Three-dimensional gender differences in facial form of children in the North East of England.

PubMed

Bugaighis, Iman; Mattick, Clare R; Tiddeman, Bernard; Hobson, Ross

2013-06-01

The aim of the prospective cross-sectional morphometric study was to explore three dimensional (3D) facial shape and form (shape plus size) variation within and between 8- and 12-year-old Caucasian children; 39 males age-matched with 41 females. The 3D images were captured using a stereophotogrammeteric system, and facial form was recorded by digitizing 39 anthropometric landmarks for each scan. The x, y, z coordinates of each landmark were extracted and used to calculate linear and angular measurements. 3D landmark asymmetry was quantified using Generalized Procrustes Analysis (GPA) and an average face was constructed for each gender. The average faces were superimposed and differences were visualized and quantified. Shape variations were explored using GPA and PrincipalComponent Analysis. Analysis of covariance and Pearson correlation coefficients were used to explore gender differences and to determine any correlation between facial measurements and height or weight. Multivariate analysis was used to ascertain differences in facial measurements or 3D landmark asymmetry. There were no differences in height or weight between genders. There was a significant positive correlation between facial measurements and height and weight and statistically significant differences in linear facial width measurements between genders. These differences were related to the larger size of males rather than differences in shape. There were no age- or gender-linked significant differences in 3D landmark asymmetry. Shape analysis confirmed similarities between both males and females for facial shape and form in 8- to 12-year-old children. Any differences found were related to differences in facial size rather than shape.

The study of craniofacial growth patterns using 3D laser scanning and geometric morphometrics

NASA Astrophysics Data System (ADS)

Friess, Martin

2006-02-01

Throughout childhood, braincase and face grow at different rates and therefore exhibit variable proportions and positions relative to each other. Our understanding of the direction and magnitude of these growth patterns is crucial for many ergonomic applications and can be improved by advanced 3D morphometrics. The purpose of this study is to investigate this known growth allometry using 3D imaging techniques. The geometry of the head and face of 840 children, aged 2 to 19, was captured with a laser surface scanner and analyzed statistically. From each scan, 18 landmarks were extracted and registered using General Procrustes Analysis (GPA). GPA eliminates unwanted variation due to position, orientation and scale by applying a least-squares superimposition algorithm to individual landmark configurations. This approach provides the necessary normalization for the study of differences in size, shape, and their interaction (allometry). The results show that throughout adolescence, boys and girls follow a different growth trajectory, leading to marked differences not only in size but also in shape, most notably in relative proportions of the braincase. These differences can be observed during early childhood, but become most noticeable after the age of 13 years, when craniofacial growth in girls slows down significantly, whereas growth in boys continues for at least 3 more years.

Craniofacial morphometric analysis of mandibular prognathism.

PubMed

Chang, H P; Liu, P H; Yang, Y H; Lin, H C; Chang, C H

2006-03-01

The purpose of this study was to provide more information about the morphological characteristics of the craniofacial complex in mandibular prognathism. Forty young adult males having mandibular prognathism were compared with 40 having normal occlusion. This was conducted to carry out geometric morphometric assessments to localize alterations, using Procrustes analysis and thin-plate spline analysis, in addition to conventional cephalometric techniques. Procrustes analysis indicated that the mean craniofacial, midfacial and mandibular morphology was significantly different in prognathic subjects compared with normal controls. This finding was corroborated by the multivariate Hotelling T(2)-test of cephalometric variables. Mandibular prognathism demonstrated a shorter and slightly retropositioned maxilla, a greater total length and anterior positioning of the mandible. Thin-plate spline analysis revealed a developmental diminution of the palatomaxillary region anteroposteriorly and a developmental elongation of the mandible anteroposteriorly, leading to the appearance of a prognathic mandibular profile. In conclusion, thin-plate spline analysis seems to provide a valuable supplement for conventional cephalometric analysis because the complex patterns of craniofacial shape change are visualized suggestive by means of grid deformations.

Shape and size variation on the wing of Drosophila mediopunctata: influence of chromosome inversions and genotype-environment interaction.

PubMed

Hatadani, Luciane Mendes; Klaczko, Louis Bernard

2008-07-01

The second chromosome of Drosophila mediopunctata is highly polymorphic for inversions. Previous work reported a significant interaction between these inversions and collecting date on wing size, suggesting the presence of genotype-environment interaction. We performed experiments in the laboratory to test for the joint effects of temperature and chromosome inversions on size and shape of the wing in D. mediopunctata. Size was measured as the centroid size, and shape was analyzed using the generalized least squares Procrustes superimposition followed by discriminant analysis and canonical variates analysis of partial warps and uniform components scores. Our findings show that wing size and shape are influenced by temperature, sex, and karyotype. We also found evidence suggestive of an interaction between the effects of karyotype and temperature on wing shape, indicating the existence of genotype-environment interaction for this trait in D. mediopunctata. In addition, the association between wing size and chromosome inversions is in agreement with previous results indicating that these inversions might be accumulating alleles adapted to different temperatures. However, no significant interaction between temperature and karyotype for size was found--in spite of the significant presence of temperature-genotype (cross) interaction. We suggest that other ecological factors--such as larval crowding--or seasonal variation of genetic content within inversions may explain the previous results.

Shape Analysis of 3D Head Scan Data for U.S. Respirator Users

NASA Astrophysics Data System (ADS)

Zhuang, Ziqing; Slice, DennisE; Benson, Stacey; Lynch, Stephanie; Viscusi, DennisJ

2010-12-01

In 2003, the National Institute for Occupational Safety and Health (NIOSH) conducted a head-and-face anthropometric survey of diverse, civilian respirator users. Of the 3,997 subjects measured using traditional anthropometric techniques, surface scans and 26 three-dimensional (3D) landmark locations were collected for 947 subjects. The objective of this study was to report the size and shape variation of the survey participants using the 3D data. Generalized Procrustes Analysis (GPA) was conducted to standardize configurations of landmarks associated with individuals into a common coordinate system. The superimposed coordinates for each individual were used as commensurate variables that describe individual shape and were analyzed using Principal Component Analysis (PCA) to identify population variation. The first four principal components (PC) account for 49% of the total sample variation. The first PC indicates that overall size is an important component of facial variability. The second PC accounts for long and narrow or short and wide faces. Longer narrow orbits versus shorter wider orbits can be described by PC3, and PC4 represents variation in the degree of ortho/prognathism. Geometric Morphometrics provides a detailed and interpretable assessment of morphological variation that may be useful in assessing respirators and devising new test and certification standards.

Three-dimensional (3D) geometric morphometric analysis of human premolars to assess sexual dimorphism and biological ancestry in Australian populations.

PubMed

Yong, Robin; Ranjitkar, Sarbin; Lekkas, Dimitra; Halazonetis, Demetrios; Evans, Alistair; Brook, Alan; Townsend, Grant

2018-06-01

This study aimed to investigate size and shape variation of human premolars between Indigenous Australians and Australians of European ancestry, and to assess whether sex and ancestry could be differentiated between these groups using 3D geometric morphometrics. Seventy dental casts from each group, equally subdivided by sex, were scanned using a structured-light scanner. The 3D meshes of upper and lower premolars were processed using geometric morphometric methods. Seventy-two landmarks were recorded for upper premolars and 50 landmarks for lower premolars. For each tooth type, two-way ANOVA was used to assess group differences in centroid size. Shape variations were explored using principal component analysis and visualized using 3D morphing. Two-way Procrustes ANOVA was applied to test group differences for ancestry and sex, and a "leave-one-out" discriminant function was applied to assess group assignment. Centroid size and shape did not display significant difference between the sexes. Centroid size was larger in Indigenous Australians for upper premolars and lower second premolars compared to the Australians of European ancestry. Significant shape variation was noted between the two ancestral groups for upper premolars and the lower first premolar. Correct group assignment of individual teeth to their ancestral groups ranged between 80.0 and 92.8% for upper premolars and 60.0 and 75.7% for lower premolars. Our findings provide evidence of significant size and shape variation in human premolars between the two ancestral groups. High classification rates based on shape analysis of upper premolars highlight potential application of geometric morphometrics in anthropological, bioarcheological and forensic contexts. © 2018 Wiley Periodicals, Inc.

Procrustes Matching by Congruence Coefficients

ERIC Educational Resources Information Center

Korth, Bruce; Tucker, L. R.

1976-01-01

Matching by Procrustes methods involves the transformation of one matrix to match with another. A special least squares criterion, the congruence coefficient, has advantages as a criterion for some factor analytic interpretations. A Procrustes method maximizing the congruence coefficient is given. (Author/JKS)

Ontogenetic study of the skull in modern humans and the common chimpanzees: neotenic hypothesis reconsidered with a tridimensional Procrustes analysis.

PubMed

Penin, Xavier; Berge, Christine; Baylac, Michel

2002-05-01

Heterochronic studies compare ontogenetic trajectories of an organ in different species: here, the skulls of common chimpanzees and modern humans. A growth trajectory requires three parameters: size, shape, and ontogenetic age. One of the great advantages of the Procrustes method is the precise definition of size and shape for whole organs such as the skull. The estimated ontogenetic age (dental stages) is added to the plot to give a graphical representation to compare growth trajectories. We used the skulls of 41 Homo sapiens and 50 Pan troglodytes at various stages of growth. The Procrustes superimposition of all specimens was completed by statistical procedures (principal component analysis, multivariate regression, and discriminant function) to calculate separately size-related shape changes (allometry common to chimpanzees and humans), and interspecific shape differences (discriminant function). The results confirm the neotenic theory of the human skull (sensu Gould [1977] Ontogeny and Phylogeny, Cambridge: Harvard University Press; Alberch et al. [1979] Paleobiology 5:296-317), but modify it slightly. Human growth is clearly retarded in terms of both the magnitude of changes (size-shape covariation) and shape alone (size-shape dissociation) with respect to the chimpanzees. At the end of growth, the adult skull in humans reaches an allometric shape (size-related shape) which is equivalent to that of juvenile chimpanzees with no permanent teeth, and a size which is equivalent to that of adult chimpanzees. Our results show that human neoteny involves not only shape retardation (paedomorphosis), but also changes in relative growth velocity. Before the eruption of the first molar, human growth is accelerated, and then strongly decelerated, relative to the growth of the chimpanzee as a reference. This entails a complex process, which explains why these species reach the same overall (i.e., brain + face) size in adult stage. The neotenic traits seem to concern primarily the function of encephalization, but less so other parts of the skull. Our results, based on the discriminant function, reveal that additional structural traits (corresponding to the nonallometric part of the shape which is specific to humans) are rather situated in the other part of the skull. They mainly concern the equilibrium of the head related to bipedalism, and the respiratory and masticatory functions. Thus, the reduced prognathism, the flexed cranial base (forward position of the foramen magnum which is brought closer to the palate), the reduced anterior portion of the face, the reduced glabella, and the prominent nose mainly correspond to functional innovations which have nothing to do with a neotenic process in human evolution. The statistical analysis used here gives us the possibility to point out that some traits, which have been classically described as paedomorphic because they superficially resemble juvenile traits, are in reality independent of growth. Copyright 2002 Wiley-Liss, Inc.

Thin-plate spline analysis of arch form in a Southern European population with an ideal natural occlusion.

PubMed

Camporesi, Matteo; Franchi, Lorenzo; Baccetti, Tiziano; Antonini, Antonino

2006-04-01

The purpose of the present study was to identify the mean configuration of the clinical arch form in a sample of Southern European subjects with ideal natural occlusion by means of Procrustes analysis, and to compare the identified configuration with 10 commercially produced arch forms by means of thin-plate spline (TPS) analysis. The sample comprised the study casts of 50 subjects (26 males and 24 females). The mean age of the sample was 26 years +/- 4 years. All subjects were young Caucasian adults of Southern European ancestry, and presented with an ideal natural occlusion. The three-dimensional (3D) co-ordinates of all dental points (facial axis points) were digitized using a 3D electromagnetic digitizer. The morphometric technique of TPS analysis with permutation tests was used to compare the configurations of landmarks in the various specimens. No sexual dimorphism was found for either upper or lower arch forms when the shape of the arches was assessed independently from size. The commercially available arch form that showed the least, though statistically significant, shape difference with respect to the average calculated configuration was the Brader arch form.

MOSHFIT: algorithms for occlusion-tolerant mean shape and rigid motion from 3D movement data.

PubMed

Mitchelson, Joel R

2013-09-03

This work addresses the use of 3D point data to measure rigid motions, in the presence of occlusion and without reference to a prior model of relative point locations. This is a problem where cluster-based measurement techniques are used (e.g. for measuring limb movements) and no static calibration trial is available. The same problem arises when performing the task known as roving capture, in which a mobile 3D movement analysis system is moved through a volume with static markers in unknown locations and the ego-motion of the system is required in order to understand biomechanical activity in the environment. To provide a solution for both of these applications, the new concept of a visibility graph is introduced, and is combined with a generalised procrustes method adapted from ones used by the biological shape statistics and computer graphics communities. Recent results on shape space manifolds are applied to show sufficient conditions for convergence to unique solution. Algorithm source code is available and referenced here. Processing speed and rate of convergence are demonstrated using simulated data. Positional and angular accuracy are shown to be equivalent to approaches which require full calibration, to within a small fraction of input resolution. Typical processing times for sub-micron convergence are found to be fractions of a second, so the method is suitable for workflows where there may be time pressure such as in sports science and clinical analysis. Copyright © 2013 Elsevier Ltd. All rights reserved.

Chincup treatment modifies the mandibular shape in children with prognathism.

PubMed

Alarcón, José Antonio; Bastir, Markus; Rosas, Antonio; Molero, Julia

2011-07-01

Although chincups are the preferred treatment for growing children with mandibular prognathism, the mechanism by which chincups improve this condition remains unclear. The aim of this study was to use geometric morphometrics to evaluate changes in the shape of the mandible of prognathic children treated with a chincup. Geometric morphometrics were used to evaluate the short-term mandibular shape changes in 50 prognathic children treated with chincups compared with 40 untreated matched controls. Twenty-one 2-dimensional mandibular landmarks from cephalograms taken before and after 36 months of treatment or observation were analyzed by Procrustes superimposition and thin plate spline. Permutation tests of the treated patients showed highly significant differences in the mandibular shapes before and after treatment, and compared with the control group after the observation period. The thin plate spline grid deformations indicated more rectangular mandibular configuration, forward condyle orientation, condyle neck compression, gonial area compression, and symphysis narrowing. Early chincup treatment widely modifies the mandibular shape of prognathic children to improve Class III malocclusion. Copyright © 2011 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

Generalized Procrustes analysis of an ontogenetic series of modified crania: Evaluating the technique of modification in the Migration Period of Europe (4th-7th century AD).

PubMed

Mayall, Peter; Pilbrow, Varsha

2018-05-01

The arrival of the Huns into Europe in the fourth century AD increased the occurrence of intentional cranial modification among European nomads. It has been postulated that the Huns used a two-bandage cranial binding technique to differentiate themselves from surrounding nomadic groups, including those from Georgia. This study examines this hypothesis by comparing Migration Period (4th to 7th century AD) juvenile crania, which retain strong impressions of bindings, with adult modified crania from Hungary and Georgia. Twelve surface landmarks and 251 semi-landmarks were used to study ontogenetic trajectories in 9 juvenile and 16 adult modified skulls from 8 Hungarian sites and 21 adult skulls from two Georgian sites. Generalized Procrustes analysis, linear regression of Procrutes distance on dental age and log centroid size, and warping the principal components (PCs) in shape space helped to identify cranial shape changes. The PCs provide significant separation of the juvenile and adult groups from Georgia and Hungary. Variation in modified cranial shape was limited in Hungary compared to Georgia. There was stronger correlation between juvenile and adult modified cranial shape in Hungary than in Georgia. Warping along the first axis reveals the trajectory from marked flattening of the frontal and occipital regions in juveniles to diminished flattening in the same regions in adult crania, corresponding with one binding. Another depression extending from the post-bregmatic region to the temporal region, similarly strong in juveniles but diminishing in adults, marks the second binding. Hungarian crania were modified with two bindings with limited shape variation, whereas the Georgian crania had greater variation in shape being also modified with antero-posterior bindings. The findings from this study alongside contemporary historical sources help to understand the role of intentional cranial modification as a mark of social identity among nomads in the Migration Period of Europe. © 2018 Wiley Periodicals, Inc.

GeneOnEarth: fitting genetic PC plots on the globe.

PubMed

Torres-Sánchez, Sergio; Medina-Medina, Nuria; Gignoux, Chris; Abad-Grau, María M; González-Burchard, Esteban

2013-01-01

Principal component (PC) plots have become widely used to summarize genetic variation of individuals in a sample. The similarity between genetic distance in PC plots and geographical distance has shown to be quite impressive. However, in most situations, individual ancestral origins are not precisely known or they are heterogeneously distributed; hence, they are hardly linked to a geographical area. We have developed GeneOnEarth, a user-friendly web-based tool to help geneticists to understand whether a linear isolation-by-distance model may apply to a genetic data set; thus, genetic distances among a set of individuals resemble geographical distances among their origins. Its main goal is to allow users to first apply a by-view Procrustes method to visually learn whether this model holds. To do that, the user can choose the exact geographical area from an on line 2D or 3D world map by using, respectively, Google Maps or Google Earth, and rotate, flip, and resize the images. GeneOnEarth can also compute the optimal rotation angle using Procrustes analysis and assess statistical evidence of similarity when a different rotation angle has been chosen by the user. An online version of GeneOnEarth is available for testing and using purposes at http://bios.ugr.es/GeneOnEarth.

Size and shape in Melipona quadrifasciata anthidioides Lepeletier, 1836 (Hymenoptera; Meliponini).

PubMed

Nunes, L A; Passos, G B; Carvalho, C A L; Araújo, E D

2013-11-01

This study aimed to identify differences in wing shape among populations of Melipona quadrifasciata anthidioides obtained in 23 locations in the semi-arid region of Bahia state (Brazil). Analysis of the Procrustes distances among mean wing shapes indicated that population structure did not determine shape variation. Instead, populations were structured geographically according to wing size. The Partial Mantel Test between morphometric (shape and size) distance matrices and altitude, taking geographic distances into account, was used for a more detailed understanding of size and shape determinants. A partial Mantel test between morphometris (shape and size) variation and altitude, taking geographic distances into account, revealed that size (but not shape) is largely influenced by altitude (r = 0.54 p < 0.01). These results indicate greater evolutionary constraints for the shape variation, which must be directly associated with aerodynamic issues in this structure. The size, however, indicates that the bees tend to have larger wings in populations located at higher altitudes.

The skeletal maturation status estimated by statistical shape analysis: axial images of Japanese cervical vertebra.

PubMed

Shin, S M; Kim, Y-I; Choi, Y-S; Yamaguchi, T; Maki, K; Cho, B-H; Park, S-B

2015-01-01

To evaluate axial cervical vertebral (ACV) shape quantitatively and to build a prediction model for skeletal maturation level using statistical shape analysis for Japanese individuals. The sample included 24 female and 19 male patients with hand-wrist radiographs and CBCT images. Through generalized Procrustes analysis and principal components (PCs) analysis, the meaningful PCs were extracted from each ACV shape and analysed for the estimation regression model. Each ACV shape had meaningful PCs, except for the second axial cervical vertebra. Based on these models, the smallest prediction intervals (PIs) were from the combination of the shape space PCs, age and gender. Overall, the PIs of the male group were smaller than those of the female group. There was no significant correlation between centroid size as a size factor and skeletal maturation level. Our findings suggest that the ACV maturation method, which was applied by statistical shape analysis, could confirm information about skeletal maturation in Japanese individuals as an available quantifier of skeletal maturation and could be as useful a quantitative method as the skeletal maturation index.

The skeletal maturation status estimated by statistical shape analysis: axial images of Japanese cervical vertebra

PubMed Central

Shin, S M; Choi, Y-S; Yamaguchi, T; Maki, K; Cho, B-H; Park, S-B

2015-01-01

Objectives: To evaluate axial cervical vertebral (ACV) shape quantitatively and to build a prediction model for skeletal maturation level using statistical shape analysis for Japanese individuals. Methods: The sample included 24 female and 19 male patients with hand–wrist radiographs and CBCT images. Through generalized Procrustes analysis and principal components (PCs) analysis, the meaningful PCs were extracted from each ACV shape and analysed for the estimation regression model. Results: Each ACV shape had meaningful PCs, except for the second axial cervical vertebra. Based on these models, the smallest prediction intervals (PIs) were from the combination of the shape space PCs, age and gender. Overall, the PIs of the male group were smaller than those of the female group. There was no significant correlation between centroid size as a size factor and skeletal maturation level. Conclusions: Our findings suggest that the ACV maturation method, which was applied by statistical shape analysis, could confirm information about skeletal maturation in Japanese individuals as an available quantifier of skeletal maturation and could be as useful a quantitative method as the skeletal maturation index. PMID:25411713

Three-dimensional geometric morphometric analysis of talar morphology in extant gorilla taxa from highland and lowland habitats.

PubMed

Knigge, Ryan P; Tocheri, Matthew W; Orr, Caley M; Mcnulty, Kieran P

2015-01-01

Western gorillas (Gorilla gorilla) are known to climb significantly more often than eastern gorillas (Gorilla beringei), a behavioral distinction attributable to major differences in their respective habitats (i.e., highland vs. lowland). Genetic evidence suggests that the lineages leading to these taxa began diverging from one another between approximately 1 and 3 million years ago. Thus, gorillas offer a special opportunity to examine the degree to which morphology of recently diverged taxa may be "fine-tuned" to differing ecological requirements. Using three-dimensional (3D) geometric morphometrics, we compared talar morphology in a sample of 87 specimens including western (lowland), mountain (highland), and grauer gorillas (lowland and highland populations). Talar shape was captured with a series of landmarks and semilandmarks superimposed by generalized Procrustes analysis. A between-group principal components analysis of overall talar shape separates gorillas by ecological habitat and by taxon. An analysis of only the trochlea and lateral malleolar facet identifies subtle variations in trochlear shape between western lowland and lowland grauer gorillas, potentially indicative of convergent evolution of arboreal adaptations in the talus. Lastly, talar shape scales differently with centroid size for highland and lowland gorillas, suggesting that ankle morphology may track body-size mediated variation in arboreal behaviors differently depending on ecological setting. Several of the observed shape differences are linked biomechanically to the facilitation of climbing in lowland gorillas and to stability and load-bearing on terrestrial substrates in the highland taxa, providing an important comparative model for studying morphological variation in groups known only from fossils (e.g., early hominins). © 2014 Wiley Periodicals, Inc.

The Morphometrics of “Masculinity” in Human Faces

PubMed Central

Mitteroecker, Philipp; Windhager, Sonja; Müller, Gerd B.; Schaefer, Katrin

2015-01-01

In studies of social inference and human mate preference, a wide but inconsistent array of tools for computing facial masculinity has been devised. Several of these approaches implicitly assumed that the individual expression of sexually dimorphic shape features, which we refer to as maleness, resembles facial shape features perceived as masculine. We outline a morphometric strategy for estimating separately the face shape patterns that underlie perceived masculinity and maleness, and for computing individual scores for these shape patterns. We further show how faces with different degrees of masculinity or maleness can be constructed in a geometric morphometric framework. In an application of these methods to a set of human facial photographs, we found that shape features typically perceived as masculine are wide faces with a wide inter-orbital distance, a wide nose, thin lips, and a large and massive lower face. The individual expressions of this combination of shape features—the masculinity shape scores—were the best predictor of rated masculinity among the compared methods (r = 0.5). The shape features perceived as masculine only partly resembled the average face shape difference between males and females (sexual dimorphism). Discriminant functions and Procrustes distances to the female mean shape were poor predictors of perceived masculinity. PMID:25671667

The morphometrics of "masculinity" in human faces.

PubMed

Mitteroecker, Philipp; Windhager, Sonja; Müller, Gerd B; Schaefer, Katrin

2015-01-01

In studies of social inference and human mate preference, a wide but inconsistent array of tools for computing facial masculinity has been devised. Several of these approaches implicitly assumed that the individual expression of sexually dimorphic shape features, which we refer to as maleness, resembles facial shape features perceived as masculine. We outline a morphometric strategy for estimating separately the face shape patterns that underlie perceived masculinity and maleness, and for computing individual scores for these shape patterns. We further show how faces with different degrees of masculinity or maleness can be constructed in a geometric morphometric framework. In an application of these methods to a set of human facial photographs, we found that shape features typically perceived as masculine are wide faces with a wide inter-orbital distance, a wide nose, thin lips, and a large and massive lower face. The individual expressions of this combination of shape features--the masculinity shape scores--were the best predictor of rated masculinity among the compared methods (r = 0.5). The shape features perceived as masculine only partly resembled the average face shape difference between males and females (sexual dimorphism). Discriminant functions and Procrustes distances to the female mean shape were poor predictors of perceived masculinity.

Ecomorphological analysis of bovid mandibles from Laetoli Tanzania using 3D geometric morphometrics: Implications for hominin paleoenvironmental reconstruction.

PubMed

Forrest, Frances L; Plummer, Thomas W; Raaum, Ryan L

2018-01-01

The current study describes a new method of mandibular ecological morphology (ecomorphology). Three-dimensional geometric morphometrics (3D GM) was used to quantify mandibular shape variation between extant bovids with different feeding preferences. Landmark data were subjected to generalized Procrustes analysis (GPA), principal components analysis (PCA), and discriminant function analysis (DFA). The PCA resulted in a continuum from grazers to browsers along PC1 and DFA classified 88% or more of the modern specimens to the correct feeding category. The protocol was reduced to a subset of landmarks on the mandibular corpus in order to make it applicable to incomplete fossils. The reduced landmark set resulted in greater overlap between feeding categories but maintained the same continuum as the complete landmark model. The DFA resubstitution and jackknife analyses resulted in classification success rates of 85% and 80%, respectively. The reduced landmark model was applied to fossil mandibles from the Upper Laetolil Beds (∼4.3-3.5 Ma) and Upper Ndolanya Beds (∼2.7-2.6 Ma) at Laetoli, Tanzania in order to assess antelope diet, and indirectly evaluate paleo-vegetation structure. The majority of the fossils were classified by the DFA as browsers or mixed feeders preferring browse. Our results indicate a continuous presence of wooded habitats and are congruent with recent environmental studies at Laetoli indicating a mosaic woodland-bushland-grassland savanna ecosystem. Copyright © 2017 Elsevier Ltd. All rights reserved.

