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PubMed1983

The conformity of an anatomically shaped endotracheal tube to the shape of the airway.

The conformity of a pre-shaped endotracheal tube to the shape of the airway during endotracheal intubation was studied from lateral radiographs in patients lying supine on the operating table, with the neck in the normal, extended and flexed positions. A computer programme calculated the anterior contour of the pre-shaped tube and the posterior contour of the airway as mean values of the original contours on the radiographs. The mean configuration of the airway in intubated individuals with a pre-shaped endotracheal tube was then presented in a standard coordinate system. The results were compared with the shape of the airway in non-intubated patients and in patients intubated with a standard endotracheal tube.

Adult↗

PubMed2005

Ceramic nanoparticle assemblies with tailored shapes and tailored chemistries via biosculpting and shape-preserving inorganic conversion.

A novel biosynthetic paradigm is introduced for fabricating three-dimensional (3-D) ceramic nanoparticle assemblies with tailored shapes and tailored chemistries: biosculpting and shape-preserving inorganic conversion (BaSIC). Biosculpting refers to the use of biomolecules that direct the precipitation of ceramic nanoparticles to form a continuous 3-D structure with a tailored shape. We used a peptide derived from a diatom (a type of unicellular algae) to biosculpt silica nanoparticle based assemblies that, in turn, were converted into a new (nonsilica) composition via a shape-preserving gas/silica displacement reaction. Interwoven, microfilamentary silica structures were prepared by exposing a peptide, derived from the silaffin-1A protein of the diatom Cylindrotheca fusiformis, to a tetramethylorthosilicate solution under a linear shear flow condition. Subsequent exposure of the silica microfilaments to magnesium gas at 900 degrees C resulted in conversion into nanocrystalline magnesium oxide microfilaments with a retention of fine (submicrometer) features. Fluid(gas or liquid)/silica displacement reactions leading to a variety of other oxides have also been identified. This hybrid (biogenic/synthetic) approach opens the door to biosculpted ceramic microcomponents with multifarious tailored shapes and compositions for a wide range of environmental, aerospace, biomedical, chemical, telecommunications, automotive, manufacturing, and defense applications.

Biomimetics↗

PubMed2000

QSD quadratic shape descriptors. 2. Molecular docking using quadratic shape descriptors (QSDock).

We present a new shape-based polynomial time algorithm for the rapid docking of rigid ligands into their macromolecular receptors. The method exploits molecular surface complementarity existing between a putative ligand and its receptor protein. Molecular shapes are represented by using a new shape descriptor that is based on local quadratic approximations to the molecular surface. The quadratic shape descriptor is capable of representing a plethora of molecular shapes and is not limited to describing convex or concave regions of molecular surface. A single pair of complementary descriptors is sufficient for computing the transformation matrix that positions a ligand into the receptor site. We demonstrate the capabilities of our algorithm by successfully reproducing the crystallographically determined orientation for a test set of 20 ligand-protein complexes.

Algorithms↗

PubMed1994

Size and shape evaluation of astrocytoma nuclei with the shape analytical morphometry software system.

Eighteen cases of astrocytomas diagnosed as grades 1-3 of malignancy were studied with analytical morphometry to determine if different grades can be discriminated by size and shape parameters related to the nuclei. The shape analytical morphometry system was used to calculate dimensional measurements and express shape irregularities through quantitative parameters. With the shape asymmetry evaluator procedure, nuclear symmetry was evaluated. All parameters subjected to univariate and multivariate strategies were the same in easily distinguishing grade 1 from the others. Grades 2 and 3 could not be discriminated completely by either dimensional or with analytical parameters revealing strong similarities of nuclear shape and dimensions.

Astrocytoma↗

PubMed2001

What's in a shape? Children represent shape variability differently than adults when naming objects.

Children and adults often generalize a word to objects of the same shape. However, the shape properties on which generalization is based are unknown. We investigated the degree to which two shape dimensions were represented categorically by children and adults when learning names for objects. Multidimensional scaling techniques were used to establish the perceptual similarity of two sets of objects in Experiment 1. In Experiments 2 and 3, children (from 2;8 to 4;5 years of age) and adults participated in two tasks in which they learned a novel name for an exemplar. We then examined how often the novel name was generalized to different objects and to line drawings of the objects. In one task, participants generalized the names from memory; in a second task the exemplar was in front of the participant during generalization. Adults accepted names more often to objects that fell "within" the proposed shape boundaries than to objects that fell "across" the boundaries. Children, however, were just as likely to generalize names to novel objects that fell within as to objects that crossed the boundaries.

