%; prolapsed, 3%; flat, 11%; plate, 2%; funnel, 6%; and mixed, 20%. Least-squares means of somatic cell score for categories of teat-end shape were computed from a mixed model that included year, parity, and teat-end shape as fixed effects and cow as a random effect. Teat-end shape did not significantly affect somatic cell score.

Animals↗
PubMed2001

Genetic and pharmacological analyses of involvement of Src-family, Syk and Btk tyrosine kinases in platelet shape change. Src-kinases mediate integrin alphaIIb beta3 inside-out signalling during shape change.

Platelet shape change was found to be associated with an increase in protein tyrosine phosphorylation upon stimulation of thrombin-, ADP- and thromboxane A2-G-protein coupled receptors in human platelets and thromboxane A2 receptors in mouse platelets. By using PP1 and PD173956, two structurally unrelated specific inhibitors of Src-family tyrosine kinases, and mouse platelets deficient in the Src-kinase Fyn or Lyn, we show that Src-family kinases cause the increase in protein tyrosine phosphorylation. We further detected that the non-Src tyrosine kinase Syk was activated during shape change in a manner dependent on Src-family kinaseactivation. The pharmacological experiments and the studies on Fyn-, Lyn- and Syk-deficient mouse platelets showed that neither Src-family kinases nor Syk are functionally involved in shape change. Also human platelets deficient of the tyrosine kinase Btk showed a normal shape change. Binding of PAC-1 that recognizes activated integrin alphaIIb beta3 complexes on the platelet surface was enhanced during shape change and blocked by inhibition of Src-kinases. We conclude that the activation of Src-kinases and the subsequent Syk stimulation upon activation of G-protein coupled receptors are not involved in the cytoskeletal changes underlying shape change of human and mouse platelets, but that the stimulation of this evolutionary conserved pathway leads to integrin alphaIIb beta3 exposure during shape change.

Agammaglobulinaemia Tyrosine Kinase↗