Joint Procrustes Analysis for Simultaneous Nonsingular Transformation of Component Score and Loading Matrices

ERIC Educational Resources Information Center

Adachi, Kohei

2009-01-01

In component analysis solutions, post-multiplying a component score matrix by a nonsingular matrix can be compensated by applying its inverse to the corresponding loading matrix. To eliminate this indeterminacy on nonsingular transformation, we propose Joint Procrustes Analysis (JPA) in which component score and loading matrices are simultaneously…

Genomic validation of the differential preservation of population history in modern human cranial anatomy.

PubMed

Reyes-Centeno, Hugo; Ghirotto, Silvia; Harvati, Katerina

2017-01-01

In modern humans, the significant correlation between neutral genetic loci and cranial anatomy suggests that the cranium preserves a population history signature. However, there is disagreement on whether certain parts of the cranium preserve this signature to a greater degree than other parts. It is also unclear how different quantitative measures of phenotype affect the association of genetic variation and anatomy. Here, we revisit these matters by testing the correlation of genetic distances and various phenotypic distances for ten modern human populations. Geometric morphometric shape data from the crania of adult individuals (n = 224) are used to calculate phenotypic P ST , Procrustes, and Mahalanobis distances. We calculate their correlation to neutral genetic distances, F ST , derived from single nucleotide polymorphisms (SNPs). We subset the cranial data into landmark configurations that include the neurocranium, the face, and the temporal bone in order to evaluate whether these cranial regions are differentially correlated to neutral genetic variation. Our results show that P ST , Mahalanobis, and Procrustes distances are correlated with F ST distances to varying degrees. They indicate that overall cranial shape is significantly correlated with neutral genetic variation. Of the component parts examined, P ST distances for both the temporal bone and the face have a stronger association with F ST distances than the neurocranium. When controlling for population divergence time, only the whole cranium and the temporal bone have a statistically significant association with F ST distances. Our results confirm that the cranium, as a whole, and the temporal bone can be used to reconstruct modern human population history. © 2016 Wiley Periodicals, Inc.

Size and shape measurement in contemporary cephalometrics.

PubMed

McIntyre, Grant T; Mossey, Peter A

2003-06-01

The traditional method of analysing cephalograms--conventional cephalometric analysis (CCA)--involves the calculation of linear distance measurements, angular measurements, area measurements, and ratios. Because shape information cannot be determined from these 'size-based' measurements, an increasing number of studies employ geometric morphometric tools in the cephalometric analysis of craniofacial morphology. Most of the discussions surrounding the appropriateness of CCA, Procrustes superimposition, Euclidean distance matrix analysis (EDMA), thin-plate spline analysis (TPS), finite element morphometry (FEM), elliptical Fourier functions (EFF), and medial axis analysis (MAA) have centred upon mathematical and statistical arguments. Surprisingly, little information is available to assist the orthodontist in the clinical relevance of each technique. This article evaluates the advantages and limitations of the above methods currently used to analyse the craniofacial morphology on cephalograms and investigates their clinical relevance and possible applications.

Optimal Embedding for Shape Indexing in Medical Image Databases

PubMed Central

Qian, Xiaoning; Tagare, Hemant D.; Fulbright, Robert K.; Long, Rodney; Antani, Sameer

2010-01-01

This paper addresses the problem of indexing shapes in medical image databases. Shapes of organs are often indicative of disease, making shape similarity queries important in medical image databases. Mathematically, shapes with landmarks belong to shape spaces which are curved manifolds with a well defined metric. The challenge in shape indexing is to index data in such curved spaces. One natural indexing scheme is to use metric trees, but metric trees are prone to inefficiency. This paper proposes a more efficient alternative. We show that it is possible to optimally embed finite sets of shapes in shape space into a Euclidean space. After embedding, classical coordinate-based trees can be used for efficient shape retrieval. The embedding proposed in the paper is optimal in the sense that it least distorts the partial Procrustes shape distance. The proposed indexing technique is used to retrieve images by vertebral shape from the NHANES II database of cervical and lumbar spine x-ray images maintained at the National Library of Medicine. Vertebral shape strongly correlates with the presence of osteophytes, and shape similarity retrieval is proposed as a tool for retrieval by osteophyte presence and severity. Experimental results included in the paper evaluate (1) the usefulness of shape-similarity as a proxy for osteophytes, (2) the computational and disk access efficiency of the new indexing scheme, (3) the relative performance of indexing with embedding to the performance of indexing without embedding, and (4) the computational cost of indexing using the proposed embedding versus the cost of an alternate embedding. The experimental results clearly show the relevance of shape indexing and the advantage of using the proposed embedding. PMID:20163981

Optimal embedding for shape indexing in medical image databases.

PubMed

Qian, Xiaoning; Tagare, Hemant D; Fulbright, Robert K; Long, Rodney; Antani, Sameer

2010-06-01

This paper addresses the problem of indexing shapes in medical image databases. Shapes of organs are often indicative of disease, making shape similarity queries important in medical image databases. Mathematically, shapes with landmarks belong to shape spaces which are curved manifolds with a well defined metric. The challenge in shape indexing is to index data in such curved spaces. One natural indexing scheme is to use metric trees, but metric trees are prone to inefficiency. This paper proposes a more efficient alternative. We show that it is possible to optimally embed finite sets of shapes in shape space into a Euclidean space. After embedding, classical coordinate-based trees can be used for efficient shape retrieval. The embedding proposed in the paper is optimal in the sense that it least distorts the partial Procrustes shape distance. The proposed indexing technique is used to retrieve images by vertebral shape from the NHANES II database of cervical and lumbar spine X-ray images maintained at the National Library of Medicine. Vertebral shape strongly correlates with the presence of osteophytes, and shape similarity retrieval is proposed as a tool for retrieval by osteophyte presence and severity. Experimental results included in the paper evaluate (1) the usefulness of shape similarity as a proxy for osteophytes, (2) the computational and disk access efficiency of the new indexing scheme, (3) the relative performance of indexing with embedding to the performance of indexing without embedding, and (4) the computational cost of indexing using the proposed embedding versus the cost of an alternate embedding. The experimental results clearly show the relevance of shape indexing and the advantage of using the proposed embedding. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Morphological evolution through integration: a quantitative study of cranial integration in Homo, Pan, Gorilla and Pongo.

PubMed

Singh, Nandini; Harvati, Katerina; Hublin, Jean-Jacques; Klingenberg, Christian P

2012-01-01

Morphological integration refers to coordinated variation among traits that are closely related in development and/or function. Patterns of integration can offer important insight into the structural relationship between phenotypic units, providing a framework to address questions about phenotypic evolvability and constraints. Integrative features of the primate cranium have recently become a popular subject of study. However, an important question that still remains under-investigated is: what is the pattern of cranial shape integration among closely related hominoids? To address this question, we conducted a Procrustes-based geometric morphometrics study to quantify and analyze shape covariation patterns between different cranial regions in Homo, Pan, Gorilla and Pongo. A total of fifty-six 3D landmarks were collected on 407 adult individuals. We then sub-divided the landmarks corresponding to cranial units as outlined in the 'functional matrix hypothesis.' Sub-dividing the cranium in this manner allowed us to explore patterns of covariation between the face, basicranium and cranial vault, using the two-block partial least squares approach. Our results suggest that integrated shape changes in the hominoid cranium are complex, but that the overall pattern of integration is similar among human and non-human apes. Thus, despite having very distinct morphologies the way in which the face, basicranium and cranial vault covary is shared among these taxa. These results imply that the pattern of cranial integration among hominoids is conserved. Copyright © 2011 Elsevier Ltd. All rights reserved.

Morphometric Variation of the Aedes albifasciatus (Diptera: Culicidae) Wings in Three Populations From Different Ecoregions of Argentina.

PubMed

Garzón, Maximiliano J; Schweigmann, Nicolás

2018-06-23

Shape variability among individuals is important to understand some ecological relationships, since it provides the nexus between the genotype and the environment. Geometric morphometrics based on generalized procrustes analysis was applied on 17 landmarks of the wings of Aedes albifasciatus (Macquart 1838) (Diptera: Culicidae) females collected from three ecoregions of Argentina (Delta and islands of the Paraná River, Pampa, and Patagonian steppe). This methodology was used to discriminate the shapes of individuals belonging to different regions. The population of the Patagonian steppe, which was the most geographically distant, showed the most dissimilar shape. Different local variations in wing shape could have been selected according to the environmental characteristics and maintained by geographic isolation. The individuals of the two ecoregions closest to each other (Delta and islands of the Paraná River and Pampa) showed differences in shape that can be explained by a lower gene flow due to the effect of geographic isolation (by the Paraná River) and the limited dispersive capacity of Ae. albifasciatus. The results allow concluding that both environmental diversity and geographic barriers could contribute to local variations in wing shape.

Identification of petroleum hydrocarbons using a reduced number of PAHs selected by Procrustes rotation.

PubMed

Fernández-Varela, R; Andrade, J M; Muniategui, S; Prada, D; Ramírez-Villalobos, F

2010-04-01

Identifying petroleum-related products released into the environment is a complex and difficult task. To achieve this, polycyclic aromatic hydrocarbons (PAHs) are of outstanding importance nowadays. Despite traditional quantitative fingerprinting uses straightforward univariate statistical analyses to differentiate among oils and to assess their sources, a multivariate strategy based on Procrustes rotation (PR) was applied in this paper. The aim of PR is to select a reduced subset of PAHs still capable of performing a satisfactory identification of petroleum-related hydrocarbons. PR selected two subsets of three (C(2)-naphthalene, C(2)-dibenzothiophene and C(2)-phenanthrene) and five (C(1)-decahidronaphthalene, naphthalene, C(2)-phenanthrene, C(3)-phenanthrene and C(2)-fluoranthene) PAHs for each of the two datasets studied here. The classification abilities of each subset of PAHs were tested using principal components analysis, hierarchical cluster analysis and Kohonen neural networks and it was demonstrated that they unraveled the same patterns as the overall set of PAHs. (c) 2009 Elsevier Ltd. All rights reserved.

Shadow detection and removal in RGB VHR images for land use unsupervised classification

NASA Astrophysics Data System (ADS)

Movia, A.; Beinat, A.; Crosilla, F.

2016-09-01

Nowadays, high resolution aerial images are widely available thanks to the diffusion of advanced technologies such as UAVs (Unmanned Aerial Vehicles) and new satellite missions. Although these developments offer new opportunities for accurate land use analysis and change detection, cloud and terrain shadows actually limit benefits and possibilities of modern sensors. Focusing on the problem of shadow detection and removal in VHR color images, the paper proposes new solutions and analyses how they can enhance common unsupervised classification procedures for identifying land use classes related to the CO2 absorption. To this aim, an improved fully automatic procedure has been developed for detecting image shadows using exclusively RGB color information, and avoiding user interaction. Results show a significant accuracy enhancement with respect to similar methods using RGB based indexes. Furthermore, novel solutions derived from Procrustes analysis have been applied to remove shadows and restore brightness in the images. In particular, two methods implementing the so called "anisotropic Procrustes" and the "not-centered oblique Procrustes" algorithms have been developed and compared with the linear correlation correction method based on the Cholesky decomposition. To assess how shadow removal can enhance unsupervised classifications, results obtained with classical methods such as k-means, maximum likelihood, and self-organizing maps, have been compared to each other and with a supervised clustering procedure.

Biomechanical implications of intraspecific shape variation in chimpanzee crania: moving towards an integration of geometric morphometrics and finite element analysis

PubMed Central

Smith, Amanda L.; Benazzi, Stefano; Ledogar, Justin A.; Tamvada, Kelli; Smith, Leslie C. Pryor; Weber, Gerhard W.; Spencer, Mark A.; Dechow, Paul C.; Grosse, Ian R.; Ross, Callum F.; Richmond, Brian G.; Wright, Barth W.; Wang, Qian; Byron, Craig; Slice, Dennis E.; Strait, David S.

2014-01-01

In a broad range of evolutionary studies, an understanding of intraspecific variation is needed in order to contextualize and interpret the meaning of variation between species. However, mechanical analyses of primate crania using experimental or modeling methods typically encounter logistical constraints that force them to rely on data gathered from only one or a few individuals. This results in a lack of knowledge concerning the mechanical significance of intraspecific shape variation that limits our ability to infer the significance of interspecific differences. This study uses geometric morphometric methods (GM) and finite element analysis (FEA) to examine the biomechanical implications of shape variation in chimpanzee crania, thereby providing a comparative context in which to interpret shape-related mechanical variation between hominin species. Six finite element models (FEMs) of chimpanzee crania were constructed from CT scans following shape-space Principal Component Analysis (PCA) of a matrix of 709 Procrustes coordinates (digitized onto 21 specimens) to identify the individuals at the extremes of the first three principal components. The FEMs were assigned the material properties of bone and were loaded and constrained to simulate maximal bites on the P3 and M2. Resulting strains indicate that intraspecific cranial variation in morphology is associated with quantitatively high levels of variation in strain magnitudes, but qualitatively little variation in the distribution of strain concentrations. Thus, interspecific comparisons should include considerations of the spatial patterning of strains rather than focus only their magnitude. PMID:25529239

A novel point cloud registration using 2D image features

NASA Astrophysics Data System (ADS)

Lin, Chien-Chou; Tai, Yen-Chou; Lee, Jhong-Jin; Chen, Yong-Sheng

2017-01-01

Since a 3D scanner only captures a scene of a 3D object at a time, a 3D registration for multi-scene is the key issue of 3D modeling. This paper presents a novel and an efficient 3D registration method based on 2D local feature matching. The proposed method transforms the point clouds into 2D bearing angle images and then uses the 2D feature based matching method, SURF, to find matching pixel pairs between two images. The corresponding points of 3D point clouds can be obtained by those pixel pairs. Since the corresponding pairs are sorted by their distance between matching features, only the top half of the corresponding pairs are used to find the optimal rotation matrix by the least squares approximation. In this paper, the optimal rotation matrix is derived by orthogonal Procrustes method (SVD-based approach). Therefore, the 3D model of an object can be reconstructed by aligning those point clouds with the optimal transformation matrix. Experimental results show that the accuracy of the proposed method is close to the ICP, but the computation cost is reduced significantly. The performance is six times faster than the generalized-ICP algorithm. Furthermore, while the ICP requires high alignment similarity of two scenes, the proposed method is robust to a larger difference of viewing angle.

The shape of the hominoid proximal femur: a geometric morphometric analysis

PubMed Central

Harmon, Elizabeth H

2007-01-01

As part of the hip joint, the proximal femur is an integral locomotor component. Although a link between locomotion and the morphology of some aspects of the proximal femur has been identified, inclusive shapes of this element have not been compared among behaviourally heterogeneous hominoids. Previous analyses have partitioned complex proximal femoral morphology into discrete features (e.g. head, neck, greater trochanter) to facilitate conventional linear measurements. In this study, three-dimensional geometric morphometrics are used to examine the shape of the proximal femur in hominoids to determine whether femoral shape co-varies with locomotor category. Fourteen landmarks are recorded on adult femora of Homo, Pan, Gorilla, Pongo and Hylobates. Generalized Procrustes analysis (GPA) is used to adjust for position, orientation and scale among landmark configurations. Principal components analysis is used to collapse and compare variation in residuals from GPA, and thin-plate spline analysis is used to visualize shape change among taxa. The results indicate that knucklewalking African apes are similar to one another in femoral shape, whereas the more suspensory Asian apes diverge from the African ape pattern. The shape of the human and orangutan proximal femur converge, a result that is best explained in terms of the distinct requirements for locomotion in each group. These findings suggest that the shape of the proximal femur is brought about primarily by locomotor behaviour. PMID:17310545

Quantifying the Degree of Movement Dissimilarity between Two Distinct Action Scenarios: An Exploratory Approach with Procrustes Analysis.

PubMed

Passos, Pedro; Campos, Tania; Diniz, Ana

2017-01-01

Game consoles allow subjects to perform movements which are visually similar to the movements performed in 'real' world scenarios. Beyond entertainment, virtual reality devices are being used in several domains: sports performance; motor rehabilitation; training of risk professions. This article presents the Procrustes method to measure the degree of dissimilarity between movements performed in 'real' and 'virtual' scenarios. For this purpose, the 501 darts game and a video darts game played on a console were used. The participants' arm throwing movements were video recorded and digitized. The matrices of x and y coordinates of the movements of the wrist, elbow, and shoulder in both performance scenarios were subjected to the Procrustes method. The wrist displays the most extreme dissimilarity values (higher than elbow and shoulder). Results also revealed smaller dissimilarity values for movements performed under the same conditions (e.g., real-real) and larger dissimilarity values between movements performed in different scenarios.

Quantifying the Degree of Movement Dissimilarity between Two Distinct Action Scenarios: An Exploratory Approach with Procrustes Analysis

PubMed Central

Passos, Pedro; Campos, Tania; Diniz, Ana

2017-01-01

Game consoles allow subjects to perform movements which are visually similar to the movements performed in ‘real’ world scenarios. Beyond entertainment, virtual reality devices are being used in several domains: sports performance; motor rehabilitation; training of risk professions. This article presents the Procrustes method to measure the degree of dissimilarity between movements performed in ‘real’ and ‘virtual’ scenarios. For this purpose, the 501 darts game and a video darts game played on a console were used. The participants’ arm throwing movements were video recorded and digitized. The matrices of x and y coordinates of the movements of the wrist, elbow, and shoulder in both performance scenarios were subjected to the Procrustes method. The wrist displays the most extreme dissimilarity values (higher than elbow and shoulder). Results also revealed smaller dissimilarity values for movements performed under the same conditions (e.g., real–real) and larger dissimilarity values between movements performed in different scenarios. PMID:28503159

Geometric morphometric analysis of allometric variation in the mandibular morphology of the hominids of Atapuerca, Sima de los Huesos site.

PubMed

Rosas, Antonio; Bastir, Markus

2004-06-01

Allometry is an important factor of morphological integration that contributes to the organization of the phenotype and its variation. Variation in the allometric shape of the mandible is particularly important in hominid evolution because the mandible carries important taxonomic traits. Some of these traits are known to covary with size, particularly the retromolar space, symphyseal curvature, and position of the mental foramen. The mandible is a well studied system in the context of the evolutionary development of complex morphological structures because it is composed of different developmental units that are integrated within a single bone. In the present study, we investigated the allometric variation of two important developmental units that are separated by the inferior nerve (a branch of CN V3). We tested the null hypothesis that there would be no difference in allometric variation between the two components. Procrustes-based geometric morphometrics of 20 two-dimensional (2D) landmarks were analyzed by multivariate regressions of shape on size in samples from 121 humans, 48 chimpanzees, and 50 gorillas (all recent specimens), eight fossil hominids from Atapuerca, Sima de los Huesos (AT-SH), and 17 Neandertals. The findings show that in all of the examined species, there was significantly greater allometric variation in the supra-nerve unit than in the infra-nerve unit. The formation of the retromolar space exhibited an allometric relationship with the supra-nerve unit in all of the species studied. The formation of the chin-like morphology is an "apodynamic" feature of the infra-nerve unit in the AT-SH hominids. The results of this study support the hypothesis that allometry contributes to the organization of variation in complex morphological structures. Copyright 2004 Wiley-Liss, Inc.

Morphometric evaluation of the knee in Chinese population reveals sexual dimorphism and age-related differences.

PubMed

Li, Ke; Cavaignac, Etienne; Xu, Wei; Cheng, Qiang; Telmon, Nobert; Huang, Wei

2018-02-20

Morphologic data of the knee is very important in the design of total knee prostheses. Generally, the designs of the total knee prostheses are based on the knee anatomy of Caucasian population. Moreover, in forensic medicine, a person's age and sex might be estimated by the shape of their knees. The aim of this study is to utilize three-dimensional morphometric analysis of the knee in Chinese population to reveal sexual dimorphism and age-related differences. Sexually dimorphic differences and age-related differences of the distal femur were studied by using geometric morphometric analysis of ten osteometric landmarks on three-dimensional reconstructions of 259 knees in Chinese population. General Procrustes analysis, PCA, and other discriminant analysis such as Mahalanobis and Goodall's F test were conducted for the knee to identify sexually dimorphism and age-related differences of the knee. The shape of distal femur between the male and female is significantly different. A difference between males and females in distal femur shape was identified by PCA; PC1 and PC2 accounted for 61.63% of the variance measured. The correct sex was assigned in 84.9% of cases by CVA, and the cross-validation revealed a 81.1% rate of correct sex estimation. The osteometric analysis also showed significant differences between the three age-related subgroups (< 40, 40-60, > 60 years, p < 0.005). This study showed both sex-related difference and age-related difference in the distal femur in Chinese population by 3D geometric morphometric analysis. Our bone measurements and geometric morphometric analysis suggest that population characteristics should be taken into account and may provide references for design of total knee prostheses in a Chinese population. Moreover, this reliable, accurate method could be used to perform diachronic and interethnic comparisons.

Sex determination by three-dimensional geometric morphometrics of craniofacial form.

PubMed

Chovalopoulou, Maria-Eleni; Valakos, Efstratios D; Manolis, Sotiris K

The purpose of the present study is to define which regions of the cranium, the upper-face, the orbits and the nasal are the most sexually dimorphic, by using three-dimensional geometric morphometric methods, and investigate the effectiveness of this method in determining sex from the shape of these regions. The study sample consisted of 176 crania of known sex (94 males, 82 females) belonging to individuals who lived in Greece during the 20(th) century. The three-dimensional co-ordinates of 31 ecto-cranial landmarks were digitized using a MicroScribe 3DX contact digitizer. Goodall's F-test was performed in order to compare statistical differences in shape between males and females. Generalized Procrustes Analysis (GPA) was used to obtain size and shape variables for statistical analysis. Shape, Size and Form analyses were carried out by logistic regression and discriminant function analysis. The results indicate that there are shape differences between the sexes in the upper-face and the orbits. The highest shape classification rate was obtained from the upper-face region. The centroid size of the caraniofacial and the orbital regions was smaller in females than males. Moreover, it was found that size is significant for sexual dimorphism in the upper-face region. As anticipated, the classification accuracy improves when both size and shape are combined. The findings presented here constitute a firm basis upon which further research can be conducted.

Mandibular effects of maxillary distraction osteogenesis in cleft lip and palate.

PubMed

Doucet, J-C; Herlin, C; Bigorre, M; Bäumler, C; Subsol, G; Captier, G

2014-06-01

Maxillary distraction osteogenesis (DO) is a reliable treatment for severe maxillary deficiency in cleft lip and palate (CLP). The objective was to analyze its long-term effects on the mandible. A retrospective study of 24 CLP treated with maxillary DO using the Polley and Figueroa technique was done; patients were followed for more than 4 years. Preoperative (T0), 6-12 months postoperative (T1), and ≥ 4 years postoperative (T2) cephalometric radiographs were evaluated. A classical cephalometric analysis was used to assess treatment stability, and a Procrustes superimposition method was used to assess local changes in the shape of the mandible. The mean age of patients at T0 was 15.4 ± 4.1 years. SNA increased at T1 and T2 (P < 0.001), with no significant relapse between T1 and T2, indicating stability at 1 year after treatment (T0 = 72.4 ± 5.3°; T1 = 81.3 ± 6.2°; T2 = 79.9 ± 6.1°). SNB, facial angle, gonial angle, and symphyseal angle remained stable. Long-term analysis of the mandible demonstrated a minimal counter-clockwise rotation of the body (mandibular plane = -0.2 ± 3.2°) and ramus (-0.6 ± 4.3°). Maxillary DO in CLP had no significant effect on the shape or rotation of the mandible. The maxillary advancement remained stable after 1 year. Copyright © 2014 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Sex determination by three-dimensional geometric morphometrics of the vault and midsagittal curve of the neurocranium in a modern Greek population sample.

PubMed

Chovalopoulou, Maria-Eleni; Valakos, Efstratios D; Manolis, Sotiris K

2016-06-01

The aim of this study is to assess sexual dimorphism of adult crania in the vault and midsagittal curve of the vault using three-dimensional geometric morphometric methods. The study sample consisted of 176 crania of known sex (94 males, 82 females) belonging to individuals who lived during the 20th century in Greece. The three-dimensional co-ordinates of 31 ecto-cranial landmarks and 30 semi-landmarks were digitized using a MicroScribe 3DX contact digitizer. Generalized Procrustes analysis (GPA) was used to obtain size and shape variables for statistical analysis. Shape, size and form analyses were carried out by logistic regression and three discriminant function analyses. Results indicate that there are shape differences between sexes. Females in the region of the parietal bones are narrower and the axis forming the frontal and occipital bones is more elongated; the frontal bone is more vertical. Sex-specific shape differences give better classification results in the vault (79%) compared with the midsagittal curve of the neurocranium (68.8%). Size alone yielded better results for cranial vault (82%), while for the midsagittal curve of the vault the result is poorer (68.1%). As anticipated, the classification accuracy improves when both size and shape are combined (89.2% for vault, and 79.4% for midsagittal curve of the vault). These latter findings imply that, in contrast to the midsagittal curve of the neurocranium, the shape of the cranial vault can be used as an indicator of sex in the modern Greek population. Copyright © 2016. Published by Elsevier GmbH.