Adolescent↗

PubMed1994

Rethinking "shape space": evidence from simulated docking suggests that steric shape complementarity is not limiting for antibody-antigen recognition and idiotypic interactions.

The concept of "shape space" is based on the assumption that the relevant properties of individual molecules can be adequately specified by a finite list of N parameters; and that cij, the affinity between molecules i and j, can be specified by an equation of the form: cij = f(xi, xj), where xi and xj are N-dimensional vectors representing the absolute positions of molecules i and j in an objective, referential "shape space", and f is an appropriate function. We have performed simulated docking of the combining sites of immunoglobulin molecules, based on their crystallographic structures. The results suggest that shape complementarity cannot account for the specificity of idiotypic interactions, since in the simulations each pair of docked proteins had a buried surface area as great as that occurring in known complexes. It therefore seems likely that the atomic interactions accounting for the specificity of immunoglobulin recognition are highly relational. This casts doubt on the basic assumptions underlying the shape-space concept, at least in the simple form hitherto used in theoretical modelling of the immune system. In order to be realistic, the dimensionality N would have to be high (more than 20), and the function f would be irregular and discontinuous. Alternatively, if the equation cij = f(xi, xj) is interpreted as a purely formal construction in an abstract "inversion space", its validity is entirely relative to the empirical affinity matrix on which the construction is based. We conclude that at present there is no sure way of adequately characterizing the internal structure of idiotypic affinity matrices; and that models of the immune system should therefore aim at being generic and robust with respect to the structure of the idiotypic affinity matrices of unselected immunoglobulins.

Algorithms↗

PubMed2003

Neural activity in prefrontal cortex during copying geometrical shapes. I. Single cells encode shape, sequence, and metric parameters.

In drawing a copy of a geometrical shape, a sequence of movements must be produced to represent the sides of the object in the proper spatial relationship. We investigated neural mechanisms of this process by training monkeys to draw (using a joystick) copies of geometrical shapes (triangles, squares, trapezoids and inverted triangles) presented on a video monitor while recording single cell activity in prefrontal cortex. The drawing trajectories monkeys produced were divided into a series of discrete segments, varying in direction and length. We performed a stepwise multiple linear regression analysis to identify those copy parameters significantly influencing cell activity. The copied shape (e.g., triangle, square) and the serial position of the segment within each trajectory were the most prevalent effects (in 46% and 43% of cells, respectively), followed by segment direction (32%) and length (16%). Effects of temporal factors (maximum segment speed and time to maximum segment speed) were less frequent. These results demonstrate that prefrontal neurons encode several spatial and sequence variables that define copy trajectories. We also found that specific groupings of significant effects tended to occur together in single neurons. Specifically, single neurons simultaneously processed the serial position of a segment within each trajectory along with the corresponding spatial (but not temporal) attributes of that segment (i.e., direction and length), as well as with the overall shape to which the segments belong. Finally, we discovered that relationships between neural activity and segment serial position were systematic in many instances, described by monotonically increasing and decreasing functions, as well as parabolic functions. These findings indicate that, within the copying task, the serial segment position is a key factor for neural activity in the periprincipalis area of the prefrontal cortex.

Action Potentials↗

PubMed1994

The seventh Datta Lecture. Membrane bending energy concept of vesicle- and cell-shapes and shape-transitions.

The main objective of this lecture is to discuss the role of lipid-bilayer elasticity (1) for the self-organization of lipid/protein-bilayers (2) for the stabilization of domain structures and shapes of cell membranes and (3) for the control of shape transitions (e.g. bud- and pit-formation) and shape instabilities (vesicle fission). It is demonstrated that many complex shape transitions of cell membranes can be mimicked by single lipid bilayer vesicles by simply varying the area-to-volume ratio or by chemically induced bending moments suggesting that these processes are governed by the universal minimum bending energy concept of closed shells composed of stratified membranes. The essential role of the coupling between curvature and phase separation in mixed membranes for the formation and stabilization of local pits and buds or the fission of budded vesicles is demonstrated. Finally, we discuss the consequences of the pronounced thermally excited bending undulations of the hyperelastic membranes for the membrane tension, the material exchange at membrane surfaces and the control of the adhesion of vesicles (or cells) on solid substrates.

Biophysical Phenomena↗

PubMed1996

A neurological dissociation between shape from shading and shape from edges.