Geometric morphometric footprint analysis of young women

PubMed Central

2013-01-01

Background Most published attempts to quantify footprint shape are based on a small number of measurements. We applied geometric morphometric methods to study shape variation of the complete footprint outline in a sample of 83 adult women. Methods The outline of the footprint, including the toes, was represented by a comprehensive set of 85 landmarks and semilandmarks. Shape coordinates were computed by Generalized Procrustes Analysis. Results The first four principal components represented the major axes of variation in foot morphology: low-arched versus high-arched feet, long and narrow versus short and wide feet, the relative length of the hallux, and the relative length of the forefoot. These shape features varied across the measured individuals without any distinct clusters or discrete types of footprint shape. A high body mass index (BMI) was associated with wide and flat feet, and a high frequency of wearing high-heeled shoes was associated with a larger forefoot area of the footprint and a relatively long hallux. Larger feet had an increased length-to-width ratio of the footprint, a lower-arched foot, and longer toes relative to the remaining foot. Footprint shape differed on average between left and right feet, and the variability of footprint asymmetry increased with BMI. Conclusions Foot shape is affected by lifestyle factors even in a sample of young women (median age 23 years). Geometric morphometrics proved to be a powerful tool for the detailed analysis of footprint shape that is applicable in various scientific disciplines, including forensics, orthopedics, and footwear design. PMID:23886074

Shape Analysis of the Peripapillary RPE Layer in Papilledema and Ischemic Optic Neuropathy

PubMed Central

Kupersmith, Mark J.; Rohlf, F. James

2011-01-01

Purpose. Geometric morphometrics (GM) was used to analyze the shape of the peripapillary retinal pigment epithelium–Bruch's membrane (RPE/BM) layer imaged on the SD-OCT 5-line raster in normal subjects and in patients with papilledema and ischemic optic neuropathy. Methods. Three groups of subjects were compared: 30 normals, 20 with anterior ischemic optic neuropathy (AION), and 25 with papilledema and intracranial hypertension. Twenty equidistant semilandmarks were digitized on OCT images of the RPE/BM layer spanning 2500 μm on each side of the neural canal opening (NCO). The data were analyzed using standard GM techniques, including a generalized least-squares Procrustes superimposition, principal component analysis, thin-plate spline (to visualize deformations), and permutation statistical analysis to evaluate differences in shape variables. Results. The RPE/BM layer in normals and AION have a characteristic V shape pointing away from the vitreous; the RPE/BM layer in papilledema has an inverted U shape, skewed nasally inward toward the vitreous. The differences were statistically significant. There was no significant difference in shapes between normals and AION. Pre- and posttreatment OCTs, in select cases of papilledema, showed that the inverted U-shaped RPE/BM moved posteriorly into a normal V shape as the papilledema resolved with weight loss or shunting. Conclusions. The shape difference in papilledema, absent in AION, cannot be explained by disc edema alone. The difference is a consequence of both the translaminar pressure gradient and the material properties of the peripapillary sclera. GM offers a novel way of statistically assessing shape differences of the peripapillary optic nerve head. PMID:21896851

Recovering Wood and McCarthy's ERP-prototypes by means of ERP-specific procrustes-rotation.

PubMed

Beauducel, André

2018-02-01

The misallocation of treatment-variance on the wrong component has been discussed in the context of temporal principal component analysis of event-related potentials. There is, until now, no rotation-method that can perfectly recover Wood and McCarthy's prototypes without making use of additional information on treatment-effects. In order to close this gap, two new methods: for component rotation were proposed. After Varimax-prerotation, the first method identifies very small slopes of successive loadings. The corresponding loadings are set to zero in a target-matrix for event-related orthogonal partial Procrustes- (EPP-) rotation. The second method generates Gaussian normal distributions around the peaks of the Varimax-loadings and performs orthogonal Procrustes-rotation towards these Gaussian distributions. Oblique versions of this Gaussian event-related Procrustes- (GEP) rotation and of EPP-rotation are based on Promax-rotation. A simulation study revealed that the new orthogonal rotations recover Wood and McCarthy's prototypes and eliminate misallocation of treatment-variance. In an additional simulation study with a more pronounced overlap of the prototypes GEP Promax-rotation reduced the variance misallocation slightly more than EPP Promax-rotation. Comparison with Existing Method(s): Varimax- and conventional Promax-rotations resulted in substantial misallocations of variance in simulation studies when components had temporal overlap. A substantially reduced misallocation of variance occurred with the EPP-, EPP Promax-, GEP-, and GEP Promax-rotations. Misallocation of variance can be minimized by means of the new rotation methods: Making use of information on the temporal order of the loadings may allow for improvements of the rotation of temporal PCA components. Copyright © 2017 Elsevier B.V. All rights reserved.

Information Geometry for Landmark Shape Analysis: Unifying Shape Representation and Deformation

PubMed Central

Peter, Adrian M.; Rangarajan, Anand

2010-01-01

Shape matching plays a prominent role in the comparison of similar structures. We present a unifying framework for shape matching that uses mixture models to couple both the shape representation and deformation. The theoretical foundation is drawn from information geometry wherein information matrices are used to establish intrinsic distances between parametric densities. When a parameterized probability density function is used to represent a landmark-based shape, the modes of deformation are automatically established through the information matrix of the density. We first show that given two shapes parameterized by Gaussian mixture models (GMMs), the well-known Fisher information matrix of the mixture model is also a Riemannian metric (actually, the Fisher-Rao Riemannian metric) and can therefore be used for computing shape geodesics. The Fisher-Rao metric has the advantage of being an intrinsic metric and invariant to reparameterization. The geodesic—computed using this metric—establishes an intrinsic deformation between the shapes, thus unifying both shape representation and deformation. A fundamental drawback of the Fisher-Rao metric is that it is not available in closed form for the GMM. Consequently, shape comparisons are computationally very expensive. To address this, we develop a new Riemannian metric based on generalized ϕ-entropy measures. In sharp contrast to the Fisher-Rao metric, the new metric is available in closed form. Geodesic computations using the new metric are considerably more efficient. We validate the performance and discriminative capabilities of these new information geometry-based metrics by pairwise matching of corpus callosum shapes. We also study the deformations of fish shapes that have various topological properties. A comprehensive comparative analysis is also provided using other landmark-based distances, including the Hausdorff distance, the Procrustes metric, landmark-based diffeomorphisms, and the bending energies of the thin-plate (TPS) and Wendland splines. PMID:19110497

Comparing primate crania: The importance of fossils.

PubMed

Fleagle, John G; Gilbert, Christopher C; Baden, Andrea L

2016-10-01

Extant primate crania represent a small subset of primate crania that have existed. The main objective here is to examine how the inclusion of fossil crania changes our understanding of primate cranial diversity relative to analyses of extant primates. We hypothesize that fossil taxa will change the major axes of cranial shape, occupy new areas of morphospace, change the relative diversity of major primate clades, and fill in notable gaps separating major primate taxa/clades. Eighteen 3D landmarks were collected on 157 extant and fossil crania representing 90 genera. Data were subjected to a Generalized Procrustes Analysis then principal components analysis. Relative diversity between clades was assessed using an F-statistic. Fossil taxa do not significantly alter major axes of cranial shape, but they do occupy unique areas of morphospace, change the relative diversity between clades, and fill in notable gaps in primate cranial evolution. Strepsirrhines remain significantly less diverse than anthropoids. Fossil hominins fill the gap in cranial morphospace between extant great apes and modern humans. The morphospace outlined by living primates largely includes that occupied by fossil taxa, suggesting that the cranial diversity of living primates generally encompasses the total diversity that has evolved in this Order. The evolution of the anthropoid cranium was a significant event allowing anthropoids to achieve significantly greater cranial diversity compared to strepsirrhines. Fossil taxa fill in notable gaps within and between clades, highlighting their transitional nature and eliminating the appearance of large morphological distances between extant taxa, particularly in the case of extant hominids. © 2016 Wiley Periodicals, Inc.

Pelvic form and locomotor adaptation in strepsirrhine primates.

PubMed

Lewton, Kristi L

2015-01-01

The pelvic girdle is a complex structure with a critical role in locomotion, but efforts to model the mechanical effects of locomotion on its shape remain difficult. Traditional approaches to understanding form and function include univariate adaptive hypothesis-testing derived from mechanical models. Geometric morphometric (GM) methods can yield novel insight into overall three-dimensional shape similarities and differences across groups, although the utility of GM in assessing functional differences has been questioned. This study evaluates the contributions of both univariate and GM approaches to unraveling the trait-function associations between pelvic form and locomotion. Three-dimensional landmarks were collected on a phylogenetically-broad sample of 180 pelves from nine primate taxa. Euclidean interlandmark distances were calculated to facilitate testing of biomechanical hypotheses, and a principal components (PC) analysis was performed on Procrustes coordinates to examine overall shape differences. Both linear dimensions and PC scores were subjected to phylogenetic ANOVA. Many of the null hypotheses relating linear dimensions to locomotor loading were not rejected. Although both analytical approaches suggest that ilium width and robusticity differ among locomotor groups, the GM analysis also suggests that ischiopubic shape differentiates groups. Although GM provides additional quantitative results beyond the univariate analyses, this study highlights the need for new GM methods to more specifically address functional shape differences among species. Until these methods are developed, it would be prudent to accompany tests of directional biomechanical hypotheses with current GM methods for a more nuanced understanding of shape and function. © 2014 Wiley Periodicals, Inc.

Thin-plate spline analysis of mandibular morphological changes induced by early class III treatment: a long-term evaluation.

PubMed

Franchi, Lorenzo; Pavoni, Chiara; Cerroni, Silvia; Cozza, Paola

2014-08-01

To evaluate the long-term mandibular morphological changes induced by early treatment of class III malocclusion with rapid maxillary expansion (RME) and facial mask (FM). Twenty-five subjects [10 boys, 15 girls; mean age at T1 (start of treatment) 9.3±1.6 years] with class III disharmony were treated with RME and FM therapy followed by fixed appliances. The patients were re-evaluated at the end of growth (T2), about 8.5 years after the end of the treatment (mean age, 18.6±2.0 years). Sixteen subjects with untreated class III malocclusion comprised the control group. Mandibular shape changes were analysed on the lateral cephalograms of the subjects of both groups by means of thin-plate spline (TPS) analysis. Procrustes average mandibular configurations were subjected to TPS analysis by means of both cross-sectional between-group comparisons at T1 and at T2 and longitudinal within-group comparisons. Statistical analysis of shape differences was performed using a generalized Goodall F test. In the long term, the treated group exhibited a significant upward and forward direction of condylar growth. On the contrary, untreated class III subjects showed an upward and backward direction of condylar growth associated with a downward and forward deformation of the mandibular symphysis. Limitations are related to the small sample size of both treated and control groups and to the retrospective nature of the study. Early treatment of class III malocclusion with RME and FM is able to produce significant and favourable long-term mandibular shape changes characterized by an anterior morphogenetic rotation. © The Author 2013. Published by Oxford University Press on behalf of the European Orthodontic Society. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Shape change in the atlas with congenital midline non-union of its posterior arch: a morphometric geometric study.

PubMed

Ríos, Luis; Palancar, Carlos; Pastor, Francisco; Llidó, Susana; Sanchís-Gimeno, Juan Alberto; Bastir, Markus

2017-10-01

The congenital midline non-union of the posterior arch of the atlas is a developmental variant present at a frequency ranging from 0.7% to 3.9%. Most of the reported cases correspond to incidental findings during routine medical examination. In cases of posterior non-union, hypertrophy of the anterior arch and cortical bone thickening of the posterior arches have been observed and interpreted as adaptive responses of the atlas to increased mechanical stress. We sought to determine if the congenital non-union of the posterior arch results in a change in the shape of the atlas. This study is an analysis of the first cervical vertebrae from osteological collections through morphometric geometric techniques. A total of 21 vertebrae were scanned with a high-resolution three-dimensional scanner (Artec Space Spider, Artec Group, Luxembourg). To capture vertebral shape, 19 landmarks and 100 semilandmarks were placed on the vertebrae. Procrustes superimposition was applied to obtain size and shape data (MorphoJ 1.02; Klingenberg, 2011), which were analyzed through principal component analysis (PCA) and mean shape comparisons. The PCA resulted in two components explaining 22.32% and 18.8% of the total shape variance. The graphic plotting of both components indicates a clear shape difference between the control atlas and the atlas with posterior non-union. This observation was supported by statistically significant differences in mean shape comparisons between both types of vertebra (p<.0001). Changes in shape were observed in the superior and inferior articular facets, the transverse processes, and the neural canal between the control and non-union vertebrae. Non-union of the posterior arch of the atlas is associated with significant changes in the shape of the vertebra. Copyright © 2017 Elsevier Inc. All rights reserved.

Age-related changes in the craniofacial region in a modern Greek population sample of known age and sex.

PubMed

Chovalopoulou, Maria-Eleni; Bertsatos, Andreas; Papageorgopoulou, Christina

2017-07-01

The aim of this paper is to investigate ageing changes in craniofacial region in both sexes and evaluate whether these shape changes are substantial to achieve age discrimination of samples used in anthropological analyses. The study sample consisted of 157 crania of known sex and age (81 males and 76 females) belonging to individuals who lived in Greece during the twentieth century. The sample was divided in three age groups: young adults (YA, 18-39 years old), middle adults (MA, 40-59 years old) and old adults (OA, >60 years old). The three-dimensional coordinates of 31 ecto-cranial landmarks were digitized using a Microscribe 3DX contact digitizer, and landmark configurations were analyzed using the generalized least-squares Procrustes method. The results indicate that both males and females show significant difference among the age groups; however, shape differences can not be used for age group discrimination due to a large range on the accuracy of age group classification. The morphometric changes related to age were different between sexes.

Morphometric Modifications in Canthon quinquemaculatus Castelnau 1840 (Coleoptera: Scarabaeinae): Sublethal Effects of Transgenic Maize?

PubMed Central

Alves, Victor Michelon; Hernández, Malva Isabel Medina

2017-01-01

The effects of transgenic compounds on non-target organisms remain poorly understood, especially in native insect species. Morphological changes (e.g., changes in body size and shape) may reflect possible responses to environmental stressors, like transgenic toxins. The dung beetle Canthon quinquemaculatus (Coleoptera: Scarabaeinae) is a non-target species found in transgenic crops. We evaluated whether C. quinquemaculatus individuals inhabiting corn fields cultivated with different seed types (conventional, creole and transgenic) present modifications in body shape compared to individuals inhabiting adjacent native forest fragments. We collected C. quinquemaculatus specimens across an agricultural landscape in southern Brazil, during the summer of 2015. Six populations were sampled: three maize crop populations each under a different seed type, and three populations of adjacent forests. After sampling, specimens were subjected to morphometric analyses to discover differences in body shape. We chose fifteen landmarks to describe body shape, and morphometric data were tested with Procrustes ANOVA and Discriminant Analysis. We found that body shape did not differ between individuals collected in conventional and creole crops with their respective adjacent forests (p > 0.05); however, transgenic crop populations differed significantly from those collected in adjacent forests (p < 0.05). Insects in transgenic maize are more oval and have a retraction in the abdominal region, compared with the respective adjacent forest, this result shows the possible effect of transgenic crops on non-target species. This may have implications for the ecosystem service of organic matter removal, carried out by these organisms. PMID:29065452

Discrimination of snipefish Macroramphosus species and boarfish Capros aper morphotypes through multivariate analysis of body shape

NASA Astrophysics Data System (ADS)

Lopes, Marta; Murta, Alberto G.; Cabral, Henrique N.

2006-03-01

The existence of two species of the genus Macroramphosus Lacepède 1803, has been discussed based on morphometric characters, diet composition and depth distribution. Another species, the boarfish Capros aper (Linnaeus 1758), caugth along the Portuguese coast, shows two different morphotypes, one type with smaller eyes and a deeper body than the other, occurring with intermediate forms. In both snipefish and boarfish no sexual dimorphism was found with respect to shape and length relationships. However, females in both genera were on average bigger than males. A multidimensional scaling analysis was performed using Procrustes distances, in order to check if shape geometry was effective in distinguishing the species of snipefish as well as the morphotypes of boarfish. A multivariate discriminant analysis using morphometric characters of snipefish and boarfish was carried out to validate the visual criteria for a distinction of species and morphotypes, respectively. Morphometric characters revealed a great discriminatory power to distinguish morphotypes. Both snipefish and boarfish are very abundant in Portuguese waters, showing two well-defined morphologies and intermediate forms. This study suggests that there may be two different species in each genus and that further studies on these fish should be carried out to investigate if there is reproductive isolation between the morphotypes of boarfish and to validate the species of snipefish.

Morphometric analysis of Passiflora leaves: the relationship between landmarks of the vasculature and elliptical Fourier descriptors of the blade

PubMed Central

2017-01-01

Abstract Background: Leaf shape among Passiflora species is spectacularly diverse. Underlying this diversity in leaf shape are profound changes in the patterning of the primary vasculature and laminar outgrowth. Each of these aspects of leaf morphology—vasculature and blade—provides different insights into leaf patterning. Results: Here, we morphometrically analyze >3300 leaves from 40 different Passiflora species collected sequentially across the vine. Each leaf is measured in two different ways: using 1) 15 homologous Procrustes-adjusted landmarks of the vasculature, sinuses, and lobes; and 2) Elliptical Fourier Descriptors (EFDs), which quantify the outline of the leaf. The ability of landmarks, EFDs, and both datasets together are compared to determine their relative ability to predict species and node position within the vine. Pairwise correlation of x and y landmark coordinates and EFD harmonic coefficients reveals close associations between traits and insights into the relationship between vasculature and blade patterning. Conclusions: Landmarks, more reflective of the vasculature, and EFDs, more reflective of the blade contour, describe both similar and distinct features of leaf morphology. Landmarks and EFDs vary in ability to predict species identity and node position in the vine and exhibit a correlational structure (both within landmark or EFD traits and between the two data types) revealing constraints between vascular and blade patterning underlying natural variation in leaf morphology among Passiflora species. PMID:28369351

Erratum to: Morphometric analysis of Passiflora leaves: the relationship between landmarks of the vasculature and elliptical Fourier descriptors of the blade.

PubMed

Chitwood, Daniel H; Otoni, Wagner C

2017-10-01

Leaf shape among Passiflora species is spectacularly diverse. Underlying this diversity in leaf shape are profound changes in the patterning of the primary vasculature and laminar outgrowth. Each of these aspects of leaf morphology-vasculature and blade-provides different insights into leaf patterning. Here, we morphometrically analyze >3300 leaves from 40 different Passiflora species collected sequentially across the vine. Each leaf is measured in two different ways: using 1) 15 homologous Procrustes-adjusted landmarks of the vasculature, sinuses, and lobes; and 2) Elliptical Fourier Descriptors (EFDs), which quantify the outline of the leaf. The ability of landmarks, EFDs, and both datasets together are compared to determine their relative ability to predict species and node position within the vine. Pairwise correlation of x and y landmark coordinates and EFD harmonic coefficients reveals close associations between traits and insights into the relationship between vasculature and blade patterning. Landmarks, more reflective of the vasculature, and EFDs, more reflective of the blade contour, describe both similar and distinct features of leaf morphology. Landmarks and EFDs vary in ability to predict species identity and node position in the vine and exhibit a correlational structure (both within landmark or EFD traits and between the two data types) revealing constraints between vascular and blade patterning underlying natural variation in leaf morphology among Passiflora species. © The Authors 2017. Published by Oxford University Press.

Morphometric analysis of Passiflora leaves: the relationship between landmarks of the vasculature and elliptical Fourier descriptors of the blade.

PubMed

Chitwood, Daniel H; Otoni, Wagner C

2017-01-01

Leaf shape among Passiflora species is spectacularly diverse. Underlying this diversity in leaf shape are profound changes in the patterning of the primary vasculature and laminar outgrowth. Each of these aspects of leaf morphology-vasculature and blade-provides different insights into leaf patterning. Here, we morphometrically analyze >3300 leaves from 40 different Passiflora species collected sequentially across the vine. Each leaf is measured in two different ways: using 1) 15 homologous Procrustes-adjusted landmarks of the vasculature, sinuses, and lobes; and 2) Elliptical Fourier Descriptors (EFDs), which quantify the outline of the leaf. The ability of landmarks, EFDs, and both datasets together are compared to determine their relative ability to predict species and node position within the vine. Pairwise correlation of x and y landmark coordinates and EFD harmonic coefficients reveals close associations between traits and insights into the relationship between vasculature and blade patterning. Landmarks, more reflective of the vasculature, and EFDs, more reflective of the blade contour, describe both similar and distinct features of leaf morphology. Landmarks and EFDs vary in ability to predict species identity and node position in the vine and exhibit a correlational structure (both within landmark or EFD traits and between the two data types) revealing constraints between vascular and blade patterning underlying natural variation in leaf morphology among Passiflora species. © The Author 2017. Published by Oxford University Press.

Midline corpus callosum is a neuroanatomical focus of fetal alcohol damage.

PubMed

Bookstein, Fred L; Sampson, Paul D; Connor, Paul D; Streissguth, Ann P

2002-06-15

Prenatal exposure to high levels of alcohol often induces birth defects that combine morphological stigmata with neurological or neuropsychological deficits. But it has proved problematic to diagnose these syndromes in adolescents and adults, in whom the morphological signs are absent or attenuated, the behavioral deficits nonspecific, and the exposure history often difficult to reconstruct. Localizing the associated brain abnormalities might circumvent most of these difficulties. To this end, three-dimensional (3D) locations were recorded for 67 homologous points on or near the corpus callosum in magnetic resonance (MR) brain images from 60 adolescents and adults who were normal, 60 diagnosed with fetal alcohol syndrome, and 60 diagnosed with fetal alcohol effects. We combined the standard statistical approach to this type of geometric data, Procrustes analysis, with a multivariate strategy focusing on differences in variability. In this data set, the shape of the corpus callosum and its vicinity proves systematically much more variable in the alcohol-affected brains than in those of the normal subjects. From this excess variability follows a promising classification rule, having both high sensitivity (100 out of 117) and high specificity (49 out of 60) in this sample. The discrimination uses four landmark points and two summary scores of callosal outline shape. The information from the corpus callosum and vicinity, as viewed in MR brain images of full-grown subjects, may serve as a permanent record of the prenatal effects of alcohol, even in patients who are first suspected of these syndromes relatively late in life or who lack the facial signs of prenatal alcohol damage. The statistical pattern underlying the callosal diagnosis also leads to speculations on mechanisms of the prenatal damage. Copyright 2002 Wiley-Liss, Inc.

Virtual reconstruction of very large skull defects featuring partly and completely missing midsagittal planes.

PubMed

Senck, Sascha; Coquerelle, Michael; Weber, Gerhard W; Benazzi, Stefano

2013-05-01

Despite the development of computer-based methods, cranial reconstruction of very large skull defects remains a challenge particularly if the damage affects the midsagittal region hampering the usage of mirror imaging techniques. This pilot study aims to deliver a new method that goes beyond mirror imaging, giving the possibility to reconstruct crania characterized by large missing areas, which might be useful in the fields of paleoanthropology, bioarcheology, and forensics. We test the accuracy of digital reconstructions in cases where two-thirds or more of a human cranium were missing. A three-dimensional (3D) virtual model of a human cranium was virtually damaged twice to compare two destruction-reconstruction scenarios. In the first case, a small fraction of the midsagittal region was still preserved, allowing the application of mirror imaging techniques. In the second case, the damage affected the complete midsagittal region, which demands a new approach to estimate the position of the midsagittal plane. Reconstructions were carried out using CT scans from a sample of modern humans (12 males and 13 females), to which 3D digital modeling techniques and geometric morphometric methods were applied. As expected, the second simulation showed a larger variability than the first one, which underlines the fact that the individual midsagittal plane is of course preferable in order to minimize the reconstruction error. However, in both simulations the Procrustes mean shape was an effective reference for the reconstruction of the entire cranium, producing models that showed a remarkably low error of about 3 mm, given the extent of missing data. Copyright © 2013 Wiley Periodicals, Inc.

Comparison of Unsupervised Vegetation Classification Methods from Vhr Images after Shadows Removal by Innovative Algorithms

NASA Astrophysics Data System (ADS)

Movia, A.; Beinat, A.; Crosilla, F.

2015-04-01

The recognition of vegetation by the analysis of very high resolution (VHR) aerial images provides meaningful information about environmental features; nevertheless, VHR images frequently contain shadows that generate significant problems for the classification of the image components and for the extraction of the needed information. The aim of this research is to classify, from VHR aerial images, vegetation involved in the balance process of the environmental biochemical cycle, and to discriminate it with respect to urban and agricultural features. Three classification algorithms have been experimented in order to better recognize vegetation, and compared to NDVI index; unfortunately all these methods are conditioned by the presence of shadows on the images. Literature presents several algorithms to detect and remove shadows in the scene: most of them are based on the RGB to HSI transformations. In this work some of them have been implemented and compared with one based on RGB bands. Successively, in order to remove shadows and restore brightness on the images, some innovative algorithms, based on Procrustes theory, have been implemented and applied. Among these, we evaluate the capability of the so called "not-centered oblique Procrustes" and "anisotropic Procrustes" methods to efficiently restore brightness with respect to a linear correlation correction based on the Cholesky decomposition. Some experimental results obtained by different classification methods after shadows removal carried out with the innovative algorithms are presented and discussed.

Functional aspects of metatarsal head shape in humans, apes, and Old World monkeys.

PubMed

Fernández, Peter J; Almécija, Sergio; Patel, Biren A; Orr, Caley M; Tocheri, Matthew W; Jungers, William L

2015-09-01

Modern human metatarsal heads are typically described as "dorsally domed," mediolaterally wide, and dorsally flat. Despite the apparent functional importance of these features in forefoot stability during bipedalism, the distinctiveness of this morphology has not been quantitatively evaluated within a broad comparative framework. In order to use these features to reconstruct fossil hominin locomotor behaviors with any confidence, their connection to human bipedalism should be validated through a comparative analysis of other primates with different locomotor behaviors and foot postures, including species with biomechanical demands potentially similar to those of bipedalism (e.g., terrestrial digitigrady). This study explores shape variation in the distal metatarsus among humans and other extant catarrhines using three-dimensional geometric morphometrics (3 DGM). Shape differences among species in metatarsal head morphology are well captured by the first two principal components of Procrustes shape coordinates, and these two components summarize most of the variance related to "dorsal doming" and "dorsal expansion." Multivariate statistical tests reveal significant differences among clades in overall shape, and humans are reliably distinguishable from other species by aspects of shape related to a greater degree of dorsal doming. Within quadrupeds, terrestrial species also trend toward more domed metatarsal heads, but not to the extent seen in humans. Certain aspects of distal metatarsus shape are likely related to habitual dorsiflexion of the metatarsophalangeal joints, but the total morphological pattern seen in humans is distinct. These comparative results indicate that this geometric morphometric approach is useful to characterize the complexity of metatarsal head morphology and will help clarify its relationship with function in fossil primates, including early hominins. Published by Elsevier Ltd.

Diversity among African Pygmies

PubMed Central

Ramírez Rozzi, Fernando V.; Sardi, Marina L.

2010-01-01

Although dissimilarities in cranial and post-cranial morphology among African pygmies groups have been recognized, comparative studies on skull morphology usually pull all pygmies together assuming that morphological characters are similar among them and different with respect to other populations. The main aim of this study is to compare cranial morphology between African pygmies and non-pygmies populations from Equatorial Africa derived from both the Eastern and the Western regions in order to test if the greatest morphological difference is obtained in the comparison between pygmies and non-pygmies. Thirty three-dimensional (3D) landmarks registered with Microscribe in four cranial samples (Western and Eastern pygmies and non-pygmies) were obtained. Multivariate analysis (generalized Procrustes analysis, Mahalanobis distances, multivariate regression) and complementary dimensions of size were evaluated with ANOVA and post hoc LSD. Results suggest that important cranial shape differentiation does occur between pygmies and non-pygmies but also between Eastern and Western populations and that size changes and allometries do not affect similarly Eastern and Western pygmies. Therefore, our findings raise serious doubt about the fact to consider African pygmies as a homogenous group in studies on skull morphology. Differences in cranial morphology among pygmies would suggest differentiation after divergence. Although not directly related to skull differentiation, the diversity among pygmies would probably suggest that the process responsible for reduced stature occurred after the split of the ancestors of modern Eastern and Western pygmies. PMID:21049030

Diversity among African pygmies.

PubMed

Ramírez Rozzi, Fernando V; Sardi, Marina L

2010-10-26

Although dissimilarities in cranial and post-cranial morphology among African pygmies groups have been recognized, comparative studies on skull morphology usually pull all pygmies together assuming that morphological characters are similar among them and different with respect to other populations. The main aim of this study is to compare cranial morphology between African pygmies and non-pygmies populations from Equatorial Africa derived from both the Eastern and the Western regions in order to test if the greatest morphological difference is obtained in the comparison between pygmies and non-pygmies. Thirty three-dimensional (3D) landmarks registered with Microscribe in four cranial samples (Western and Eastern pygmies and non-pygmies) were obtained. Multivariate analysis (generalized Procrustes analysis, Mahalanobis distances, multivariate regression) and complementary dimensions of size were evaluated with ANOVA and post hoc LSD. Results suggest that important cranial shape differentiation does occur between pygmies and non-pygmies but also between Eastern and Western populations and that size changes and allometries do not affect similarly Eastern and Western pygmies. Therefore, our findings raise serious doubt about the fact to consider African pygmies as a homogenous group in studies on skull morphology. Differences in cranial morphology among pygmies would suggest differentiation after divergence. Although not directly related to skull differentiation, the diversity among pygmies would probably suggest that the process responsible for reduced stature occurred after the split of the ancestors of modern Eastern and Western pygmies.

Multiple mechanisms in the perception of face gender: Effect of sex-irrelevant features.

PubMed

Komori, Masashi; Kawamura, Satoru; Ishihara, Shigekazu

2011-06-01

Effects of sex-relevant and sex-irrelevant facial features on the evaluation of facial gender were investigated. Participants rated masculinity of 48 male facial photographs and femininity of 48 female facial photographs. Eighty feature points were measured on each of the facial photographs. Using a generalized Procrustes analysis, facial shapes were converted into multidimensional vectors, with the average face as a starting point. Each vector was decomposed into a sex-relevant subvector and a sex-irrelevant subvector which were, respectively, parallel and orthogonal to the main male-female axis. Principal components analysis (PCA) was performed on the sex-irrelevant subvectors. One principal component was negatively correlated with both perceived masculinity and femininity, and another was correlated only with femininity, though both components were orthogonal to the male-female dimension (and thus by definition sex-irrelevant). These results indicate that evaluation of facial gender depends on sex-irrelevant as well as sex-relevant facial features.

Effect of sex and carcass weight on sensory quality of goat meat of Cabrito Transmontano.

PubMed

Rodrigues, S; Teixeira, A

2009-02-01

The main purpose of this work was the characterization of Cabrito Transmontana goat kid carcass and meat, which is a Protected Origin Designation product. The effects of sex and carcass weight were studied. Sensory attributes of toughness, juiciness, flavor intensity, flavor quality, odor intensity, fiber presence (stringy), sweet intensity, and overall acceptability were evaluated in 60 males and females allocated to 3 carcass weight groups: 4, 6, and 8 kg. Sensory quality of meat was evaluated by a trained taste panel of 11 experts in 5 sessions. Generalized Procrustes analysis was performed, and 93% of total variability was explained by the 2 first factors (axes). Correlation between sensory traits and factors 1 and 2 allowed the factors to be renamed as toughness/aroma and juiciness/acceptability, respectively. Procrustes analysis indicated that a sex effect was detected by experts. Meat from males presented greater juiciness, flavor quality, and general acceptability than did meat from females. Cabrito Transmontano Protected Origin Designation includes animals from 4 to 9 kg of carcass weight. However, differences among them can be important, because the taste panel found differences between animals from distinct carcass weight ranges. Lighter weight carcasses were considered more tender with less flavor and odor intensity than heavier carcasses.

Evaluation of morphological changes in the adult skull with age and sex.

PubMed

Urban, Jillian E; Weaver, Ashley A; Lillie, Elizabeth M; Maldjian, Joseph A; Whitlow, Christopher T; Stitzel, Joel D

2016-12-01

The morphology of the brain and skull are important in the evaluation of the aging human; however, little is known about how the skull may change with age. The objective of this study was to evaluate the morphological changes of the adult skull using three-dimensional geometric morphometric analysis of thousands of landmarks with the focus on anatomic regions that may be correlated with brain atrophy and head injury. Computed tomography data were collected between ages 20 and 100. Each scan was segmented using thresholding techniques. An atlas image of a 50th percentile skull was registered to each subject scan by computing a series of rigid, affine, and non-linear transformations between atlas space and subject space. Landmarks on the atlas skull were transformed to each subject and partitioned into the inner and outer cranial vault and the cranial fossae. A generalized Procrustes analysis was completed for the landmark sets. The coordinate locations describing the shape of each region were regressed with age to generate a model predicting the landmark location with age. Permutation testing was performed to assess significant changes with age. For the males, all anatomic regions reveal significant changes in shape with age except for the posterior cranial fossa. For the females, only the middle cranial fossa and anterior cranial fossa were found to change significantly in shape. Results of this study are important for understanding the adult skull and how shape changes may pertain to brain atrophy, aging, and injury. © 2014 Anatomical Society.

Wing geometry of Culex coronator (Diptera: Culicidae) from South and Southeast Brazil

PubMed Central

2014-01-01

Background The Coronator Group encompasses Culex coronator Dyar & Knab, Culex camposi Dyar, Culex covagarciai Forattini, Culex ousqua Dyar, Culex usquatissimus Dyar, Culex usquatus Dyar and Culex yojoae Strickman. Culex coronator has the largest geographic distribution, occurring in North, Central and South America. Moreover, it is a potential vector-borne mosquito species because females have been found naturally infected with several arboviruses, i.e., Saint Louis Encephalitis Virus, Venezuelan Equine Encephalitis Virus and West Nile Virus. Considering the epidemiological importance of Cx. coronator, we investigated the wing shape diversity of Cx. coronator from South and Southeast Brazil, a method to preliminarily estimate population diversity. Methods Field-collected immature stages of seven populations from a large geographical area in Brazil were maintained in the laboratory to obtain both females and males linked with pupal and/or larval exuviae. For each individual female, 18 landmarks of left wings were marked and digitalized. After Procrustes superimposition, discriminant analysis of shape was employed to quantify wing shape variation among populations. The isometric estimator centroid size was calculated to assess the overall wing size and allometry. Results Wing shape was polymorphic among populations of Cx. coronator. However, dissimilarities among populations were higher than those observed within each population, suggesting populational differentiation in Cx. coronator. Morphological distances between populations were not correlated to geographical distances, indicating that other factors may act on wing shape and thus, determining microevolutionary patterns in Cx. coronator. Despite the population differentiation, intrapopulational wing shape variability was equivalent among all seven populations. Conclusion The wing variability found in Cx. coronator populations brings to light a new biological problem to be investigated: the population genetics of Cx. coronator. Because of differences in the male genitalia, we also transferred Cx. yojoae to the Apicinus Subgroup. PMID:24721508

[Differentiation by geometric morphometrics among 11 Anopheles (Nyssorhynchus) in Colombia].

PubMed

Calle, David Alonso; Quiñones, Martha Lucía; Erazo, Holmes Francisco; Jaramillo, Nicolás

2008-09-01

The correct identification of the Anopheles species of the subgenus Nyssorhynchus is important because this subgenus includes the main malaria vectors in Colombia. This information is necessary for focusing a malaria control program. Geometric morphometrics were used to evaluate morphometric variation of 11 species of subgenus Nyssorhynchus present in Colombia and to distinguish females of each species. Materials and methods. The specimens were obtained from series and family broods from females collected with protected human hosts as attractants. The field collected specimens and their progeny were identified at each of the associated stages by conventional keys. For some species, wild females were used. Landmarks were selected on wings from digital pictures from 336 individuals, and digitized with coordinates. The coordinate matrix was processed by generalized Procrustes analysis which generated size and shape variables, free of non-biological variation. Size and shape variables were analyzed by univariate and multivariate statistics. The subdivision of subgenus Nyssorhynchus in sections is not correlated with wing shape. Discriminant analyses correctly classified 97% of females in the section Albimanus and 86% in the section Argyritarsis. In addition, these methodologies allowed the correct identification of 3 sympatric species from Putumayo which have been difficult to identify in the adult female stage. The geometric morphometrics were demonstrated to be a very useful tool as an adjunct to taxonomy of females the use of this method is recommended in studies of the subgenus Nyssorhynchus in Colombia.

Axial cervical vertebrae-based multivariate regression model for the estimation of skeletal-maturation status.

PubMed

Yang, Y-M; Lee, J; Kim, Y-I; Cho, B-H; Park, S-B

2014-08-01

This study aimed to determine the viability of using axial cervical vertebrae (ACV) as biological indicators of skeletal maturation and to build models that estimate ossification level with improved explanatory power over models based only on chronological age. The study population comprised 74 female and 47 male patients with available hand-wrist radiographs and cone-beam computed tomography images. Generalized Procrustes analysis was used to analyze the shape, size, and form of the ACV regions of interest. The variabilities of these factors were analyzed by principal component analysis. Skeletal maturation was then estimated using a multiple regression model. Separate models were developed for male and female participants. For the female estimation model, the adjusted R(2) explained 84.8% of the variability of the Sempé maturation level (SML), representing a 7.9% increase in SML explanatory power over that using chronological age alone (76.9%). For the male estimation model, the adjusted R(2) was over 90%, representing a 1.7% increase relative to the reference model. The simplest possible ACV morphometric information provided a statistically significant explanation of the portion of skeletal-maturation variability not dependent on chronological age. These results verify that ACV is a strong biological indicator of ossification status. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Bayesian comparison of protein structures using partial Procrustes distance.

PubMed

Ejlali, Nasim; Faghihi, Mohammad Reza; Sadeghi, Mehdi

2017-09-26

An important topic in bioinformatics is the protein structure alignment. Some statistical methods have been proposed for this problem, but most of them align two protein structures based on the global geometric information without considering the effect of neighbourhood in the structures. In this paper, we provide a Bayesian model to align protein structures, by considering the effect of both local and global geometric information of protein structures. Local geometric information is incorporated to the model through the partial Procrustes distance of small substructures. These substructures are composed of β-carbon atoms from the side chains. Parameters are estimated using a Markov chain Monte Carlo (MCMC) approach. We evaluate the performance of our model through some simulation studies. Furthermore, we apply our model to a real dataset and assess the accuracy and convergence rate. Results show that our model is much more efficient than previous approaches.

Ancestry Estimation in Forensic Anthropology: Geometric Morphometric versus Standard and Nonstandard Interlandmark Distances.

PubMed

Katherine Spradley, M; Jantz, Richard L

2016-07-01

Standard cranial measurements are commonly used for ancestry estimation; however, 3D digitizers have made cranial landmark data collection and geometric morphometric (GM) analyses more popular within forensic anthropology. Yet there has been little focus on which data type works best. The goal of the present research is to test the discrimination ability of standard and nonstandard craniometric measurements and data derived from GM analysis. A total of 31 cranial landmarks were used to generate 465 interlandmark distances, including a subset of 20 commonly used measurements, and to generate principal component scores from procrustes coordinates. All were subjected to discriminant function analysis to ascertain which type of data performed best for ancestry estimation of American Black and White and Hispanic males and females. The nonstandard interlandmark distances generated the highest classification rates for females (90.5%) and males (88.2%). Using nonstandard interlandmark distances over more commonly used measurements leads to better ancestry estimates for our current population structure. © 2016 American Academy of Forensic Sciences.

3D dentofacial photogrammetry reference values: a novel approach to orthodontic diagnosis.

PubMed

Masoud, Mohamed I; Bansal, Neetu; C Castillo, Jose; Manosudprasit, Amornrut; Allareddy, Veerasathpurush; Haghi, Arshan; Hawkins, Hannah C; Otárola-Castillo, Erik

2017-04-01

Orthodontic diagnostic standards generally use the cranial base as a reference and rely on samples selected by orthodontists. The purpose of this study was to provide male and female standards for a novel non-radiographic approach for orthodontic diagnosis that utilizes 3D dentofacial photogrammetry using the eyes and natural head orientation as references instead of the cranial base. One hundred and eighty females and 200 males between the ages of 18 and 35 years from 2 modeling agencies were orthodontically screened for near ideal occlusion. Subjects that met the inclusion criteria were rated by a sample of 40 lay people for attractiveness on a visual analogue scale. The final sample that had 3D facial and dental imaging included 49 subjects 25 males and 24 females with near ideal occlusion and considered attractive by the public. Inter and Intra-examiner ICC were greater than 0.8 for both landmarking and indexing. Relative to a coronal plane contacting the pupils (MC), the mean sagittal position of the alar curvature (representing the nasomaxillary complex) was 14.36 ± 3.08 mm in males and 12.4 ± 3.58 mm in females. The sagittal position of soft tissue pogonion relative to the pupils was 14.84 ± 3.63 mm in males and 12.78 ± 5.68 mm in females. The angle between the alar curvature and pogonion relative to the pupils was 9° in males and 10° in females. With the exception of the occlusal plane which was steeper in females, no ratios or angular facial measurements showed a significant gender difference. Relative to MC, males had more proclined upper incisors (20° vs 16°) and more retroclined Lower incisors (27° vs 31°; P > 0.05). A Procrustes ANOVA and permutation test showed that the shapes of males and females are different enough to be considered two distinct populations. 1. When using the proposed method for orthodontic diagnosis, male and female patients should be compared to their respective dentofacial standards. 2. Validation of the proposed method and standards on an orthodontic population is underway to determine the scope its use. © The Author 2016. Published by Oxford University Press on behalf of the European Orthodontic Society. All rights reserved. For permissions, please email: journals.permissions@oup.com

An analysis of beak shape variation in two ages of domestic turkeys (Meleagris gallopavo) using landmark-based geometric morphometrics.

PubMed

Dalton, Hillary A; Wood, Benjamin J; Widowski, Tina M; Guerin, Michele T; Torrey, Stephanie

2017-01-01

The objective of this study was to assess beak shape variation in domestic turkeys (Meleagris gallopavo) and determine the effects of age, sex, and beak size on beak shape variation using geometric morphometrics. Dorsal and right lateral images were taken of 2442 turkeys at 6 and 18.5 weeks of age. Landmarks were digitized in tpsDig in three analyses of the dorsal upper mandible, lateral upper mandible, and lateral lower mandible shape of each turkey at both ages. The coordinate data were then subjected to a principal components analysis (PCA), multivariate regression, and a canonical variates analysis (CVA) with a Procrustes ANOVA in MorphoJ. For the dorsal images, three principal components (PCs) showed beak shape variation ranged from long, narrow, and pointed to short, wide, and blunt upper mandibles at both ages (6 weeks: 95.36%, 18.5 weeks: 92.21%). Three PCs showed the lateral upper mandible shape variation ranged from long, wide beaks with long, curved beak tips to short, narrow beaks with short, pointed beak tips at both ages (6 weeks: 94.91%, 18.5 weeks: 94.33%). Three PCs also explained 97.80% (6 weeks) and 97.11% (18.5 weeks) of the lateral lower mandible shape variation ranging from wide and round to narrow and thin lower mandibles with superior/inferior beak tip shifts. Beak size accounted for varying proportions of the beak shape variation (0.96-54.76%; P < 0.0001) in the three analyses of each age group. For all the analyses, the CVA showed sexual dimorphism in beak shape (P < 0.0001) with female upper mandibles appearing wider and blunter dorsally with long, curved beak tips laterally. Whereas male turkey upper mandibles had a narrow, pointed dorsal appearance and short, pointed beak tips laterally. Future applications of beak shape variability could have a genetic and welfare value by incorporating beak shape variation to select for specific turkey beak phenotypes as an alternative to beak treatment.

An analysis of beak shape variation in two ages of domestic turkeys (Meleagris gallopavo) using landmark-based geometric morphometrics

PubMed Central

Widowski, Tina M.; Guerin, Michele T.

2017-01-01

The objective of this study was to assess beak shape variation in domestic turkeys (Meleagris gallopavo) and determine the effects of age, sex, and beak size on beak shape variation using geometric morphometrics. Dorsal and right lateral images were taken of 2442 turkeys at 6 and 18.5 weeks of age. Landmarks were digitized in tpsDig in three analyses of the dorsal upper mandible, lateral upper mandible, and lateral lower mandible shape of each turkey at both ages. The coordinate data were then subjected to a principal components analysis (PCA), multivariate regression, and a canonical variates analysis (CVA) with a Procrustes ANOVA in MorphoJ. For the dorsal images, three principal components (PCs) showed beak shape variation ranged from long, narrow, and pointed to short, wide, and blunt upper mandibles at both ages (6 weeks: 95.36%, 18.5 weeks: 92.21%). Three PCs showed the lateral upper mandible shape variation ranged from long, wide beaks with long, curved beak tips to short, narrow beaks with short, pointed beak tips at both ages (6 weeks: 94.91%, 18.5 weeks: 94.33%). Three PCs also explained 97.80% (6 weeks) and 97.11% (18.5 weeks) of the lateral lower mandible shape variation ranging from wide and round to narrow and thin lower mandibles with superior/inferior beak tip shifts. Beak size accounted for varying proportions of the beak shape variation (0.96–54.76%; P < 0.0001) in the three analyses of each age group. For all the analyses, the CVA showed sexual dimorphism in beak shape (P < 0.0001) with female upper mandibles appearing wider and blunter dorsally with long, curved beak tips laterally. Whereas male turkey upper mandibles had a narrow, pointed dorsal appearance and short, pointed beak tips laterally. Future applications of beak shape variability could have a genetic and welfare value by incorporating beak shape variation to select for specific turkey beak phenotypes as an alternative to beak treatment. PMID:28934330

Photometric calibration of the COMBO-17 survey with the Softassign Procrustes Matching method

NASA Astrophysics Data System (ADS)

Sheikhbahaee, Z.; Nakajima, R.; Erben, T.; Schneider, P.; Hildebrandt, H.; Becker, A. C.

2017-11-01

Accurate photometric calibration of optical data is crucial for photometric redshift estimation. We present the Softassign Procrustes Matching (SPM) method to improve the colour calibration upon the commonly used Stellar Locus Regression (SLR) method for the COMBO-17 survey. Our colour calibration approach can be categorised as a point-set matching method, which is frequently used in medical imaging and pattern recognition. We attain a photometric redshift precision Δz/(1 + zs) of better than 2 per cent. Our method is based on aligning the stellar locus of the uncalibrated stars to that of a spectroscopic sample of the Sloan Digital Sky Survey standard stars. We achieve our goal by finding a correspondence matrix between the two point-sets and applying the matrix to estimate the appropriate translations in multidimensional colour space. The SPM method is able to find the translation between two point-sets, despite the existence of noise and incompleteness of the common structures in the sets, as long as there is a distinct structure in at least one of the colour-colour pairs. We demonstrate the precision of our colour calibration method with a mock catalogue. The SPM colour calibration code is publicly available at https://neuronphysics@bitbucket.org/neuronphysics/spm.git.

Relation between consumers' perceptions of color and texture of dairy desserts and instrumental measurements using a generalized procrustes analysis.

PubMed

González-Tomás, L; Costell, E

2006-12-01

Consumers' perceptions of the color and texture of 8 commercial vanilla dairy desserts were studied and related to color and rheological measurements. First, the 8 desserts were evaluated by a group of consumers by means of the Free Choice Profile. For both color and texture, a 2-dimensional solution was chosen, with dimension 1 highly related to yellow color intensity in the case of color and to thickness in the case of texture. Second, mechanical spectra, flow behavior, and instrumental color were determined. All the samples showed a time-dependent and shear-thinning flow and a mechanical spectrum typical of a weak gel. Differences were found in the flow index, in the apparent viscosity at 10 s(-1), and in the values of the storage modulus, the loss modulus, the loss angle tangent, and the complex viscosity at 1 Hz, as well as in the color parameters. Finally, sensory and instrumental relationships were investigated by a generalized Procrustes analysis. For both color and texture, a 3-dimensional solution explained a high percentage of the total variance (>80%). In these particular samples, the instrumental color parameters provided more accurate information on consumers' color perceptions than was provided by the rheological parameters of consumers' perceptions of texture.

Abnormal ventricular development in preterm neonates with visually normal MRIs

NASA Astrophysics Data System (ADS)

Shi, Jie; Wang, Yalin; Lao, Yi; Ceschin, Rafael; Mi, Liang; Nelson, Marvin D.; Panigrahy, Ashok; Leporé, Natasha

2015-12-01

Children born preterm are at risk for a wide range of neurocognitive and neurobehavioral disorders. Some of these may stem from early brain abnormalities at the neonatal age. Hence, a precise characterization of neonatal neuroanatomy may help inform treatment strategies. In particular, the ventricles are often enlarged in neurocognitive disorders, due to atrophy of surrounding tissues. Here we present a new pipeline for the detection of morphological and relative pose differences in the ventricles of premature neonates compared to controls. To this end, we use a new hyperbolic Ricci flow based mapping of the ventricular surfaces of each subjects to the Poincaré disk. Resulting surfaces are then registered to a template, and a between group comparison is performed using multivariate tensor-based morphometry. We also statistically compare the relative pose of the ventricles within the brain between the two groups, by performing a Procrustes alignment between each subject's ventricles and an average shape. For both types of analyses, differences were found in the left ventricles between the two groups.

A parametric ribcage geometry model accounting for variations among the adult population.

PubMed

Wang, Yulong; Cao, Libo; Bai, Zhonghao; Reed, Matthew P; Rupp, Jonathan D; Hoff, Carrie N; Hu, Jingwen

2016-09-06

The objective of this study is to develop a parametric ribcage model that can account for morphological variations among the adult population. Ribcage geometries, including 12 pair of ribs, sternum, and thoracic spine, were collected from CT scans of 101 adult subjects through image segmentation, landmark identification (1016 for each subject), symmetry adjustment, and template mesh mapping (26,180 elements for each subject). Generalized procrustes analysis (GPA), principal component analysis (PCA), and regression analysis were used to develop a parametric ribcage model, which can predict nodal locations of the template mesh according to age, sex, height, and body mass index (BMI). Two regression models, a quadratic model for estimating the ribcage size and a linear model for estimating the ribcage shape, were developed. The results showed that the ribcage size was dominated by the height (p=0.000) and age-sex-interaction (p=0.007) and the ribcage shape was significantly affected by the age (p=0.0005), sex (p=0.0002), height (p=0.0064) and BMI (p=0.0000). Along with proper assignment of cortical bone thickness, material properties and failure properties, this parametric ribcage model can directly serve as the mesh of finite element ribcage models for quantifying effects of human characteristics on thoracic injury risks. Copyright © 2016 Elsevier Ltd. All rights reserved.

Marquardt's Phi mask: pitfalls of relying on fashion models and the golden ratio to describe a beautiful face.

PubMed

Holland, E

2008-03-01

Stephen Marquardt has derived a mask from the golden ratio that he claims represents the "ideal" facial archetype. Many have found his mask convincing, including cosmetic surgeons. However, Marquardt's mask is associated with numerous problems. The method used to examine goodness of fit with the proportions in the mask is faulty. The mask is ill-suited for non-European populations, especially sub-Saharan Africans and East Asians. The mask also appears to approximate the face shape of masculinized European women. Given that the general public strongly and overwhelmingly prefers above average facial femininity in women, white women seeking aesthetic facial surgery would be ill-advised to aim toward a better fit with Marquardt's mask. This article aims to show the proper way of assessing goodness of fit with Marquardt's mask, to address the shape of the mask as it pertains to masculinity-femininity, and to discuss the broader issue of an objective assessment of facial attractiveness. Generalized Procrustes analysis is used to show how goodness of fit with Marquardt's mask can be assessed. Thin-plate spline analysis is used to illustrate visually how sample faces, including northwestern European averages, differ from Marquardt's mask. Marquardt's mask best describes the facial proportions of masculinized white women as seen in fashion models. Marquardt's mask does not appear to describe "ideal" face shape even for white women because its proportions are inconsistent with the optimal preferences of most people, especially with regard to femininity.

Kinetic Shapes: Analysis, Verification, and Applications.