We studied the ability of a neurological patient, who has deficits in various aspects of form perception, to perform region segregation tasks requiring discriminations based on several image properties that are related to the three-dimensional structure of objects. The patient could discriminate the apparent three-dimensional structure and orientation of shapes defined by shading gradients, but could not make such discriminations for shapes in which edges were depicted as lines or as luminance discontinuities. These results suggest that the neural pathways that compute shape from shading gradients may be independent of those that compute shape based on edges, and, based on the patient's pattern of brain damage, they also indicate a relatively early functional separation in the requisite inputs.

Adult↗

PubMed2004

Shape-controlled synthesis and shape-induced texture of MnFe2O4 nanoparticles.

Monodisperse MnFe2O4 nanoparticles with cubelike and polyhedron shapes were synthesized by reaction of Fe(acac)3 and Mn(acac)2 with 1,2-hexadecanediol, oleic acid, and oleylamine. Controlled evaporation of the particle dispersion led to nanoparticle superlattices. The crystal orientation of the particle in the assembly depends on the shape of the particles, with particles in a cubelike shape showing (100) texture and those in the polyhedron shape exhibiting (110) texture.

Journal Article↗

PubMed2006

Pore size or geometry: which determines the shape and inverse-shape selective adsorption of alkane isomers?

The adsorption of pure pentane (C(5)) isomers and their ternary mixture is simulated in a series of carbon nanoslits. With decreasing nanoslit pore size, shape selective adsorption first occurs in the order of nC(5) > or = iC(5) > neoC(5) due to the configurational entropy effect, then inverse-shape selective adsorption occurs in the order of nC(5) < iC(5) < or = neoC(5) due to the area entropy effect, and finally no adsorption occurs. The entropy effects lead to a large adsorptive separation among the C(5) isomers from their mixture. Similar behavior has been observed from the simulation of C(5) adsorption in carbon nanotubes with variation in pore size. These results reveal that pore size rather than geometry determines the shape and inverse-shape selective adsorption of alkane isomers in nanopores.

Journal Article↗

PubMed2006

Shape resonances in molecular clusters: the 2t(2g) shape resonances in S 2p-excited sulfur hexafluoride clusters.

Sulfur hexafluoride clusters are investigated in the S 2p excitation regime. For the first time special emphasis is put on high-energy resolution spectroscopy of shape resonances in free clusters. We have investigated the 2t(2g)-shape resonance occurring above the S 2p threshold as one typical example to study size effects that are related to shape resonances. A small redshift of this resonance of 30 +/- 5 meV occurs in clusters relative to the free molecule and changes in line shape are observed. A double-barrier optical potential model is applied for the analysis of intra- and intermolecular effects occurring in SF6 clusters, which is suitable for rationalizing the experimentally observed spectral changes. The experimental and theoretical results are briefly discussed in comparison to previous work on core-excited van der Waals clusters containing diatomic molecules.

Cluster Analysis↗

PubMed1999

Vertebral shape: automatic measurement with active shape models.

The shape and appearance of the spine on lateral dual x-ray absorptiometry scans were statistically modeled. To measure vertebral shape accurately, rapidly, and automatically with a computer, this trained model was matched to findings on previously unseen scans. The technique obtained entire shape information, was faster than manual analysis, and was as accurate as human observers in the measurement of vertebral shape.

Absorptiometry, Photon↗

PubMed1980

Shaping the location of a pigeon's peck: effect of rate and size of shaping steps.

For several pigeons, pecking at particular locations within a ten-inch-wide response area was reinforced by grain presentations. The reinforced locations changed systematically to "shape" response location back and forth across the area. The rate and size of these shifts in reinforced locations were varied in both between-subject and within-subject comparisons to evaluate the influence of these variables on the shaping process. Larger step sizes produced larger shifts in location for all sizes inspected, with all sizes from .5 to 3.0 inches effective in shaping behavior. More rapid steps were approximately as effective as slower steps for all rates of shift inspected from 25 reinforcers to 400 reinforcers per step. These data suggest that shaping peck location proceeds most efficiently with rapid, relatively large shifts in criterion performance.

Animals↗

PubMed2003

Genetic analysis of three-dimensional shape of mouse lung tumors reveals eight lung tumor shape-determining (Ltsd) loci that are associated with tumor heterogeneity and symmetry.