PubMed

Handz̆ić, Ismet; Reed, Kyle B

2014-06-01

A circular shape placed on an incline will roll; similarly, an irregularly shaped object, such as the Archimedean spiral, will roll on a flat surface when a force is applied to its axle. This rolling is dependent on the specific shape and the applied force (magnitude and location). In this paper, we derive formulas that define the behavior of irregular 2D and 3D shapes on a flat plane when a weight is applied to the shape's axle. These kinetic shape (KS) formulas also define and predict shapes that exert given ground reaction forces when a known weight is applied at the axle rotation point. Three 2D KS design examples are physically verified statically with good correlation to predicted values. Motion simulations of unrestrained 2D KS yielded expected results in shape dynamics and self-stabilization. We also put forth practical application ideas and research for 2D and 3D KS such as in robotics and gait rehabilitation.

Global Optimality of the Successive Maxbet Algorithm.

ERIC Educational Resources Information Center

Hanafi, Mohamed; ten Berge, Jos M. F.

2003-01-01

It is known that the Maxbet algorithm, which is an alternative to the method of generalized canonical correlation analysis and Procrustes analysis, may converge to local maxima. Discusses an eigenvalue criterion that is sufficient, but not necessary, for global optimality of the successive Maxbet algorithm. (SLD)

Recognizing an individual face: 3D shape contributes earlier than 2D surface reflectance information.

PubMed

Caharel, Stéphanie; Jiang, Fang; Blanz, Volker; Rossion, Bruno

2009-10-01

The human brain recognizes faces by means of two main diagnostic sources of information: three-dimensional (3D) shape and two-dimensional (2D) surface reflectance. Here we used event-related potentials (ERPs) in a face adaptation paradigm to examine the time-course of processing for these two types of information. With a 3D morphable model, we generated pairs of faces that were either identical, varied in 3D shape only, in 2D surface reflectance only, or in both. Sixteen human observers discriminated individual faces in these 4 types of pairs, in which a first (adapting) face was followed shortly by a second (test) face. Behaviorally, observers were as accurate and as fast for discriminating individual faces based on either 3D shape or 2D surface reflectance alone, but were faster when both sources of information were present. As early as the face-sensitive N170 component (approximately 160 ms following the test face), there was larger amplitude for changes in 3D shape relative to the repetition of the same face, especially over the right occipito-temporal electrodes. However, changes in 2D reflectance between the adapter and target face did not increase the N170 amplitude. At about 250 ms, both 3D shape and 2D reflectance contributed equally, and the largest difference in amplitude compared to the repetition of the same face was found when both 3D shape and 2D reflectance were combined, in line with observers' behavior. These observations indicate that evidence to recognize individual faces accumulate faster in the right hemisphere human visual cortex from diagnostic 3D shape information than from 2D surface reflectance information.

On Browne's Solution for Oblique Procrustes Rotation

ERIC Educational Resources Information Center

Cramer, Elliot M.

1974-01-01

A form of Browne's (1967) solution of finding a least squares fit to a specified factor structure is given which does not involve solution of an eigenvalue problem. It suggests the possible existence of a singularity, and a simple modification of Browne's computational procedure is proposed. (Author/RC)

Rotator cuff tear shape characterization: a comparison of two-dimensional imaging and three-dimensional magnetic resonance reconstructions.

PubMed

Gyftopoulos, Soterios; Beltran, Luis S; Gibbs, Kevin; Jazrawi, Laith; Berman, Phillip; Babb, James; Meislin, Robert

2016-01-01

The purpose of this study was to see if 3-dimensional (3D) magnetic resonance imaging (MRI) could improve our understanding of rotator cuff tendon tear shapes. We believed that 3D MRI would be more accurate than two-dimensional (2D) MRI for classifying tear shapes. We performed a retrospective review of MRI studies of patients with arthroscopically proven full-thickness rotator cuff tears. Two orthopedic surgeons reviewed the information for each case, including scope images, and characterized the shape of the cuff tear into crescent, longitudinal, U- or L-shaped longitudinal, and massive type. Two musculoskeletal radiologists reviewed the corresponding MRI studies independently and blind to the arthroscopic findings and characterized the shape on the basis of the tear's retraction and size using 2D MRI. The 3D reconstructions of each cuff tear were reviewed by each radiologist to characterize the shape. Statistical analysis included 95% confidence intervals and intraclass correlation coefficients. The study reviewed 34 patients. The accuracy for differentiating between crescent-shaped, longitudinal, and massive tears using measurements on 2D MRI was 70.6% for reader 1 and 67.6% for reader 2. The accuracy for tear shape characterization into crescent and longitudinal U- or L-shaped using 3D MRI was 97.1% for reader 1 and 82.4% for reader 2. When further characterizing the longitudinal tears as massive or not using 3D MRI, both readers had an accuracy of 76.9% (10 of 13). The overall accuracy of 3D MRI was 82.4% (56 of 68), significantly different (P = .021) from 2D MRI accuracy (64.7%). Our study has demonstrated that 3D MR reconstructions of the rotator cuff improve the accuracy of characterizing rotator cuff tear shapes compared with current 2D MRI-based techniques. Copyright © 2016 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

Genes mirror geography in Daphnia magna.

PubMed

Fields, Peter D; Reisser, Céline; Dukić, Marinela; Haag, Christoph R; Ebert, Dieter

2015-09-01

Identifying the presence and magnitude of population genetic structure remains a major consideration in evolutionary biology as doing so allows one to understand the demographic history of a species as well as make predictions of how the evolutionary process will proceed. Next-generation sequencing methods allow us to reconsider previous ideas and conclusions concerning the distribution of genetic variation, and what this distribution implies about a given species evolutionary history. A previous phylogeographic study of the crustacean Daphnia magna suggested that, despite strong genetic differentiation among populations at a local scale, the species shows only moderate genetic structure across its European range, with a spatially patchy occurrence of individual lineages. We apply RAD sequencing to a sample of D. magna collected across a wide swath of the species' Eurasian range and analyse the data using principle component analysis (PCA) of genetic variation and Procrustes analytical approaches, to quantify spatial genetic structure. We find remarkable consistency between the first two PCA axes and the geographic coordinates of individual sampling points, suggesting that, on a continent-wide scale, genetic differentiation is driven to a large extent by geographic distance. The observed pattern is consistent with unimpeded (i.e. no barriers, landscape or otherwise) migration at large spatial scales, despite the fragmented and patchy nature of favourable habitats at local scales. With high-resolution genetic data similar patterns may be uncovered for other species with wide geographic distributions, allowing an increased understanding of how genetic drift and selection have shaped their evolutionary history. © 2015 John Wiley & Sons Ltd.

Metatarsal Shape and Foot Type: A Geometric Morphometric Analysis.

PubMed

Telfer, Scott; Kindig, Matthew W; Sangeorzan, Bruce J; Ledoux, William R

2017-03-01

Planus and cavus foot types have been associated with an increased risk of pain and disability. Improving our understanding of the geometric differences between bones in different foot types may provide insights into injury risk profiles and have implications for the design of musculoskeletal and finite-element models. In this study, we performed a geometric morphometric analysis on the geometry of metatarsal bones from 65 feet, segmented from computed tomography (CT) scans. These were categorized into four foot types: pes cavus, neutrally aligned, asymptomatic pes planus, and symptomatic pes planus. Generalized procrustes analysis (GPA) followed by permutation tests was used to determine significant shape differences associated with foot type and sex, and principal component analysis was used to find the modes of variation for each metatarsal. Significant shape differences were found between foot types for all the metatarsals (p < 0.01), most notably in the case of the second metatarsal which showed significant pairwise differences across all the foot types. Analysis of the principal components of variation showed pes cavus bones to have reduced cross-sectional areas in the sagittal and frontal planes. The first (p = 0.02) and fourth metatarsals (p = 0.003) were found to have significant sex-based differences, with first metatarsals from females shown to have reduced width, and fourth metatarsals from females shown to have reduced frontal and sagittal plane cross-sectional areas. Overall, these findings suggest that metatarsal bones have distinct morphological characteristics that are associated with foot type and sex, with implications for our understanding of anatomy and numerical modeling of the foot.

Early modern human diversity suggests subdivided population structure and a complex out-of-Africa scenario

PubMed Central

Gunz, Philipp; Bookstein, Fred L.; Mitteroecker, Philipp; Stadlmayr, Andrea; Seidler, Horst; Weber, Gerhard W.

2009-01-01

The interpretation of genetic evidence regarding modern human origins depends, among other things, on assessments of the structure and the variation of ancient populations. Because we lack genetic data from the time when the first anatomically modern humans appeared, between 200,000 and 60,000 years ago, instead we exploit the phenotype of neurocranial geometry to compare the variation in early modern human fossils with that in other groups of fossil Homo and recent modern humans. Variation is assessed as the mean-squared Procrustes distance from the group average shape in a representation based on several hundred neurocranial landmarks and semilandmarks. We find that the early modern group has more shape variation than any other group in our sample, which covers 1.8 million years, and that they are morphologically similar to recent modern humans of diverse geographically dispersed populations but not to archaic groups. Of the currently competing models of modern human origins, some are inconsistent with these findings. Rather than a single out-of-Africa dispersal scenario, we suggest that early modern humans were already divided into different populations in Pleistocene Africa, after which there followed a complex migration pattern. Our conclusions bear implications for the inference of ancient human demography from genetic models and emphasize the importance of focusing research on those early modern humans, in particular, in Africa. PMID:19307568

The role of plant mycorrhizal type and status in modulating the relationship between plant and arbuscular mycorrhizal fungal communities.

PubMed

Neuenkamp, Lena; Moora, Mari; Öpik, Maarja; Davison, John; Gerz, Maret; Männistö, Minna; Jairus, Teele; Vasar, Martti; Zobel, Martin

2018-01-25

Interactions between communities of plants and arbuscular mycorrhizal (AM) fungi shape fundamental ecosystem properties. Experimental evidence suggests that compositional changes in plant and AM fungal communities should be correlated, but empirical data from natural ecosystems are scarce. We investigated the dynamics of covariation between plant and AM fungal communities during three stages of grassland succession, and the biotic and abiotic factors shaping these dynamics. Plant communities were characterised using vegetation surveys. AM fungal communities were characterised by 454-sequencing of the small subunit rRNA gene and identification against the AM fungal reference database MaarjAM. AM fungal abundance was estimated using neutral-lipid fatty acids (NLFAs). Multivariate correlation analysis (Procrustes) revealed a significant relationship between plant and AM fungal community composition. The strength of plant-AM fungal correlation weakened during succession following cessation of grassland management, reflecting changes in the proportion of plants exhibiting different AM status. Plant-AM fungal correlation was strong when the abundance of obligate AM plants was high, and declined as the proportion of facultative AM plants increased. We conclude that the extent to which plants rely on AM symbiosis can determine how tightly communities of plants and AM fungi are interlinked, regulating community assembly of both symbiotic partners. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Geometric Morphometrics on Gene Expression Patterns Within Phenotypes: A Case Example on Limb Development

PubMed Central

Martínez-Abadías, Neus; Mateu, Roger; Niksic, Martina; Russo, Lucia; Sharpe, James

2016-01-01

How the genotype translates into the phenotype through development is critical to fully understand the evolution of phenotypes. We propose a novel approach to directly assess how changes in gene expression patterns are associated with changes in morphology using the limb as a case example. Our method combines molecular biology techniques, such as whole-mount in situ hybridization, with image and shape analysis, extending the use of Geometric Morphometrics to the analysis of nonanatomical shapes, such as gene expression domains. Elliptical Fourier and Procrustes-based semilandmark analyses were used to analyze the variation and covariation patterns of the limb bud shape with the expression patterns of two relevant genes for limb morphogenesis, Hoxa11 and Hoxa13. We devised a multiple thresholding method to semiautomatically segment gene domains at several expression levels in large samples of limb buds from C57Bl6 mouse embryos between 10 and 12 postfertilization days. Besides providing an accurate phenotyping tool to quantify the spatiotemporal dynamics of gene expression patterns within developing structures, our morphometric analyses revealed high, non-random, and gene-specific variation undergoing canalization during limb development. Our results demonstrate that Hoxa11 and Hoxa13, despite being paralogs with analogous functions in limb patterning, show clearly distinct dynamic patterns, both in shape and size, and are associated differently with the limb bud shape. The correspondence between our results and already well-established molecular processes underlying limb development confirms that this morphometric approach is a powerful tool to extract features of development regulating morphogenesis. Such multilevel analyses are promising in systems where not so much molecular information is available and will advance our understanding of the genotype–phenotype map. In systematics, this knowledge will increase our ability to infer how evolution modified a common developmental pattern to generate a wide diversity of morphologies, as in the vertebrate limb. PMID:26377442

The mammalian bony labyrinth reconsidered, introducing a comprehensive geometric morphometric approach

PubMed Central

Gunz, Philipp; Ramsier, Marissa; Kuhrig, Melanie; Hublin, Jean-Jacques; Spoor, Fred

2012-01-01

The bony labyrinth in the temporal bone houses the sensory systems of balance and hearing. While the overall structure of the semicircular canals and cochlea is similar across therian mammals, their detailed morphology varies even among closely related groups. As such, the shape of the labyrinth carries valuable functional and phylogenetic information. Here we introduce a new, semilandmark-based three-dimensional geometric morphometric approach to shape analysis of the labyrinth, as a major improvement upon previous metric studies based on linear measurements and angles. We first provide a detailed, step-by-step description of the measurement protocol. Subsequently, we test our approach using a geographically diverse sample of 50 recent modern humans and 30 chimpanzee specimens belonging to Pan troglodytes troglodytes and P. t. verus. Our measurement protocol can be applied to CT scans of different spatial resolutions because it primarily quantifies the midline skeleton of the bony labyrinth. Accurately locating the lumen centre of the semicircular canals and the cochlea is not affected by the partial volume and thresholding effects that can make the comparison of the outer border problematic. After virtually extracting the bony labyrinth from CT scans of the temporal bone, we computed its midline skeleton by thinning the encased volume. On the resulting medial axes of the semicircular canals and cochlea we placed a sequence of semilandmarks. After Procrustes superimposition, the shape coordinates were analysed using multivariate statistics. We found statistically significant shape differences between humans and chimpanzees which corroborate previous analyses of the labyrinth based on traditional measurements. As the geometric relationship among the semilandmark coordinates was preserved throughout the analysis, we were able to quantify and visualize even small-scale shape differences. Notably, our approach made it possible to detect and visualize subtle, yet statistically significant (P = 0.009), differences between two chimpanzee subspecies in the shape of their semicircular canals. The ability to discriminate labyrinth shape at the subspecies level demonstrates that the approach presented here has great potential in future taxonomic studies of fossil specimens. PMID:22404255

Multiple Mechanisms in the Perception of Face Gender: Effect of Sex-Irrelevant Features

ERIC Educational Resources Information Center

Komori, Masashi; Kawamura, Satoru; Ishihara, Shigekazu

2011-01-01

Effects of sex-relevant and sex-irrelevant facial features on the evaluation of facial gender were investigated. Participants rated masculinity of 48 male facial photographs and femininity of 48 female facial photographs. Eighty feature points were measured on each of the facial photographs. Using a generalized Procrustes analysis, facial shapes…

The Rigid Orthogonal Procrustes Rotation Problem

ERIC Educational Resources Information Center

ten Berge, Jos M. F.

2006-01-01

The problem of rotating a matrix orthogonally to a best least squares fit with another matrix of the same order has a closed-form solution based on a singular value decomposition. The optimal rotation matrix is not necessarily rigid, but may also involve a reflection. In some applications, only rigid rotations are permitted. Gower (1976) has…

Least-Squares Approximation of an Improper Correlation Matrix by a Proper One.

ERIC Educational Resources Information Center

Knol, Dirk L.; ten Berge, Jos M. F.

1989-01-01

An algorithm, based on a solution for C. I. Mosier's oblique Procrustes rotation problem, is presented for the best least-squares fitting correlation matrix approximating a given missing value or improper correlation matrix. Results are of interest for missing value and tetrachoric correlation, indefinite matrix correlation, and constrained…

Profound Effect of Profiling Platform and Normalization Strategy on Detection of Differentially Expressed MicroRNAs – A Comparative Study

PubMed Central

Meyer, Swanhild U.; Kaiser, Sebastian; Wagner, Carola; Thirion, Christian; Pfaffl, Michael W.

2012-01-01

Background Adequate normalization minimizes the effects of systematic technical variations and is a prerequisite for getting meaningful biological changes. However, there is inconsistency about miRNA normalization performances and recommendations. Thus, we investigated the impact of seven different normalization methods (reference gene index, global geometric mean, quantile, invariant selection, loess, loessM, and generalized procrustes analysis) on intra- and inter-platform performance of two distinct and commonly used miRNA profiling platforms. Methodology/Principal Findings We included data from miRNA profiling analyses derived from a hybridization-based platform (Agilent Technologies) and an RT-qPCR platform (Applied Biosystems). Furthermore, we validated a subset of miRNAs by individual RT-qPCR assays. Our analyses incorporated data from the effect of differentiation and tumor necrosis factor alpha treatment on primary human skeletal muscle cells and a murine skeletal muscle cell line. Distinct normalization methods differed in their impact on (i) standard deviations, (ii) the area under the receiver operating characteristic (ROC) curve, (iii) the similarity of differential expression. Loess, loessM, and quantile analysis were most effective in minimizing standard deviations on the Agilent and TLDA platform. Moreover, loess, loessM, invariant selection and generalized procrustes analysis increased the area under the ROC curve, a measure for the statistical performance of a test. The Jaccard index revealed that inter-platform concordance of differential expression tended to be increased by loess, loessM, quantile, and GPA normalization of AGL and TLDA data as well as RGI normalization of TLDA data. Conclusions/Significance We recommend the application of loess, or loessM, and GPA normalization for miRNA Agilent arrays and qPCR cards as these normalization approaches showed to (i) effectively reduce standard deviations, (ii) increase sensitivity and accuracy of differential miRNA expression detection as well as (iii) increase inter-platform concordance. Results showed the successful adoption of loessM and generalized procrustes analysis to one-color miRNA profiling experiments. PMID:22723911

Differences between sliding semi-landmark methods in geometric morphometrics, with an application to human craniofacial and dental variation

PubMed Central

Ivan Perez, S; Bernal, Valeria; Gonzalez, Paula N

2006-01-01

Over the last decade, geometric morphometric methods have been applied increasingly to the study of human form. When too few landmarks are available, outlines can be digitized as series of discrete points. The individual points must be slid along a tangential direction so as to remove tangential variation, because contours should be homologous from subject to subject whereas their individual points need not. This variation can be removed by minimizing either bending energy (BE) or Procrustes distance (D) with respect to a mean reference form. Because these two criteria make different assumptions, it becomes necessary to study how these differences modify the results obtained. We performed bootstrapped-based Goodall's F-test, Foote's measurement, principal component (PC) and discriminant function analyses on human molars and craniometric data to compare the results obtained by the two criteria. Results show that: (1) F-scores and P-values were similar for both criteria; (2) results of Foote's measurement show that both criteria yield different estimates of within- and between-sample variation; (3) there is low correlation between the first PC axes obtained by D and BE; (4) the percentage of correct classification is similar for BE and D, but the ordination of groups along discriminant scores differs between them. The differences between criteria can alter the results when morphological variation in the sample is small, as in the analysis of modern human populations. PMID:16761977

Quantifying floral shape variation in 3D using microcomputed tomography: a case study of a hybrid line between actinomorphic and zygomorphic flowers.

PubMed

Wang, Chun-Neng; Hsu, Hao-Chun; Wang, Cheng-Chun; Lee, Tzu-Kuei; Kuo, Yan-Fu

2015-01-01

The quantification of floral shape variations is difficult because flower structures are both diverse and complex. Traditionally, floral shape variations are quantified using the qualitative and linear measurements of two-dimensional (2D) images. The 2D images cannot adequately describe flower structures, and thus lead to unsatisfactory discrimination of the flower shape. This study aimed to acquire three-dimensional (3D) images by using microcomputed tomography (μCT) and to examine the floral shape variations by using geometric morphometrics (GM). To demonstrate the advantages of the 3D-μCT-GM approach, we applied the approach to a second-generation population of florist's gloxinia (Sinningia speciosa) crossed from parents of zygomorphic and actinomorphic flowers. The flowers in the population considerably vary in size and shape, thereby served as good materials to test the applicability of the proposed phenotyping approach. Procedures were developed to acquire 3D volumetric flower images using a μCT scanner, to segment the flower regions from the background, and to select homologous characteristic points (i.e., landmarks) from the flower images for the subsequent GM analysis. The procedures identified 95 landmarks for each flower and thus improved the capability of describing and illustrating the flower shapes, compared with typically lower number of landmarks in 2D analyses. The GM analysis demonstrated that flower opening and dorsoventral symmetry were the principal shape variations of the flowers. The degrees of flower opening and corolla asymmetry were then subsequently quantified directly from the 3D flower images. The 3D-μCT-GM approach revealed shape variations that could not be identified using typical 2D approaches and accurately quantified the flower traits that presented a challenge in 2D images. The approach opens new avenues to investigate floral shape variations.

Progressive 3D shape abstraction via hierarchical CSG tree

NASA Astrophysics Data System (ADS)

Chen, Xingyou; Tang, Jin; Li, Chenglong

2017-06-01

A constructive solid geometry(CSG) tree model is proposed to progressively abstract 3D geometric shape of general object from 2D image. Unlike conventional ones, our method applies to general object without the need for massive CAD models, and represents the object shapes in a coarse-to-fine manner that allows users to view temporal shape representations at any time. It stands in a transitional position between 2D image feature and CAD model, benefits from state-of-the-art object detection approaches and better initializes CAD model for finer fitting, estimates 3D shape and pose parameters of object at different levels according to visual perception objective, in a coarse-to-fine manner. Two main contributions are the application of CSG building up procedure into visual perception, and the ability of extending object estimation result into a more flexible and expressive model than 2D/3D primitive shapes. Experimental results demonstrate the feasibility and effectiveness of the proposed approach.

From Procrustes to Proteus: Trends and Practices in the Assessment of Education Research

ERIC Educational Resources Information Center

Oancea, Alis

2007-01-01

This article is a reflection on an area of particular interest in the current research environment, but which has not yet been explored satisfactorily in the education literature: the evaluation of educational research. The particular focus is on the UK context, but the article is informed by comparative evidence from six countries (gathered…

Evaluation of a New Method of Fossil Retrodeformation by Algorithmic Symmetrization: Crania of Papionins (Primates, Cercopithecidae) as a Test Case

PubMed Central

Tallman, Melissa; Amenta, Nina; Delson, Eric; Frost, Stephen R.; Ghosh, Deboshmita; Klukkert, Zachary S.; Morrow, Andrea; Sawyer, Gary J.

2014-01-01

Diagenetic distortion can be a major obstacle to collecting quantitative shape data on paleontological specimens, especially for three-dimensional geometric morphometric analysis. Here we utilize the recently -published algorithmic symmetrization method of fossil reconstruction and compare it to the more traditional reflection & averaging approach. In order to have an objective test of this method, five casts of a female cranium of Papio hamadryas kindae were manually deformed while the plaster hardened. These were subsequently “retrodeformed” using both algorithmic symmetrization and reflection & averaging and then compared to the original, undeformed specimen. We found that in all cases, algorithmic retrodeformation improved the shape of the deformed cranium and in four out of five cases, the algorithmically symmetrized crania were more similar in shape to the original crania than the reflected & averaged reconstructions. In three out of five cases, the difference between the algorithmically symmetrized crania and the original cranium could be contained within the magnitude of variation among individuals in a single subspecies of Papio. Instances of asymmetric distortion, such as breakage on one side, or bending in the axis of symmetry, were well handled, whereas symmetrical distortion remained uncorrected. This technique was further tested on a naturally deformed and fossilized cranium of Paradolichopithecus arvernensis. Results, based on a principal components analysis and Procrustes distances, showed that the algorithmically symmetrized Paradolichopithecus cranium was more similar to other, less-deformed crania from the same species than was the original. These results illustrate the efficacy of this method of retrodeformation by algorithmic symmetrization for the correction of asymmetrical distortion in fossils. Symmetrical distortion remains a problem for all currently developed methods of retrodeformation. PMID:24992483

A Nonrigid Kernel-Based Framework for 2D-3D Pose Estimation and 2D Image Segmentation

PubMed Central

Sandhu, Romeil; Dambreville, Samuel; Yezzi, Anthony; Tannenbaum, Allen

2013-01-01

In this work, we present a nonrigid approach to jointly solving the tasks of 2D-3D pose estimation and 2D image segmentation. In general, most frameworks that couple both pose estimation and segmentation assume that one has exact knowledge of the 3D object. However, under nonideal conditions, this assumption may be violated if only a general class to which a given shape belongs is given (e.g., cars, boats, or planes). Thus, we propose to solve the 2D-3D pose estimation and 2D image segmentation via nonlinear manifold learning of 3D embedded shapes for a general class of objects or deformations for which one may not be able to associate a skeleton model. Thus, the novelty of our method is threefold: First, we present and derive a gradient flow for the task of nonrigid pose estimation and segmentation. Second, due to the possible nonlinear structures of one’s training set, we evolve the preimage obtained through kernel PCA for the task of shape analysis. Third, we show that the derivation for shape weights is general. This allows us to use various kernels, as well as other statistical learning methodologies, with only minimal changes needing to be made to the overall shape evolution scheme. In contrast with other techniques, we approach the nonrigid problem, which is an infinite-dimensional task, with a finite-dimensional optimization scheme. More importantly, we do not explicitly need to know the interaction between various shapes such as that needed for skeleton models as this is done implicitly through shape learning. We provide experimental results on several challenging pose estimation and segmentation scenarios. PMID:20733218

Interspecific variation in the tetradactyl manus of modern tapirs (Perissodactyla: Tapirus) exposed using geometric morphometrics.

PubMed

MacLaren, Jamie A; Nauwelaerts, Sandra

2017-11-01

The distal forelimb (autopodium) of quadrupedal mammals is a key morphological unit involved in locomotion, body support, and interaction with the substrate. The manus of the tapir (Perissodactyla: Tapirus) is unique within modern perissodactyls, as it retains the plesiomorphic tetradactyl (four-toed) condition also exhibited by basal equids and rhinoceroses. Tapirs are known to exhibit anatomical mesaxonic symmetry in the manus, although interspecific differences and biomechanical mesaxony have yet to be rigorously tested. Here, we investigate variation in the manus morphology of four modern tapir species (Tapirus indicus, Tapirus bairdii, Tapirus pinchaque, and Tapirus terrestris) using a geometric morphometric approach. Autopodial bones were laser scanned to capture surface shape and morphology was quantified using 3D-landmark analysis. Landmarks were aligned using Generalised Procrustes Analysis, with discriminant function and partial least square analyses performed on aligned coordinate data to identify features that significantly separate tapir species. Overall, our results support the previously held hypothesis that T. indicus is morphologically separate from neotropical tapirs; however, previous conclusions regarding function from morphological differences are shown to require reassessment. We find evidence indicating that T. bairdii exhibits reduced reliance on the lateral fifth digit compared to other tapirs. Morphometric assessment of the metacarpophalangeal joint and the morphology of the distal facets of the lunate lend evidence toward high loading on the lateral digits of both the large T. indicus (large body mass) and the small, long limbed T. pinchaque (ground impact). Our results support other recent studies on T. pinchaque, suggesting subtle but important adaptations to a compliant but inclined habitat. In conclusion, we demonstrate further evidence that the modern tapir forelimb is a variable locomotor unit with a range of interspecific features tailored to habitual and biomechanical needs of each species. © 2017 Wiley Periodicals, Inc.

The Extraction of 3D Shape from Texture and Shading in the Human Brain

PubMed Central

Georgieva, Svetlana S.; Todd, James T.; Peeters, Ronald

2008-01-01

We used functional magnetic resonance imaging to investigate the human cortical areas involved in processing 3-dimensional (3D) shape from texture (SfT) and shading. The stimuli included monocular images of randomly shaped 3D surfaces and a wide variety of 2-dimensional (2D) controls. The results of both passive and active experiments reveal that the extraction of 3D SfT involves the bilateral caudal inferior temporal gyrus (caudal ITG), lateral occipital sulcus (LOS) and several bilateral sites along the intraparietal sulcus. These areas are largely consistent with those involved in the processing of 3D shape from motion and stereo. The experiments also demonstrate, however, that the analysis of 3D shape from shading is primarily restricted to the caudal ITG areas. Additional results from psychophysical experiments reveal that this difference in neuronal substrate cannot be explained by a difference in strength between the 2 cues. These results underscore the importance of the posterior part of the lateral occipital complex for the extraction of visual 3D shape information from all depth cues, and they suggest strongly that the importance of shading is diminished relative to other cues for the analysis of 3D shape in parietal regions. PMID:18281304

Characterization of wood dust from furniture by scanning electron microscopy and energy-dispersive x-ray analysis.

PubMed

Gómez Yepes, Milena Elizabeth; Cremades, Lázaro V

2011-01-01

Study characterized and analyzed form factor, elementary composition and particle size of wood dust, in order to understand its harmful health effects on carpenters in Quindío (Colombia). Once particle characteristics (size distributions, aerodynamic equivalent diameter (D(α)), elemental composition and shape factors) were analyzed, particles were then characterized via scanning electron microscopy (SEM) in conjunction with energy dispersive X-ray analysis (EDXRA). SEM analysis of particulate matter showed: 1) cone-shaped particle ranged from 2.09 to 48.79 µm D(α); 2) rectangular prism-shaped particle from 2.47 to 72.9 µm D(α); 3) cylindrically-shaped particle from 2.5 to 48.79 µm D(α); and 4) spherically-shaped particle from 2.61 to 51.93 µm D(α). EDXRA reveals presence of chemical elements from paints and varnishes such as Ca, K, Na and Cr. SEM/EDXRA contributes in a significant manner to the morphological characterization of wood dust. It is obvious that the type of particles sampled is a complex function of shapes and sizes of particles. Thus, it is important to investigate the influence of particles characteristics, morphology, shapes and D(α) that may affect the health of carpenters in Quindío.

The design and implementation of stereoscopic 3D scalable vector graphics based on WebKit

NASA Astrophysics Data System (ADS)

Liu, Zhongxin; Wang, Wenmin; Wang, Ronggang

2014-03-01

Scalable Vector Graphics (SVG), which is a language designed based on eXtensible Markup Language (XML), is used to describe basic shapes embedded in webpages, such as circles and rectangles. However, it can only depict 2D shapes. As a consequence, web pages using classical SVG can only display 2D shapes on a screen. With the increasing development of stereoscopic 3D (S3D) technology, binocular 3D devices have been widely used. Under this circumstance, we intend to extend the widely used web rendering engine WebKit to support the description and display of S3D webpages. Therefore, the extension of SVG is of necessity. In this paper, we will describe how to design and implement SVG shapes with stereoscopic 3D mode. Two attributes representing the depth and thickness are added to support S3D shapes. The elimination of hidden lines and hidden surfaces, which is an important process in this project, is described as well. The modification of WebKit is also discussed, which is made to support the generation of both left view and right view at the same time. As is shown in the result, in contrast to the 2D shapes generated by the Google Chrome web browser, the shapes got from our modified browser are in S3D mode. With the feeling of depth and thickness, the shapes seem to be real 3D objects away from the screen, rather than simple curves and lines as before.

Packing of flexible 2D materials in vesicles

NASA Astrophysics Data System (ADS)

Zou, Guijin; Yi, Xin; Zhu, Wenpeng; Gao, Huajian

2018-06-01

To understand the mechanics of cellular packing of two-dimensional (2D) materials, we perform systematic molecular dynamics simulations and theoretical analysis to investigate the packing of a flexible circular sheet in a spherical vesicle and the 2D packing problem of a strip in a cylindrical vesicle. Depending on the system dimensions and the bending rigidity ratio between the confined sheet and the vesicle membrane, a variety of packing morphologies are observed, including a conical shape, a shape of three-fold symmetry, a cylindrically curved shape, an axisymmetrically buckled shape, as well as the initial circular shape. A set of buckling analyses lead to phase diagrams of the packing morphologies of the encapsulated sheets. These results may have important implications on the mechanism of intracellular packing and toxicity of 2D materials.

3D deblending of simultaneous source data based on 3D multi-scale shaping operator

NASA Astrophysics Data System (ADS)

Zu, Shaohuan; Zhou, Hui; Mao, Weijian; Gong, Fei; Huang, Weilin

2018-04-01

We propose an iterative three-dimensional (3D) deblending scheme using 3D multi-scale shaping operator to separate 3D simultaneous source data. The proposed scheme is based on the property that signal is coherent, whereas interference is incoherent in some domains, e.g., common receiver domain and common midpoint domain. In two-dimensional (2D) blended record, the coherency difference of signal and interference is in only one spatial direction. Compared with 2D deblending, the 3D deblending can take more sparse constraints into consideration to obtain better performance, e.g., in 3D common receiver gather, the coherency difference is in two spatial directions. Furthermore, with different levels of coherency, signal and interference distribute in different scale curvelet domains. In both 2D and 3D blended records, most coherent signal locates in coarse scale curvelet domain, while most incoherent interference distributes in fine scale curvelet domain. The scale difference is larger in 3D deblending, thus, we apply the multi-scale shaping scheme to further improve the 3D deblending performance. We evaluate the performance of 3D and 2D deblending with the multi-scale and global shaping operators, respectively. One synthetic and one field data examples demonstrate the advantage of the 3D deblending with 3D multi-scale shaping operator.

Statistical shape modeling of human cochlea: alignment and principal component analysis

NASA Astrophysics Data System (ADS)

Poznyakovskiy, Anton A.; Zahnert, Thomas; Fischer, Björn; Lasurashvili, Nikoloz; Kalaidzidis, Yannis; Mürbe, Dirk

2013-02-01

The modeling of the cochlear labyrinth in living subjects is hampered by insufficient resolution of available clinical imaging methods. These methods usually provide resolutions higher than 125 μm. This is too crude to record the position of basilar membrane and, as a result, keep apart even the scala tympani from other scalae. This problem could be avoided by the means of atlas-based segmentation. The specimens can endure higher radiation loads and, conversely, provide better-resolved images. The resulting surface can be used as the seed for atlas-based segmentation. To serve this purpose, we have developed a statistical shape model (SSM) of human scala tympani based on segmentations obtained from 10 μCT image stacks. After segmentation, we aligned the resulting surfaces using Procrustes alignment. This algorithm was slightly modified to accommodate single models with nodes which do not necessarily correspond to salient features and vary in number between models. We have established correspondence by mutual proximity between nodes. Rather than using the standard Euclidean norm, we have applied an alternative logarithmic norm to improve outlier treatment. The minimization was done using BFGS method. We have also split the surface nodes along an octree to reduce computation cost. Subsequently, we have performed the principal component analysis of the training set with Jacobi eigenvalue algorithm. We expect the resulting method to help acquiring not only better understanding in interindividual variations of cochlear anatomy, but also a step towards individual models for pre-operative diagnostics prior to cochlear implant insertions.

Adding a dimension to the infrared spectra of interfaces: 2D SFG spectroscopy via mid-IR pulse shaping

NASA Astrophysics Data System (ADS)

Zanni, Martin

2012-02-01

Sum-frequency generation spectroscopy provides an infrared spectrum of interfaces and thus has widespread use in the materials and chemical sciences. In this presentation, I will present our recent work in developing a 2D pulse sequence to generate 2D SFG spectra of interfaces, in analogy to 2D infrared spectra used to measure bulk species. To develop this spectroscopy, we have utilized many of the tricks-of-the-trade developed in the 2D IR and 2D Vis communities in the last decade, including mid-IR pulse shaping. With mid-IR pulse shaping, the 2D pulse sequence is manipulated by computer programming in the desired frequency resolution, rotating frame, and signal pathway. We believe that 2D SFG will become an important tool in the interfacial sciences in an analogous way that 2D IR is now being used in many disciplines.

View subspaces for indexing and retrieval of 3D models

NASA Astrophysics Data System (ADS)

Dutagaci, Helin; Godil, Afzal; Sankur, Bülent; Yemez, Yücel

2010-02-01

View-based indexing schemes for 3D object retrieval are gaining popularity since they provide good retrieval results. These schemes are coherent with the theory that humans recognize objects based on their 2D appearances. The viewbased techniques also allow users to search with various queries such as binary images, range images and even 2D sketches. The previous view-based techniques use classical 2D shape descriptors such as Fourier invariants, Zernike moments, Scale Invariant Feature Transform-based local features and 2D Digital Fourier Transform coefficients. These methods describe each object independent of others. In this work, we explore data driven subspace models, such as Principal Component Analysis, Independent Component Analysis and Nonnegative Matrix Factorization to describe the shape information of the views. We treat the depth images obtained from various points of the view sphere as 2D intensity images and train a subspace to extract the inherent structure of the views within a database. We also show the benefit of categorizing shapes according to their eigenvalue spread. Both the shape categorization and data-driven feature set conjectures are tested on the PSB database and compared with the competitor view-based 3D shape retrieval algorithms.

Ontogeny of the female femur: geometric morphometric analysis applied on current living individuals of a Spanish population

PubMed Central

Pujol, Aniol; Rissech, Carme; Ventura, Jacint; Badosa, Joaquim; Turbón, Daniel

2014-01-01

In this study we describe the development of the female femur based on the analysis of high-resolution radiographic images by means of geometric morphometrics, while assessing the usefulness of this method in these kinds of studies. The material analysed consisted of digital images in DICOM format (telemetries), corresponding to 184 left femora in anterior view, obtained from the database of the Hospital Sant Joan de Déu of Barcelona (Spain). Bones analysed corresponded to individuals from 9 to 14 years old. Size and shape variation of the entire femur was quantified by 22 two-dimensional landmarks. Landmark digitisation errors were assessed using Procrustes anova test. Centroid size (CS) variation with age was evaluated by an anova test. Shape variation was assessed by principal component analysis. A mancova test between the first five principal components and age, using the CS as covariable, was applied. Results indicated that both size and shape vary significantly with age. Several age-related shape changes remained significant after removing the allometric effect. In general, an increase in the robustness of the bone and noticeable phenotypic changes in certain areas of the femur were observed. During growth in the proximal region of the femur, the collo-diaphyseal angle decreases, the neck of the femur widens and the fovea moves to a lower position, standing more in line with the plane of the neck. Likewise, the size of the greater and lesser trochanters increase. In the distal region, a significant increase of epiphyseal dimensions was recorded, mainly in the medial condyle. The angular remodelling of the neck and the bicondylar region of the femur in females continues until 13 years old. The information provided in the present study increases our knowledge on the timing and morphology of the femur during development, and in particular the morphology of the different femoral ossification centres during development. PMID:24975495

Specific-age group sex estimation of infants through geometric morphometrics analysis of pubis and ischium.

PubMed

Estévez Campo, Enrique José; López-Lázaro, Sandra; López-Morago Rodríguez, Claudia; Alemán Aguilera, Inmaculada; Botella López, Miguel Cecilio

2018-05-01

Sex determination of unknown individuals is one of the primary goals of Physical and Forensic Anthropology. The adult skeleton can be sexed using both morphological and metric traits on a large number of bones. The human pelvis is often used as an important element of adult sex determination. However, studies carried out about the pelvic bone in subadult individuals present several limitations due the absence of sexually dimorphic characteristics. In this study, we analyse the sexual dimorphism of the immature pubis and ischium bones, attending to their shape (Procrustes residuals) and size (centroid size), using an identified sample of subadult individuals composed of 58 individuals for the pubis and 83 for the ischium, aged between birth and 1year of life, from the Granada osteological collection of identified infants (Granada, Spain). Geometric morphometric methods and discriminant analysis were applied to this study. The results of intra- and inter-observer error showed good and excellent agreement in the location of coordinates of landmarks and semilandmarks, respectively. Principal component analysis performed on shape and size variables showed superposition of the two sexes, suggesting a low degree of sexual dimorphism. Canonical variable analysis did not show significant changes between the male and female shapes. As a consequence, discriminant analysis with leave-one-out cross validation provided low classification accuracy. The results suggested a low degree of sexual dimorphism supported by significant sexual dimorphism in the subadult sample and poor cross-validated classification accuracy. The inclusion of centroid size as a discriminant variable does not imply a significant improvement in the results of the analysis. The similarities found between the sexes prevent consideration of pubic and ischial morphology as a sex estimator in early stages of development. The authors suggest extending this study by analysing the different trajectories of shape and size in later ontogeny between males and females. Copyright © 2018 Elsevier B.V. All rights reserved.

Evaluation of facial attractiveness for patients with malocclusion: a machine-learning technique employing Procrustes.

PubMed

Yu, Xiaonan; Liu, Bin; Pei, Yuru; Xu, Tianmin

2014-05-01

To establish an objective method for evaluating facial attractiveness from a set of orthodontic photographs. One hundred eight malocclusion patients randomly selected from six universities in China were randomly divided into nine groups, with each group containing an equal number of patients with Class I, II, and III malocclusions. Sixty-nine expert Chinese orthodontists ranked photographs of the patients (frontal, lateral, and frontal smiling photos) before and after orthodontic treatment from "most attractive" to "least attractive" in each group. A weighted mean ranking was then calculated for each patient, based on which a three-point scale was created. Procrustes superimposition was conducted on 101 landmarks identified on the photographs. A support vector regression (SVR) function was set up according to the coordinate values of identified landmarks of each photographic set and its corresponding grading. Its predictive ability was tested for each group in turn. The average coincidence rate obtained for comparisons of the subjective ratings with the SVR evaluation was 71.8% according to 18 verification tests. Geometric morphometrics combined with SVR may be a prospective method for objective comprehensive evaluation of facial attractiveness in the near future.

Validation of a computer modelled forensic facial reconstruction technique using CT data from live subjects: a pilot study.

PubMed

Short, Laura J; Khambay, Balvinder; Ayoub, Ashraf; Erolin, Caroline; Rynn, Chris; Wilkinson, Caroline

2014-04-01

Human forensic facial soft tissue reconstructions are used when post-mortem deterioration makes identification difficult by usual means. The aim is to trigger recognition of the in vivo countenance of the individual by a friend or family member. A further use is in the field of archaeology. There are a number of different methods that can be applied to complete the facial reconstruction, ranging from two dimensional drawings, three dimensional clay models and now, with the advances of three dimensional technology, three dimensional computerised modelling. Studies carried out to assess the accuracy of facial reconstructions have produced variable results over the years. Advances in three dimensional imaging techniques in the field of oral and maxillofacial surgery, particularly cone beam computed tomography (CBCT), now provides an opportunity to utilise the data of live subjects and assess the accuracy of the three dimensional computerised facial reconstruction technique. The aim of this study was to assess the accuracy of a computer modelled facial reconstruction technique using CBCT data from live subjects. This retrospective pilot study was carried out at the Glasgow Dental Hospital Orthodontic Department and the Centre of Anatomy and Human Identification, Dundee University School of Life Sciences. Ten patients (5 male and 5 female; mean age 23 years) with mild skeletal discrepancies with pre-surgical cone beam CT data (CBCT) were included in this study. The actual and forensic reconstruction soft tissues were analysed using 3D software to look at differences between landmarks, linear and angular measurements and surface meshes. There were no statistical differences for 18 out of the 23 linear and 7 out of 8 angular measurements between the reconstruction and the target (p<0.05). The use of Procrustes superimposition has highlighted potential problems with soft tissue depth and anatomical landmarks' position. Surface mesh analysis showed that this virtual sculpture technique can be objectively assessed using the distance between the meshes. This study found that the percentage of faces with less than ±2.5mm error ranged from 56% to 90%. This may be improved if Procrustes superimposition could be applied to all the mesh points rather than specific landmarks. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

A statistical shape modelling framework to extract 3D shape biomarkers from medical imaging data: assessing arch morphology of repaired coarctation of the aorta.

PubMed

Bruse, Jan L; McLeod, Kristin; Biglino, Giovanni; Ntsinjana, Hopewell N; Capelli, Claudio; Hsia, Tain-Yen; Sermesant, Maxime; Pennec, Xavier; Taylor, Andrew M; Schievano, Silvia

2016-05-31

Medical image analysis in clinical practice is commonly carried out on 2D image data, without fully exploiting the detailed 3D anatomical information that is provided by modern non-invasive medical imaging techniques. In this paper, a statistical shape analysis method is presented, which enables the extraction of 3D anatomical shape features from cardiovascular magnetic resonance (CMR) image data, with no need for manual landmarking. The method was applied to repaired aortic coarctation arches that present complex shapes, with the aim of capturing shape features as biomarkers of potential functional relevance. The method is presented from the user-perspective and is evaluated by comparing results with traditional morphometric measurements. Steps required to set up the statistical shape modelling analyses, from pre-processing of the CMR images to parameter setting and strategies to account for size differences and outliers, are described in detail. The anatomical mean shape of 20 aortic arches post-aortic coarctation repair (CoA) was computed based on surface models reconstructed from CMR data. By analysing transformations that deform the mean shape towards each of the individual patient's anatomy, shape patterns related to differences in body surface area (BSA) and ejection fraction (EF) were extracted. The resulting shape vectors, describing shape features in 3D, were compared with traditionally measured 2D and 3D morphometric parameters. The computed 3D mean shape was close to population mean values of geometric shape descriptors and visually integrated characteristic shape features associated with our population of CoA shapes. After removing size effects due to differences in body surface area (BSA) between patients, distinct 3D shape features of the aortic arch correlated significantly with EF (r = 0.521, p = .022) and were well in agreement with trends as shown by traditional shape descriptors. The suggested method has the potential to discover previously unknown 3D shape biomarkers from medical imaging data. Thus, it could contribute to improving diagnosis and risk stratification in complex cardiac disease.

3D foot shape generation from 2D information.

PubMed

Luximon, Ameersing; Goonetilleke, Ravindra S; Zhang, Ming

2005-05-15

Two methods to generate an individual 3D foot shape from 2D information are proposed. A standard foot shape was first generated and then scaled based on known 2D information. In the first method, the foot outline and the foot height were used, and in the second, the foot outline and the foot profile were used. The models were developed using 40 participants and then validated using a different set of 40 participants. Results show that each individual foot shape can be predicted within a mean absolute error of 1.36 mm for the left foot and 1.37 mm for the right foot using the first method, and within a mean absolute error of 1.02 mm for the left foot and 1.02 mm for the right foot using the second method. The second method shows somewhat improved accuracy even though it requires two images. Both the methods are relatively cheaper than using a scanner to determine the 3D foot shape for custom footwear design.

Deep neural network using color and synthesized three-dimensional shape for face recognition

NASA Astrophysics Data System (ADS)

Rhee, Seon-Min; Yoo, ByungIn; Han, Jae-Joon; Hwang, Wonjun

2017-03-01

We present an approach for face recognition using synthesized three-dimensional (3-D) shape information together with two-dimensional (2-D) color in a deep convolutional neural network (DCNN). As 3-D facial shape is hardly affected by the extrinsic 2-D texture changes caused by illumination, make-up, and occlusions, it could provide more reliable complementary features in harmony with the 2-D color feature in face recognition. Unlike other approaches that use 3-D shape information with the help of an additional depth sensor, our approach generates a personalized 3-D face model by using only face landmarks in the 2-D input image. Using the personalized 3-D face model, we generate a frontalized 2-D color facial image as well as 3-D facial images (e.g., a depth image and a normal image). In our DCNN, we first feed 2-D and 3-D facial images into independent convolutional layers, where the low-level kernels are successfully learned according to their own characteristics. Then, we merge them and feed into higher-level layers under a single deep neural network. Our proposed approach is evaluated with labeled faces in the wild dataset and the results show that the error rate of the verification rate at false acceptance rate 1% is improved by up to 32.1% compared with the baseline where only a 2-D color image is used.

Integrating Anisakis spp. parasites data and host genetic structure in the frame of a holistic approach for stock identification of selected Mediterranean Sea fish species.

PubMed

Mattiucci, S; Cimmaruta, R; Cipriani, P; Abaunza, P; Bellisario, B; Nascetti, G

2015-01-01

The unique environment of the Mediterranean Sea makes fish stock assessment a major challenge. Stock identification of Mediterranean fisheries has been based mostly from data on biology, morphometrics, artificial tags, otolith shape and fish genetics, with less effort on the use of parasites as biomarkers. Here we use some case studies comparing Mediterranean vs Atlantic fish stocks in a multidisciplinary framework. The generalized Procrustes Rotation (PR) was used to assess the association between host genetics and larval Anisakis spp. datasets on demersal (hake) and pelagic (horse mackerel, swordfish) species. When discordant results emerged, they were due to the different features of the data. While fish population genetics can detect changes over an evolutionary timescale, providing indications on the cohesive action of gene flow, parasites are more suitable biomarkers when considering fish stocks over smaller temporal and spatial scales, hence giving information of fish movements over their lifespan. Future studies on the phylogeographic analysis of parasites suitable as biomarkers, and that of their fish host, performed on the same genes, will represent a further tool to be included in multidisciplinary studies on fish stock structure.

Thin-plate spline analysis of the effects of face mask treatment in children with maxillary retrognathism.

PubMed

Chang, Jenny Zwei-Chieng; Liu, Pao-Hsin; Chen, Yi-Jane; Yao, Jane Chung-Chen; Chang, Hong-Po; Chang, Chih-Han; Chang, Frank Hsin-Fu

2006-02-01

Face mask therapy is indicated for growing patients who suffer from maxillary retrognathia. Most previous studies used conventional cephalometric analysis to evaluate the effects of face mask treatment. Cephalometric analysis has been shown to be insufficient for complex craniofacial configurations. The purpose of this study was to investigate changes in the craniofacial structure of children with maxillary retrognathism following face mask treatment by means of thin-plate spline analysis. Thirty children with skeletal Class III malocclusions who had been treated with face masks were compared with a group of 30 untreated gender-matched, age-matched, observation period-matched, and craniofacial configuration-matched subjects. Average geometries, scaled to an equivalent size, were generated by means of Procrustes analysis. Thin-plate spline analysis was then performed for localization of the shape changes. Face mask treatment induced a forward displacement of the maxilla, a counterclockwise rotation of the palatal plane, a horizontal compression of the anterior border of the symphysis and the condylar region, and a downward deformation of the menton. The cranial base exhibited a counterclockwise deformation as a whole. We conclude that thin-plate spline analysis is a valuable supplement to conventional cephalometric analysis.

An Elliptic PDE Approach for Shape Characterization

PubMed Central

Haidar, Haissam; Bouix, Sylvain; Levitt, James; McCarley, Robert W.; Shenton, Martha E.; Soul, Janet S.

2009-01-01

This paper presents a novel approach to analyze the shape of anatomical structures. Our methodology is rooted in classical physics and in particular Poisson's equation, a fundamental partial differential equation [1]. The solution to this equation and more specifically its equipotential surfaces display properties that are useful for shape analysis. We present a numerical algorithm to calculate the length of streamlines formed by the gradient field of the solution to this equation for 2D and 3D objects. The length of the streamlines along the equipotential surfaces was used to build a new function which can characterize the shape of objects. We illustrate our method on 2D synthetic and natural shapes as well as 3D medical data. PMID:17271986

Shape Analysis of Planar Multiply-Connected Objects Using Conformal Welding.

PubMed

Lok Ming Lui; Wei Zeng; Shing-Tung Yau; Xianfeng Gu

2014-07-01

Shape analysis is a central problem in the field of computer vision. In 2D shape analysis, classification and recognition of objects from their observed silhouettes are extremely crucial but difficult. It usually involves an efficient representation of 2D shape space with a metric, so that its mathematical structure can be used for further analysis. Although the study of 2D simply-connected shapes has been subject to a corpus of literatures, the analysis of multiply-connected shapes is comparatively less studied. In this work, we propose a representation for general 2D multiply-connected domains with arbitrary topologies using conformal welding. A metric can be defined on the proposed representation space, which gives a metric to measure dissimilarities between objects. The main idea is to map the exterior and interior of the domain conformally to unit disks and circle domains (unit disk with several inner disks removed), using holomorphic 1-forms. A set of diffeomorphisms of the unit circle S(1) can be obtained, which together with the conformal modules are used to define the shape signature. A shape distance between shape signatures can be defined to measure dissimilarities between shapes. We prove theoretically that the proposed shape signature uniquely determines the multiply-connected objects under suitable normalization. We also introduce a reconstruction algorithm to obtain shapes from their signatures. This completes our framework and allows us to move back and forth between shapes and signatures. With that, a morphing algorithm between shapes can be developed through the interpolation of the Beltrami coefficients associated with the signatures. Experiments have been carried out on shapes extracted from real images. Results demonstrate the efficacy of our proposed algorithm as a stable shape representation scheme.