Most lung tumor linkage studies focus on identifying loci that confer susceptibility or resistance irrespective of the tumor types developed. However, different mouse strains develop different types of lung tumors. A major obstacle for genetic studies of these differences is the lack of reproducible, quantitative, and uniform assessment of tumor type. We have previously described a new variable (Rratio) that assesses the three-dimensional shape of lung tumors in a quantifiable way and showed that nonspherical tumors are correlated with tumor heterogeneity and with a tendency to asymmetrical growth (N. Tripodis and P. Demant, Exp. Lung Res., 27: 521-531, 2001). In the present study, we use the Rratio variable to search for quantitative trait loci affecting tumor phenotype. We tested the F(2) cross between the susceptible strain O20 and the recombinant congenic strain OcB-9. Both develop mixed alveolar and papillary lung tumors, and the OcB9 tumors are, on average, more elongated than the O20 ones. We mapped eight new lung tumor shape-determining loci (Ltsd1-8) involved in mutual interactions. Two of these loci, Ltsd1 and Ltsd3, seem to play a major role in tumor shape formation. The Ltsd4 locus was confirmed in a second F(2) cross between strain O20 and the recombinant congenic strain OcB-6. Genotype-phenotype associations show that nonspherical tumors are correlated with tumor heterogeneity and nonsymmetrical (focal) development of structures. Most of the new Ltsd loci map in regions where susceptibility to lung cancer (Sluc) loci have been previously mapped, raising the question of whether they are identical or closely linked loci. Based on models of tumor growth indicating that supply of nutrients and the ability to create a capillary network may be shape-determining factors (G. P. Pescarmona et al., Med. Hypoth., 53: 497-503, 1999), we suggest as likely candidates for the Ltsd loci genes involved in angiogenesis, vascularization, and capillary patterning. This is the first set of loci that affects qualitative aspects of lung tumors and may provide biologically and clinically interesting indicators of lung tumor progression.

Animals↗

PubMed1998

Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape.

The size and shape of macromolecules such as proteins and nucleic acids play an important role in their functions. Prior efforts to quantify these properties have been based on various discretization or tessellation procedures involving analytical or numerical computations. In this article, we present an analytically exact method for computing the metric properties of macromolecules based on the alpha shape theory. This method uses the duality between alpha complex and the weighted Voronoi decomposition of a molecule. We describe the intuitive ideas and concepts behind the alpha shape theory and the algorithm for computing areas and volumes of macromolecules. We apply our method to compute areas and volumes of a number of protein systems. We also discuss several difficulties commonly encountered in molecular shape computations and outline methods to overcome these problems.

Algorithms↗

PubMed2006

Synthesis of novel rod-shaped and star-shaped fluorescent phosphane oxides--nonlinear optical properties and photophysical properties.

The design of a new class of fluorophores is presented. Some push-pull chromophores (D-pi-A) containing polyphenylethynyl units and a phosphane oxide moiety were efficiently prepared from common intermediates. Straightforward syntheses gave novel one-armed, rod-shaped and three-armed, star-shaped fluorophores. The optical properties of the resulting star-shaped derivatives were evaluated, showed high fluorescence quantum yields, and their excitation induces very efficient charge redistribution. Moreover, thanks to their push-pull character, the molecules exhibited significant second-order NLO properties with good transparency, up to 67x10(-30) esu at 1907 nm, with an absorption lambdamax at 369 nm. The effect of the donor group and of the number of phenylethynyl arms have been studied in this work.

Journal Article↗

PubMed2006

Evaluating oneself by shape and weight is not the same as being dissatisfied about shape and weight: A longitudinal examination in severely obese gastric bypass patients.

OBJECTIVE: This study examined two related and confused body image constructs--overevaluation and body image dissatisfaction--and tested their distinctiveness by examining their longitudinal associations with changes in self-esteem and negative affect. METHOD: One hundred forty-five obese (mean BMI = 51.6, SD = 7.5) patients (16 men and 129 women) completed a battery of self-report measures prior to and six months after undergoing gastric bypass surgery. Measures of body image (overevaluation of shape and weight, and body image dissatisfaction), self-esteem, and negative affect were assessed. RESULTS: Overevaluation and body image dissatisfaction both improved substantially following surgery. Change in overevaluation was significantly correlated only with change in self-esteem (after controlling for negative affect). Whereas change in body image dissatisfaction was significantly correlated with changes in both self-esteem and negative affect; findings for partial correlations remained unchanged. CONCLUSION: These findings demonstrate that evaluating oneself by shape and weight is related to, but not the same as, being dissatisfied about shape and weight. Given that overevaluation is less likely to be influenced by mood, it appears to be a more stable marker for disturbance in body image than body image dissatisfaction. This distinction has important implications for how clinicians and researchers assess these constructs.

Adult↗