Pull-Up Nets

ERIC Educational Resources Information Center

Meenan, Liz

2008-01-01

When the author began teaching, she always hit a problem when it came to 3D shapes. She wanted the pupils to get a feel for them, and she would get them to make the shapes from their nets. The pupils would first try to visualize how the 2D nets could become 3D shapes and then they would physically fold the nets into the shapes for themselves.…

Extrinsic Calibration of Camera Networks Based on Pedestrians

PubMed Central

Guan, Junzhi; Deboeverie, Francis; Slembrouck, Maarten; Van Haerenborgh, Dirk; Van Cauwelaert, Dimitri; Veelaert, Peter; Philips, Wilfried

2016-01-01

In this paper, we propose a novel extrinsic calibration method for camera networks by analyzing tracks of pedestrians. First of all, we extract the center lines of walking persons by detecting their heads and feet in the camera images. We propose an easy and accurate method to estimate the 3D positions of the head and feet w.r.t. a local camera coordinate system from these center lines. We also propose a RANSAC-based orthogonal Procrustes approach to compute relative extrinsic parameters connecting the coordinate systems of cameras in a pairwise fashion. Finally, we refine the extrinsic calibration matrices using a method that minimizes the reprojection error. While existing state-of-the-art calibration methods explore epipolar geometry and use image positions directly, the proposed method first computes 3D positions per camera and then fuses the data. This results in simpler computations and a more flexible and accurate calibration method. Another advantage of our method is that it can also handle the case of persons walking along straight lines, which cannot be handled by most of the existing state-of-the-art calibration methods since all head and feet positions are co-planar. This situation often happens in real life. PMID:27171080

Localisation of deformations of the midfacial complex in subjects with class III malocclusions employing thin-plate spline analysis

PubMed Central

SINGH, G. D.; McNAMARA JR, J. A.; LOZANOFF, S.

1997-01-01

This study determines deformations of the midface that contribute to a class III appearance, employing thin-plate spline analysis. A total of 135 lateral cephalographs of prepubertal children of European-American descent with either class III malocclusions or a class I molar occlusion were compared. The cephalographs were traced and checked, and 7 homologous landmarks of the midface were identified and digitised. The data sets were scaled to an equivalent size and subjected to Procrustes analysis. These statistical tests indicated significant differences (P<0.05) between the averaged class I and class III morphologies. Thin-plate spline analysis indicated that both affine and nonaffine transformations contribute towards the total spline for the averaged midfacial configuration. For nonaffine transformations, partial warp 3 had the highest magnitude, indicating the large scale deformations of the midfacial configuration. These deformations affected the palatal landmarks, and were associated with compression of the midfacial complex in the anteroposterior plane predominantly. Partial warp 4 produced some vertical compression of the posterior aspect of the midfacial complex whereas partial warps 1 and 2 indicated localised shape changes of the maxillary alveolus region. Large spatial-scale deformations therefore affect the midfacial complex in an anteroposterior axis, in combination with vertical compression and localised distortions. These deformations may represent a developmental diminution of the palatal complex anteroposteriorly that, allied with vertical shortening of midfacial height posteriorly, results in class III malocclusions with a retrusive midfacial profile. PMID:9449078

Localisation of deformations of the midfacial complex in subjects with class III malocclusions employing thin-plate spline analysis.

PubMed

Singh, G D; McNamara, J A; Lozanoff, S

1997-11-01

This study determines deformations of the midface that contribute to a class III appearance, employing thinplate spline analysis. A total of 135 lateral cephalographs of prepubertal children of European-American descent with either class III malocclusions or a class I molar occlusion were compared. The cephalographs were traced and checked, and 7 homologous landmarks of the midface were identified and digitised. The data sets were scaled to an equivalent size and subjected to Procrustes analysis. These statistical tests indicated significant differences (P < 0.05) between the averaged class I and class III morphologies. Thinplate spline analysis indicated that both affine and nonaffine transformations contribute towards the total spline for the averaged midfacial configuration. For nonaffine transformations, partial warp 3 had the highest magnitude, indicating the large scale deformations of the midfacial configuration. These deformations affected the palatal landmarks, and were associated with compression of the midfacial complex in the anteroposterior plane predominantly. Partial warp 4 produced some vertical compression of the posterior aspect of the midfacial complex whereas partial warps 1 and 2 indicated localised shape changes of the maxillary alveolus region. large spatial-scale deformations therefore affect the midfacial complex in an anteroposterior axis, in combination with vertical compression and localised distortions. These deformations may represent a developmental diminution of the palatal complex anteroposteriorly that, allied with vertical shortening of midfacial height posteriorly, results in class III malocclusions with a retrusive midfacial profile.

An Effective 3D Shape Descriptor for Object Recognition with RGB-D Sensors

PubMed Central

Liu, Zhong; Zhao, Changchen; Wu, Xingming; Chen, Weihai

2017-01-01

RGB-D sensors have been widely used in various areas of computer vision and graphics. A good descriptor will effectively improve the performance of operation. This article further analyzes the recognition performance of shape features extracted from multi-modality source data using RGB-D sensors. A hybrid shape descriptor is proposed as a representation of objects for recognition. We first extracted five 2D shape features from contour-based images and five 3D shape features over point cloud data to capture the global and local shape characteristics of an object. The recognition performance was tested for category recognition and instance recognition. Experimental results show that the proposed shape descriptor outperforms several common global-to-global shape descriptors and is comparable to some partial-to-global shape descriptors that achieved the best accuracies in category and instance recognition. Contribution of partial features and computational complexity were also analyzed. The results indicate that the proposed shape features are strong cues for object recognition and can be combined with other features to boost accuracy. PMID:28245553

Least-Squares Approximation of an Improper by a Proper Correlation Matrix Using a Semi-Infinite Convex Program. Research Report 87-7.

ERIC Educational Resources Information Center

Knol, Dirk L.; ten Berge, Jos M. F.

An algorithm is presented for the best least-squares fitting correlation matrix approximating a given missing value or improper correlation matrix. The proposed algorithm is based on a solution for C. I. Mosier's oblique Procrustes rotation problem offered by J. M. F. ten Berge and K. Nevels (1977). It is shown that the minimization problem…

Orthogonal Procrustes Analysis for Dictionary Learning in Sparse Linear Representation.

PubMed

Grossi, Giuliano; Lanzarotti, Raffaella; Lin, Jianyi

2017-01-01

In the sparse representation model, the design of overcomplete dictionaries plays a key role for the effectiveness and applicability in different domains. Recent research has produced several dictionary learning approaches, being proven that dictionaries learnt by data examples significantly outperform structured ones, e.g. wavelet transforms. In this context, learning consists in adapting the dictionary atoms to a set of training signals in order to promote a sparse representation that minimizes the reconstruction error. Finding the best fitting dictionary remains a very difficult task, leaving the question still open. A well-established heuristic method for tackling this problem is an iterative alternating scheme, adopted for instance in the well-known K-SVD algorithm. Essentially, it consists in repeating two stages; the former promotes sparse coding of the training set and the latter adapts the dictionary to reduce the error. In this paper we present R-SVD, a new method that, while maintaining the alternating scheme, adopts the Orthogonal Procrustes analysis to update the dictionary atoms suitably arranged into groups. Comparative experiments on synthetic data prove the effectiveness of R-SVD with respect to well known dictionary learning algorithms such as K-SVD, ILS-DLA and the online method OSDL. Moreover, experiments on natural data such as ECG compression, EEG sparse representation, and image modeling confirm R-SVD's robustness and wide applicability.

A New 3D Object Pose Detection Method Using LIDAR Shape Set

PubMed Central

Kim, Jung-Un

2018-01-01

In object detection systems for autonomous driving, LIDAR sensors provide very useful information. However, problems occur because the object representation is greatly distorted by changes in distance. To solve this problem, we propose a LIDAR shape set that reconstructs the shape surrounding the object more clearly by using the LIDAR point information projected on the object. The LIDAR shape set restores object shape edges from a bird’s eye view by filtering LIDAR points projected on a 2D pixel-based front view. In this study, we use this shape set for two purposes. The first is to supplement the shape set with a LIDAR Feature map, and the second is to divide the entire shape set according to the gradient of the depth and density to create a 2D and 3D bounding box proposal for each object. We present a multimodal fusion framework that classifies objects and restores the 3D pose of each object using enhanced feature maps and shape-based proposals. The network structure consists of a VGG -based object classifier that receives multiple inputs and a LIDAR-based Region Proposal Networks (RPN) that identifies object poses. It works in a very intuitive and efficient manner and can be extended to other classes other than vehicles. Our research has outperformed object classification accuracy (Average Precision, AP) and 3D pose restoration accuracy (3D bounding box recall rate) based on the latest studies conducted with KITTI data sets. PMID:29547551

A New 3D Object Pose Detection Method Using LIDAR Shape Set.

PubMed

Kim, Jung-Un; Kang, Hang-Bong

2018-03-16

In object detection systems for autonomous driving, LIDAR sensors provide very useful information. However, problems occur because the object representation is greatly distorted by changes in distance. To solve this problem, we propose a LIDAR shape set that reconstructs the shape surrounding the object more clearly by using the LIDAR point information projected on the object. The LIDAR shape set restores object shape edges from a bird's eye view by filtering LIDAR points projected on a 2D pixel-based front view. In this study, we use this shape set for two purposes. The first is to supplement the shape set with a LIDAR Feature map, and the second is to divide the entire shape set according to the gradient of the depth and density to create a 2D and 3D bounding box proposal for each object. We present a multimodal fusion framework that classifies objects and restores the 3D pose of each object using enhanced feature maps and shape-based proposals. The network structure consists of a VGG -based object classifier that receives multiple inputs and a LIDAR-based Region Proposal Networks (RPN) that identifies object poses. It works in a very intuitive and efficient manner and can be extended to other classes other than vehicles. Our research has outperformed object classification accuracy (Average Precision, AP) and 3D pose restoration accuracy (3D bounding box recall rate) based on the latest studies conducted with KITTI data sets.

The role of dimension and shape in colloidal liquids and glasses

NASA Astrophysics Data System (ADS)

Vivek, Skanda

In two-dimensions, the laws of physics give rise to intriguing phenomena such as long-range correlations that do not decay at infinity. However, reality can only be quasi-2D at best. This thesis is an effort to bridge the gap between 2D theory and reality, by doing experiments. Here we consider two different model systems - soap films as 2D fluids, and 2D colloidal glass formers. We look at diffusion of tracer particles in soap films and test the validity of 2D theory. We find that for thin films, both 2D surface viscosity and 3D viscosity are important. To a good approximation, soap films are thin films and can be considered 2D for flow. Next, we look at glassy dynamics in 2D and 3D colloidal glass formers. We demonstrate that the differences between 2D and 3D are long-wavelength fluctuations, precisely those that distinguish 2D and 3D phase transitions. Through a novel analysis method that removes the influence of these fluctuations, we show that 2D and 3D glass transitions are otherwise similar. Finally, we look at the effect of shape anisotropy of dimers in 2D glasses, and find that glass dynamics are highly dependent on shape, both in experiments and simulations. These colloidal and simulation results are a prediction of aspect ratio dependent diffusion in real glasses.

Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis.

PubMed

Hurst, Travis; Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

2018-05-10

The selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) method probes RNA local structural and dynamic information at single nucleotide resolution. To gain quantitative insights into the relationship between nucleotide flexibility, RNA 3D structure, and SHAPE reactivity, we develop a 3D Structure-SHAPE Relationship model (3DSSR) to rebuild SHAPE profiles from 3D structures. The model starts from RNA structures and combines nucleotide interaction strength and conformational propensity, ligand (SHAPE reagent) accessibility, and base-pairing pattern through a composite function to quantify the correlation between SHAPE reactivity and nucleotide conformational stability. The 3DSSR model shows the relationship between SHAPE reactivity and RNA structure and energetics. Comparisons between the 3DSSR-predicted SHAPE profile and the experimental SHAPE data show correlation, suggesting that the extracted analytical function may have captured the key factors that determine the SHAPE reactivity profile. Furthermore, the theory offers an effective method to sieve RNA 3D models and exclude models that are incompatible with experimental SHAPE data.

Reconstructing liver shape and position from MR image slices using an active shape model

NASA Astrophysics Data System (ADS)

Fenchel, Matthias; Thesen, Stefan; Schilling, Andreas

2008-03-01

We present an algorithm for fully automatic reconstruction of 3D position, orientation and shape of the human liver from a sparsely covering set of n 2D MR slice images. Reconstructing the shape of an organ from slice images can be used for scan planning, for surgical planning or other purposes where 3D anatomical knowledge has to be inferred from sparse slices. The algorithm is based on adapting an active shape model of the liver surface to a given set of slice images. The active shape model is created from a training set of liver segmentations from a group of volunteers. The training set is set up with semi-manual segmentations of T1-weighted volumetric MR images. Searching for the optimal shape model that best fits to the image data is done by maximizing a similarity measure based on local appearance at the surface. Two different algorithms for the active shape model search are proposed and compared: both algorithms seek to maximize the a-posteriori probability of the grey level appearance around the surface while constraining the surface to the space of valid shapes. The first algorithm works by using grey value profile statistics in normal direction. The second algorithm uses average and variance images to calculate the local surface appearance on the fly. Both algorithms are validated by fitting the active shape model to abdominal 2D slice images and comparing the shapes, which have been reconstructed, to the manual segmentations and to the results of active shape model searches from 3D image data. The results turn out to be promising and competitive to active shape model segmentations from 3D data.

Seeing the tipping point: Balance perception and visual shape.

PubMed

Firestone, Chaz; Keil, Frank C

2016-07-01

In a brief glance at an object or shape, we can appreciate a rich suite of its functional properties, including the organization of the object's parts, its optimal contact points for grasping, and its center of mass, or balancing point. However, in the real world and the laboratory, balance perception shows systematic biases whereby observers may misjudge a shape's center of mass by a severe margin. Are such biases simply quirks of physical reasoning? Or might they instead reflect more fundamental principles of object representation? Here we demonstrate systematically biased center-of-mass estimation for two-dimensional (2D) shapes (Study 1) and advance a surprising explanation of such biases. We suggest that the mind implicitly represents ordinary 2D shapes as rich, volumetric, three-dimensional (3D) objects, and that these "inflated" shape representations intrude on and bias perception of the 2D shape's geometric properties. Such "inflation" is a computer-graphics technique for segmenting shapes into parts, and we show that a model derived from this technique best accounts for the biases in center-of-mass estimation in Study 1. Further supporting this account, we show that reducing the need for inflated shape representations diminishes such biases: Center-of-mass estimation improved when cues to shapehood were attenuated (Study 2) and when shapes' depths were explicitly depicted using real-life objects laser-cut from wood (Study 3). We suggest that the technique of shape inflation is actually implemented in the mind; thus, biases in our impressions of balance reflect a more general functional characteristic of object perception. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

An Unified Multiscale Framework for Planar, Surface, and Curve Skeletonization.

PubMed

Jalba, Andrei C; Sobiecki, Andre; Telea, Alexandru C

2016-01-01

Computing skeletons of 2D shapes, and medial surface and curve skeletons of 3D shapes, is a challenging task. In particular, there is no unified framework that detects all types of skeletons using a single model, and also produces a multiscale representation which allows to progressively simplify, or regularize, all skeleton types. In this paper, we present such a framework. We model skeleton detection and regularization by a conservative mass transport process from a shape's boundary to its surface skeleton, next to its curve skeleton, and finally to the shape center. The resulting density field can be thresholded to obtain a multiscale representation of progressively simplified surface, or curve, skeletons. We detail a numerical implementation of our framework which is demonstrably stable and has high computational efficiency. We demonstrate our framework on several complex 2D and 3D shapes.

Reproducibility of the dynamics of facial expressions in unilateral facial palsy.

PubMed

Alagha, M A; Ju, X; Morley, S; Ayoub, A

2018-02-01

The aim of this study was to assess the reproducibility of non-verbal facial expressions in unilateral facial paralysis using dynamic four-dimensional (4D) imaging. The Di4D system was used to record five facial expressions of 20 adult patients. The system captured 60 three-dimensional (3D) images per second; each facial expression took 3-4seconds which was recorded in real time. Thus a set of 180 3D facial images was generated for each expression. The procedure was repeated after 30min to assess the reproducibility of the expressions. A mathematical facial mesh consisting of thousands of quasi-point 'vertices' was conformed to the face in order to determine the morphological characteristics in a comprehensive manner. The vertices were tracked throughout the sequence of the 180 images. Five key 3D facial frames from each sequence of images were analyzed. Comparisons were made between the first and second capture of each facial expression to assess the reproducibility of facial movements. Corresponding images were aligned using partial Procrustes analysis, and the root mean square distance between them was calculated and analyzed statistically (paired Student t-test, P<0.05). Facial expressions of lip purse, cheek puff, and raising of eyebrows were reproducible. Facial expressions of maximum smile and forceful eye closure were not reproducible. The limited coordination of various groups of facial muscles contributed to the lack of reproducibility of these facial expressions. 4D imaging is a useful clinical tool for the assessment of facial expressions. Copyright © 2017 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

A novel shape-changing haptic table-top display

NASA Astrophysics Data System (ADS)

Wang, Jiabin; Zhao, Lu; Liu, Yue; Wang, Yongtian; Cai, Yi

2018-01-01

A shape-changing table-top display with haptic feedback allows its users to perceive 3D visual and texture displays interactively. Since few existing devices are developed as accurate displays with regulatory haptic feedback, a novel attentive and immersive shape changing mechanical interface (SCMI) consisting of image processing unit and transformation unit was proposed in this paper. In order to support a precise 3D table-top display with an offset of less than 2 mm, a custommade mechanism was developed to form precise surface and regulate the feedback force. The proposed image processing unit was capable of extracting texture data from 2D picture for rendering shape-changing surface and realizing 3D modeling. The preliminary evaluation result proved the feasibility of the proposed system.

Forming three-dimensional closed shapes from two-dimensional soft ribbons by controlled buckling

PubMed Central

Aoki, Michio

2018-01-01

Conventional manufacturing techniques—moulding, machining and casting—exist to produce three-dimensional (3D) shapes. However, these industrial processes are typically geared for mass production and are not directly applicable to residential settings, where inexpensive and versatile tools are desirable. Moreover, those techniques are, in general, not adequate to process soft elastic materials. Here, we introduce a new concept of forming 3D closed hollow shapes from two-dimensional (2D) elastic ribbons by controlled buckling. We numerically and experimentally characterize how the profile and thickness of the ribbon determine its buckled shape. We find a 2D master profile with which various elliptical 3D shapes can be formed. More complex natural and artificial hollow shapes, such as strawberry, hourglass and wheel, can also be achieved via strategic design and pattern engraving on the ribbons. The nonlinear response of the post-buckling regime is rationalized through finite-element analysis, which shows good quantitative agreement with experiments. This robust fabrication should complement conventional techniques and provide a rich arena for future studies on the mechanics and new applications of elastic hollow structures. PMID:29515894

Forming three-dimensional closed shapes from two-dimensional soft ribbons by controlled buckling

NASA Astrophysics Data System (ADS)

Aoki, Michio; Juang, Jia-Yang

2018-02-01

Conventional manufacturing techniques-moulding, machining and casting-exist to produce three-dimensional (3D) shapes. However, these industrial processes are typically geared for mass production and are not directly applicable to residential settings, where inexpensive and versatile tools are desirable. Moreover, those techniques are, in general, not adequate to process soft elastic materials. Here, we introduce a new concept of forming 3D closed hollow shapes from two-dimensional (2D) elastic ribbons by controlled buckling. We numerically and experimentally characterize how the profile and thickness of the ribbon determine its buckled shape. We find a 2D master profile with which various elliptical 3D shapes can be formed. More complex natural and artificial hollow shapes, such as strawberry, hourglass and wheel, can also be achieved via strategic design and pattern engraving on the ribbons. The nonlinear response of the post-buckling regime is rationalized through finite-element analysis, which shows good quantitative agreement with experiments. This robust fabrication should complement conventional techniques and provide a rich arena for future studies on the mechanics and new applications of elastic hollow structures.

Reconstruction of shapes of near symmetric and asymmetric objects

DOEpatents

Pizlo, Zygmunt; Sawada, Tadamasa; Li, Yunfeng

2013-03-26

A system processes 2D images of 2D or 3D objects, creating a model of the object that is consistent with the image and as veridical as the perception of the 2D image by humans. Vertices of the object that are hidden in the image are recovered by using planarity and symmetry constraints. The 3D shape is recovered by maximizing 3D compactness of the recovered object and minimizing its surface area. In some embodiments, these two criteria are weighted by using the geometric mean.

Laplace-Beltrami Eigenvalues and Topological Features of Eigenfunctions for Statistical Shape Analysis

PubMed Central

Reuter, Martin; Wolter, Franz-Erich; Shenton, Martha; Niethammer, Marc

2009-01-01

This paper proposes the use of the surface based Laplace-Beltrami and the volumetric Laplace eigenvalues and -functions as shape descriptors for the comparison and analysis of shapes. These spectral measures are isometry invariant and therefore allow for shape comparisons with minimal shape pre-processing. In particular, no registration, mapping, or remeshing is necessary. The discriminatory power of the 2D surface and 3D solid methods is demonstrated on a population of female caudate nuclei (a subcortical gray matter structure of the brain, involved in memory function, emotion processing, and learning) of normal control subjects and of subjects with schizotypal personality disorder. The behavior and properties of the Laplace-Beltrami eigenvalues and -functions are discussed extensively for both the Dirichlet and Neumann boundary condition showing advantages of the Neumann vs. the Dirichlet spectra in 3D. Furthermore, topological analyses employing the Morse-Smale complex (on the surfaces) and the Reeb graph (in the solids) are performed on selected eigenfunctions, yielding shape descriptors, that are capable of localizing geometric properties and detecting shape differences by indirectly registering topological features such as critical points, level sets and integral lines of the gradient field across subjects. The use of these topological features of the Laplace-Beltrami eigenfunctions in 2D and 3D for statistical shape analysis is novel. PMID:20161035

2D net shape weaving for cost effective manufacture of textile reinforced composites

NASA Astrophysics Data System (ADS)

Vo, D. M. P.; Kern, M.; Hoffmann, G.; Cherif, C.

2017-10-01

Despite significant weight and performance advantages over metal parts, the today’s demand for fibre-reinforced polymer composites (FRPC) has been limited mainly by their large manufacturing cost. The combination of dry textile preforms and low-cost consolidation processes such as resin transfer molding (RTM) has been appointed as a promising approach to low-cost FRPC manufacture. At the current state of the art, tooling and impregnation technology is well understood whereas preform fabrication technology has not been developed effectively. This paper presents an advanced 2D net shape weaving technology developed with the aim to establish a more cost effective system for the manufacture of dry textile preforms for FRPC. 2D net shape weaving is developed based on open reed weave (ORW) technology and enables the manufacture of 2D contoured woven fabrics with firm edge, so that oversize cutting and hand trimming after molding are no longer required. The introduction of 2D net shape woven fabrics helps to reduce material waste, cycle time and preform manufacturing cost significantly. Furthermore, higher grade of automation in preform fabrication can be achieved.

Programming 2D/3D shape-shifting with hobbyist 3D printers† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7mh00269f

PubMed Central

van Manen, Teunis; Janbaz, Shahram

2017-01-01

Materials and devices with advanced functionalities often need to combine complex 3D shapes with functionality-inducing surface features. Precisely controlled bio-nanopatterns, printed electronic components, and sensors/actuators are all examples of such surface features. However, the vast majority of the refined technologies that are currently available for creating functional surface features work only on flat surfaces. Here we present initially flat constructs that upon triggering by high temperatures change their shape to a pre-programmed 3D shape, thereby enabling the combination of surface-related functionalities with complex 3D shapes. A number of shape-shifting materials have been proposed during the last few years based on various types of advanced technologies. The proposed techniques often require multiple fabrication steps and special materials, while being limited in terms of the 3D shapes they could achieve. The approach presented here is a single-step printing process that requires only a hobbyist 3D printer and inexpensive off-the-shelf materials. It also lends itself to a host of design strategies based on self-folding origami, instability-driven pop-up, and ‘sequential’ shape-shifting to unprecedentedly expand the space of achievable 3D shapes. This combination of simplicity and versatility is a key to widespread applications. PMID:29308207

Effective 3-D shape discrimination survives retinal blur.

PubMed

Norman, J Farley; Beers, Amanda M; Holmin, Jessica S; Boswell, Alexandria M

2010-08-01

A single experiment evaluated observers' ability to visually discriminate 3-D object shape, where the 3-D structure was defined by motion, texture, Lambertian shading, and occluding contours. The observers' vision was degraded to varying degrees by blurring the experimental stimuli, using 2.0-, 2.5-, and 3.0-diopter convex lenses. The lenses reduced the observers' acuity from -0.091 LogMAR (in the no-blur conditions) to 0.924 LogMAR (in the conditions with the most blur; 3.0-diopter lenses). This visual degradation, although producing severe reductions in visual acuity, had only small (but significant) effects on the observers' ability to discriminate 3-D shape. The observers' shape discrimination performance was facilitated by the objects' rotation in depth, regardless of the presence or absence of blur. Our results indicate that accurate global shape discrimination survives a considerable amount of retinal blur.

From Data to Images:. a Shape Based Approach for Fluorescence Tomography

NASA Astrophysics Data System (ADS)

Dorn, O.; Prieto, K. E.

2012-12-01

Fluorescence tomography is treated as a shape reconstruction problem for a coupled system of two linear transport equations in 2D. The shape evolution is designed in order to minimize the least squares data misfit cost functional either in the excitation frequency or in the emission frequency. Furthermore, a level set technique is employed for numerically modelling the evolving shapes. Numerical results are presented which demonstrate the performance of this novel technique in the situation of noisy simulated data in 2D.

Quantitative characterization and comparison of precipitate and grain shape in Nickel -base superalloys using moment invariants

NASA Astrophysics Data System (ADS)

Callahan, Patrick Gregory

A fundamental objective of materials science and engineering is to understand the structure-property-processing-performance relationship. We need to know the true 3-D microstructure of a material to understand certain geometric properties of a material, and thus fulfill this objective. Focused ion beam (FIB) serial sectioning allows us to find the true 3-D microstructure of Ni-base superalloys. Once the true 3-D microstructure is obtained, an accurate quantitative description and characterization of precipitate and/or grain shapes is needed to understand the microstructure and describe it in an unbiased way. In this thesis, second order moment invariants, the shape quotient Q, a convexity measure relating the volume of an object to the volume of its convex hull, V/Vconv, and Gaussian curvature have been used to compare an experimentally observed polycrystalline IN100 microstructure to three synthetic microstructures. The three synthetic microstructures used different shape classes to produce starting grain shapes. The three shape classes are ellipsoids, superellipsoids, and the shapes generated when truncating a cube with an octahedron. The microstructures are compared using a distance measure, the Hellinger distance. The Hellinger distance is used to compare distributions of shape descriptors for the grains in each microstructure. The synthetic microstructure that has the smallest Hellinger distance, and so best matched the experimentally observed microstructure is the microstructure that used superellipsoids as a starting grain shape. While it has the smallest Hellinger distance, and is approaching realistic grain morphologies, the superellipsoidal microstructure is still not realistic. Second order moment invariants, Q, and V/V conv have also been used to characterize the γ' precipitate shapes from four experimental Ru-containing Ni-base superalloys with differences in alloying additions. The superalloys are designated UM-F9, UM-F18, UM-F19, and UM-F22. The different alloying additions in each sample cause differences in lattice misfit and γ' precipitate shape morphology, varying from spherical, to cuboidal, to intermediate morphologies. 3-D datasets from each alloy were collected via automated Focused Ion Beam (FIB) serial sectioning. Digital image processing methods are used to register, clean, and segment the images in each of the datasets in order to digitally reconstruct the microstructures in 3-D. The distributions of the shape descriptors of the γ' precipitates from each microstructure are compared using the Hellinger distance. The Hellinger distance determines if there are quantitative differences in the γ' precipitate morphologies, or if they are the same. It was found that comparing distributions of the second order affine moment invariant Ω 3 with the Hellinger distance is sufficient for recognizing that alloys have different compositions. The secondary γ' precipitate shapes in two Ni-based superalloys, one from a UM-F20 alloy with cuboidal precipitates, and one from a Rene-88 DT alloy with more complex dendritic precipitates, have been decomposed and reconstructed using 3-D Zernike functions, which are orthogonal over the unit ball; they can be used to decompose an arbitrary shape scaled to fit inside an embedding sphere into spherical harmonics. Relatively complex shapes can be decomposed into, and reconstructed from, 3-D Zernike functions. In this thesis we show the 3-D Zernike functions and a method to derive expressions for Zernike moments from the more familiar geometric moments. Then Zernike moment reconstructions up to order 20 of precipitates from the two Ni-base superalloys are presented. The Zernike moment reconstructions were characterized using second order moment invariants, and have yielded good reconstructions of cuboidal precipitates. More orders of Zernike moments may be needed to accurately reconstruct the dendritic precipitates. We also introduce the concept of moment invariant density maps to describe 3-D shapes using 2-D moment invariants. To do this we characterize 2-D sections of a 3-D microstructure using 2-D moment invariants. The statistical distribution of 2-D moment invariants from the sections are compared to a library of density maps produced from different shapes. The sectioning plane is random so each group of particles produces a statistical distribution of 2-D moments that can represent a microstructure. Then we show three example applications: determination of a 3-D shape by computing the Hellinger distance between moment invariant density maps derived from random 2-D section micrographs and the density map database; automated detection and quantification of rafting in cuboidal microstructures; and quantitative comparison of pairs of microstructures.

3D Shape Perception in Posterior Cortical Atrophy: A Visual Neuroscience Perspective

PubMed Central

Gillebert, Céline R.; Schaeverbeke, Jolien; Bastin, Christine; Neyens, Veerle; Bruffaerts, Rose; De Weer, An-Sofie; Seghers, Alexandra; Sunaert, Stefan; Van Laere, Koen; Versijpt, Jan; Vandenbulcke, Mathieu; Salmon, Eric; Todd, James T.; Orban, Guy A.

2015-01-01

Posterior cortical atrophy (PCA) is a rare focal neurodegenerative syndrome characterized by progressive visuoperceptual and visuospatial deficits, most often due to atypical Alzheimer's disease (AD). We applied insights from basic visual neuroscience to analyze 3D shape perception in humans affected by PCA. Thirteen PCA patients and 30 matched healthy controls participated, together with two patient control groups with diffuse Lewy body dementia (DLBD) and an amnestic-dominant phenotype of AD, respectively. The hierarchical study design consisted of 3D shape processing for 4 cues (shading, motion, texture, and binocular disparity) with corresponding 2D and elementary feature extraction control conditions. PCA and DLBD exhibited severe 3D shape-processing deficits and AD to a lesser degree. In PCA, deficient 3D shape-from-shading was associated with volume loss in the right posterior inferior temporal cortex. This region coincided with a region of functional activation during 3D shape-from-shading in healthy controls. In PCA patients who performed the same fMRI paradigm, response amplitude during 3D shape-from-shading was reduced in this region. Gray matter volume in this region also correlated with 3D shape-from-shading in AD. 3D shape-from-disparity in PCA was associated with volume loss slightly more anteriorly in posterior inferior temporal cortex as well as in ventral premotor cortex. The findings in right posterior inferior temporal cortex and right premotor cortex are consistent with neurophysiologically based models of the functional anatomy of 3D shape processing. However, in DLBD, 3D shape deficits rely on mechanisms distinct from inferior temporal structural integrity. SIGNIFICANCE STATEMENT Posterior cortical atrophy (PCA) is a neurodegenerative syndrome characterized by progressive visuoperceptual dysfunction and most often an atypical presentation of Alzheimer's disease (AD) affecting the ventral and dorsal visual streams rather than the medial temporal system. We applied insights from fundamental visual neuroscience to analyze 3D shape perception in PCA. 3D shape-processing deficits were affected beyond what could be accounted for by lower-order processing deficits. For shading and disparity, this was related to volume loss in regions previously implicated in 3D shape processing in the intact human and nonhuman primate brain. Typical amnestic-dominant AD patients also exhibited 3D shape deficits. Advanced visual neuroscience provides insight into the pathogenesis of PCA that also bears relevance for vision in typical AD. PMID:26377458

3D Printed Reversible Shape Changing Components with Stimuli Responsive Materials

PubMed Central

Mao, Yiqi; Ding, Zhen; Yuan, Chao; Ai, Shigang; Isakov, Michael; Wu, Jiangtao; Wang, Tiejun; Dunn, Martin L.; Qi, H. Jerry

2016-01-01

The creation of reversibly-actuating components that alter their shapes in a controllable manner in response to environmental stimuli is a grand challenge in active materials, structures, and robotics. Here we demonstrate a new reversible shape-changing component design concept enabled by 3D printing two stimuli responsive polymers—shape memory polymers and hydrogels—in prescribed 3D architectures. This approach uses the swelling of a hydrogel as the driving force for the shape change, and the temperature-dependent modulus of a shape memory polymer to regulate the time of such shape change. Controlling the temperature and aqueous environment allows switching between two stable configurations – the structures are relatively stiff and can carry load in each – without any mechanical loading and unloading. Specific shape changing scenarios, e.g., based on bending, or twisting in prescribed directions, are enabled via the controlled interplay between the active materials and the 3D printed architectures. The physical phenomena are complex and nonintuitive, and so to help understand the interplay of geometric, material, and environmental stimuli parameters we develop 3D nonlinear finite element models. Finally, we create several 2D and 3D shape changing components that demonstrate the role of key parameters and illustrate the broad application potential of the proposed approach. PMID:27109063

3D Printed Reversible Shape Changing Components with Stimuli Responsive Materials

NASA Astrophysics Data System (ADS)

Mao, Yiqi; Ding, Zhen; Yuan, Chao; Ai, Shigang; Isakov, Michael; Wu, Jiangtao; Wang, Tiejun; Dunn, Martin L.; Qi, H. Jerry

2016-04-01

The creation of reversibly-actuating components that alter their shapes in a controllable manner in response to environmental stimuli is a grand challenge in active materials, structures, and robotics. Here we demonstrate a new reversible shape-changing component design concept enabled by 3D printing two stimuli responsive polymers—shape memory polymers and hydrogels—in prescribed 3D architectures. This approach uses the swelling of a hydrogel as the driving force for the shape change, and the temperature-dependent modulus of a shape memory polymer to regulate the time of such shape change. Controlling the temperature and aqueous environment allows switching between two stable configurations - the structures are relatively stiff and can carry load in each - without any mechanical loading and unloading. Specific shape changing scenarios, e.g., based on bending, or twisting in prescribed directions, are enabled via the controlled interplay between the active materials and the 3D printed architectures. The physical phenomena are complex and nonintuitive, and so to help understand the interplay of geometric, material, and environmental stimuli parameters we develop 3D nonlinear finite element models. Finally, we create several 2D and 3D shape changing components that demonstrate the role of key parameters and illustrate the broad application potential of the proposed approach.

3D shape representation with spatial probabilistic distribution of intrinsic shape keypoints

NASA Astrophysics Data System (ADS)

Ghorpade, Vijaya K.; Checchin, Paul; Malaterre, Laurent; Trassoudaine, Laurent

2017-12-01

The accelerated advancement in modeling, digitizing, and visualizing techniques for 3D shapes has led to an increasing amount of 3D models creation and usage, thanks to the 3D sensors which are readily available and easy to utilize. As a result, determining the similarity between 3D shapes has become consequential and is a fundamental task in shape-based recognition, retrieval, clustering, and classification. Several decades of research in Content-Based Information Retrieval (CBIR) has resulted in diverse techniques for 2D and 3D shape or object classification/retrieval and many benchmark data sets. In this article, a novel technique for 3D shape representation and object classification has been proposed based on analyses of spatial, geometric distributions of 3D keypoints. These distributions capture the intrinsic geometric structure of 3D objects. The result of the approach is a probability distribution function (PDF) produced from spatial disposition of 3D keypoints, keypoints which are stable on object surface and invariant to pose changes. Each class/instance of an object can be uniquely represented by a PDF. This shape representation is robust yet with a simple idea, easy to implement but fast enough to compute. Both Euclidean and topological space on object's surface are considered to build the PDFs. Topology-based geodesic distances between keypoints exploit the non-planar surface properties of the object. The performance of the novel shape signature is tested with object classification accuracy. The classification efficacy of the new shape analysis method is evaluated on a new dataset acquired with a Time-of-Flight camera, and also, a comparative evaluation on a standard benchmark dataset with state-of-the-art methods is performed. Experimental results demonstrate superior classification performance of the new approach on RGB-D dataset and depth data.

[Applications of 2D and 3D landscape pattern indices in landscape pattern analysis of mountainous area at county level].

PubMed

Lu, Chao; Qi, Wei; Li, Le; Sun, Yao; Qin, Tian-Tian; Wang, Na-Na

2012-05-01

Landscape pattern indices are the commonly used tools for the quantitative analysis of landscape pattern. However, the traditional 2D landscape pattern indices neglect the effects of terrain on landscape, existing definite limitations in quantitatively describing the landscape patterns in mountains areas. Taking the Qixia City, a typical mountainous and hilly region in Shandong Province of East China, as a case, this paper compared the differences between 2D and 3D landscape pattern indices in quantitatively describing the landscape patterns and their dynamic changes in mountainous areas. On the basis of terrain structure analysis, a set of landscape pattern indices were selected, including area and density (class area and mean patch size), edge and shape (edge density, landscape shape index, and fractal dimension of mean patch), diversity (Shannon's diversity index and evenness index) , and gathering and spread (contagion index). There existed obvious differences between the 3D class area, mean patch area, and edge density and the corresponding 2D indices, but no significant differences between the 3D landscape shape index, fractal dimension of mean patch, and Shannon' s diversity index and evenness index and the corresponding 2D indices. The 3D contagion index and 2D contagion index had no difference. Because the 3D landscape pattern indices were calculated by using patch surface area and surface perimeter whereas the 2D landscape pattern indices were calculated by adopting patch projective area and projective perimeter, the 3D landscape pattern indices could be relative accurate and efficient in describing the landscape area, density and borderline, in mountainous areas. However, there were no distinct differences in describing landscape shape, diversity, and gathering and spread between the 3D and 2D landscape pattern indices. Generally, by introducing 3D landscape pattern indices to topographic pattern, the description of landscape pattern and its dynamic change would be relatively accurate.

The relation between atrial septal defect shape, diameter, and area using three-dimensional transoesophageal echocardiography and balloon sizing during percutaneous closure in children.

PubMed

Hascoet, Sébastien; Hadeed, Khaled; Marchal, Pauline; Dulac, Yves; Alacoque, Xavier; Heitz, Francois; Acar, Philippe

2015-07-01

A trans-catheter closure of an atrial septal defect (ASD) is efficient. Balloon sizing (BS) during the catheterization leads to an overestimation of ASD size. Three-dimensional transoesophageal echocardiography (3D-TEE) allows the ASD morphology to be assessed comprehensively. The aim of this study was to assess the relationships between the shape and the measurements of ASDs by 2D-, 3D-TEE, and BS in children. Thirty children who underwent percutaneous closures of a single ASD were enrolled. ASD diameters were measured by 2D-transthoracic echocardiography (TTE), 2D-TEE, 3D-TEE and compared with BS. The ASD area was measured on 3D-TEE images after multi-planar reconstruction. ASD was estimated as round or oval on 3D-TEE 'en-face' view. 2D-TTE, 2D-TEE, and 3D-TEE(max) ASD diameters were well correlated with BS (r = 0.75; 0.80, and 0.85, respectively). Mean diameters were all significantly smaller than the mean BS. The mean difference between the balloon area and 3D-TEE area was 1.6 ± 1.4 cm(2) (P < 0.0001). The mean difference between BS and 3D-TEE(max) diameters was higher in round ASDs than in oval ASDs (4.0 ± 3.3 vs. 1.1 ± 3.3, P = 0.02). With multivariate linear regression analysis, two formulas were built to predict BS. The first model was BS = 1.07 × 3D-TEE(max)- 3.1 × ASDshape + 3. The ASD shape was 0 for round and 1 for oval ASDs. A second model was BS = 4.5 × ASDarea + 11.5. The ASD shape is accurately estimated by 3D-TEE and influences the relationship between echocardiographic measurements and BS. The ASD shape, its maximal diameter and the area assessed by 3D-TEE may be sufficient to determine the device size without BS in children. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2015. For permissions please email: journals.permissions@oup.com.

Learning Spatially-Smooth Mappings in Non-Rigid Structure from Motion

PubMed Central

Hamsici, Onur C.; Gotardo, Paulo F.U.; Martinez, Aleix M.

2013-01-01

Non-rigid structure from motion (NRSFM) is a classical underconstrained problem in computer vision. A common approach to make NRSFM more tractable is to constrain 3D shape deformation to be smooth over time. This constraint has been used to compress the deformation model and reduce the number of unknowns that are estimated. However, temporal smoothness cannot be enforced when the data lacks temporal ordering and its benefits are less evident when objects undergo abrupt deformations. This paper proposes a new NRSFM method that addresses these problems by considering deformations as spatial variations in shape space and then enforcing spatial, rather than temporal, smoothness. This is done by modeling each 3D shape coefficient as a function of its input 2D shape. This mapping is learned in the feature space of a rotation invariant kernel, where spatial smoothness is intrinsically defined by the mapping function. As a result, our model represents shape variations compactly using custom-built coefficient bases learned from the input data, rather than a pre-specified set such as the Discrete Cosine Transform. The resulting kernel-based mapping is a by-product of the NRSFM solution and leads to another fundamental advantage of our approach: for a newly observed 2D shape, its 3D shape is recovered by simply evaluating the learned function. PMID:23946937

Learning Spatially-Smooth Mappings in Non-Rigid Structure from Motion.

PubMed

Hamsici, Onur C; Gotardo, Paulo F U; Martinez, Aleix M

2012-01-01

Non-rigid structure from motion (NRSFM) is a classical underconstrained problem in computer vision. A common approach to make NRSFM more tractable is to constrain 3D shape deformation to be smooth over time. This constraint has been used to compress the deformation model and reduce the number of unknowns that are estimated. However, temporal smoothness cannot be enforced when the data lacks temporal ordering and its benefits are less evident when objects undergo abrupt deformations. This paper proposes a new NRSFM method that addresses these problems by considering deformations as spatial variations in shape space and then enforcing spatial, rather than temporal, smoothness. This is done by modeling each 3D shape coefficient as a function of its input 2D shape. This mapping is learned in the feature space of a rotation invariant kernel, where spatial smoothness is intrinsically defined by the mapping function. As a result, our model represents shape variations compactly using custom-built coefficient bases learned from the input data, rather than a pre-specified set such as the Discrete Cosine Transform. The resulting kernel-based mapping is a by-product of the NRSFM solution and leads to another fundamental advantage of our approach: for a newly observed 2D shape, its 3D shape is recovered by simply evaluating the learned function.

Orthogonal Procrustes Analysis for Dictionary Learning in Sparse Linear Representation

PubMed Central

Grossi, Giuliano; Lin, Jianyi

2017-01-01

In the sparse representation model, the design of overcomplete dictionaries plays a key role for the effectiveness and applicability in different domains. Recent research has produced several dictionary learning approaches, being proven that dictionaries learnt by data examples significantly outperform structured ones, e.g. wavelet transforms. In this context, learning consists in adapting the dictionary atoms to a set of training signals in order to promote a sparse representation that minimizes the reconstruction error. Finding the best fitting dictionary remains a very difficult task, leaving the question still open. A well-established heuristic method for tackling this problem is an iterative alternating scheme, adopted for instance in the well-known K-SVD algorithm. Essentially, it consists in repeating two stages; the former promotes sparse coding of the training set and the latter adapts the dictionary to reduce the error. In this paper we present R-SVD, a new method that, while maintaining the alternating scheme, adopts the Orthogonal Procrustes analysis to update the dictionary atoms suitably arranged into groups. Comparative experiments on synthetic data prove the effectiveness of R-SVD with respect to well known dictionary learning algorithms such as K-SVD, ILS-DLA and the online method OSDL. Moreover, experiments on natural data such as ECG compression, EEG sparse representation, and image modeling confirm R-SVD’s robustness and wide applicability. PMID:28103283

Pose-oblivious shape signature.

PubMed

Gal, Ran; Shamir, Ariel; Cohen-Or, Daniel

2007-01-01

A 3D shape signature is a compact representation for some essence of a shape. Shape signatures are commonly utilized as a fast indexing mechanism for shape retrieval. Effective shape signatures capture some global geometric properties which are scale, translation, and rotation invariant. In this paper, we introduce an effective shape signature which is also pose-oblivious. This means that the signature is also insensitive to transformations which change the pose of a 3D shape such as skeletal articulations. Although some topology-based matching methods can be considered pose-oblivious as well, our new signature retains the simplicity and speed of signature indexing. Moreover, contrary to topology-based methods, the new signature is also insensitive to the topology change of the shape, allowing us to match similar shapes with different genus. Our shape signature is a 2D histogram which is a combination of the distribution of two scalar functions defined on the boundary surface of the 3D shape. The first is a definition of a novel function called the local-diameter function. This function measures the diameter of the 3D shape in the neighborhood of each vertex. The histogram of this function is an informative measure of the shape which is insensitive to pose changes. The second is the centricity function that measures the average geodesic distance from one vertex to all other vertices on the mesh. We evaluate and compare a number of methods for measuring the similarity between two signatures, and demonstrate the effectiveness of our pose-oblivious shape signature within a 3D search engine application for different databases containing hundreds of models.

Realistic Analytical Polyhedral MRI Phantoms

PubMed Central

Ngo, Tri M.; Fung, George S. K.; Han, Shuo; Chen, Min; Prince, Jerry L.; Tsui, Benjamin M. W.; McVeigh, Elliot R.; Herzka, Daniel A.

2015-01-01

Purpose Analytical phantoms have closed form Fourier transform expressions and are used to simulate MRI acquisitions. Existing 3D analytical phantoms are unable to accurately model shapes of biomedical interest. It is demonstrated that polyhedral analytical phantoms have closed form Fourier transform expressions and can accurately represent 3D biomedical shapes. Theory The derivations of the Fourier transform of a polygon and polyhedron are presented. Methods The Fourier transform of a polyhedron was implemented and its accuracy in representing faceted and smooth surfaces was characterized. Realistic anthropomorphic polyhedral brain and torso phantoms were constructed and their use in simulated 3D/2D MRI acquisitions was described. Results Using polyhedra, the Fourier transform of faceted shapes can be computed to within machine precision. Smooth surfaces can be approximated with increasing accuracy by increasing the number of facets in the polyhedron; the additional accumulated numerical imprecision of the Fourier transform of polyhedra with many faces remained small. Simulations of 3D/2D brain and 2D torso cine acquisitions produced realistic reconstructions free of high frequency edge aliasing as compared to equivalent voxelized/rasterized phantoms. Conclusion Analytical polyhedral phantoms are easy to construct and can accurately simulate shapes of biomedical interest. PMID:26479724

3D Shape Perception in Posterior Cortical Atrophy: A Visual Neuroscience Perspective.

PubMed

Gillebert, Céline R; Schaeverbeke, Jolien; Bastin, Christine; Neyens, Veerle; Bruffaerts, Rose; De Weer, An-Sofie; Seghers, Alexandra; Sunaert, Stefan; Van Laere, Koen; Versijpt, Jan; Vandenbulcke, Mathieu; Salmon, Eric; Todd, James T; Orban, Guy A; Vandenberghe, Rik

2015-09-16

Posterior cortical atrophy (PCA) is a rare focal neurodegenerative syndrome characterized by progressive visuoperceptual and visuospatial deficits, most often due to atypical Alzheimer's disease (AD). We applied insights from basic visual neuroscience to analyze 3D shape perception in humans affected by PCA. Thirteen PCA patients and 30 matched healthy controls participated, together with two patient control groups with diffuse Lewy body dementia (DLBD) and an amnestic-dominant phenotype of AD, respectively. The hierarchical study design consisted of 3D shape processing for 4 cues (shading, motion, texture, and binocular disparity) with corresponding 2D and elementary feature extraction control conditions. PCA and DLBD exhibited severe 3D shape-processing deficits and AD to a lesser degree. In PCA, deficient 3D shape-from-shading was associated with volume loss in the right posterior inferior temporal cortex. This region coincided with a region of functional activation during 3D shape-from-shading in healthy controls. In PCA patients who performed the same fMRI paradigm, response amplitude during 3D shape-from-shading was reduced in this region. Gray matter volume in this region also correlated with 3D shape-from-shading in AD. 3D shape-from-disparity in PCA was associated with volume loss slightly more anteriorly in posterior inferior temporal cortex as well as in ventral premotor cortex. The findings in right posterior inferior temporal cortex and right premotor cortex are consistent with neurophysiologically based models of the functional anatomy of 3D shape processing. However, in DLBD, 3D shape deficits rely on mechanisms distinct from inferior temporal structural integrity. Posterior cortical atrophy (PCA) is a neurodegenerative syndrome characterized by progressive visuoperceptual dysfunction and most often an atypical presentation of Alzheimer's disease (AD) affecting the ventral and dorsal visual streams rather than the medial temporal system. We applied insights from fundamental visual neuroscience to analyze 3D shape perception in PCA. 3D shape-processing deficits were affected beyond what could be accounted for by lower-order processing deficits. For shading and disparity, this was related to volume loss in regions previously implicated in 3D shape processing in the intact human and nonhuman primate brain. Typical amnestic-dominant AD patients also exhibited 3D shape deficits. Advanced visual neuroscience provides insight into the pathogenesis of PCA that also bears relevance for vision in typical AD. Copyright © 2015 Gillebert, Schaeverbeke et al.

Weighted regularized statistical shape space projection for breast 3D model reconstruction.

PubMed

Ruiz, Guillermo; Ramon, Eduard; García, Jaime; Sukno, Federico M; Ballester, Miguel A González

2018-07-01

The use of 3D imaging has increased as a practical and useful tool for plastic and aesthetic surgery planning. Specifically, the possibility of representing the patient breast anatomy in a 3D shape and simulate aesthetic or plastic procedures is a great tool for communication between surgeon and patient during surgery planning. For the purpose of obtaining the specific 3D model of the breast of a patient, model-based reconstruction methods can be used. In particular, 3D morphable models (3DMM) are a robust and widely used method to perform 3D reconstruction. However, if additional prior information (i.e., known landmarks) is combined with the 3DMM statistical model, shape constraints can be imposed to improve the 3DMM fitting accuracy. In this paper, we present a framework to fit a 3DMM of the breast to two possible inputs: 2D photos and 3D point clouds (scans). Our method consists in a Weighted Regularized (WR) projection into the shape space. The contribution of each point in the 3DMM shape is weighted allowing to assign more relevance to those points that we want to impose as constraints. Our method is applied at multiple stages of the 3D reconstruction process. Firstly, it can be used to obtain a 3DMM initialization from a sparse set of 3D points. Additionally, we embed our method in the 3DMM fitting process in which more reliable or already known 3D points or regions of points, can be weighted in order to preserve their shape information. The proposed method has been tested in two different input settings: scans and 2D pictures assessing both reconstruction frameworks with very positive results. Copyright © 2018 Elsevier B.V. All rights reserved.

3D shape recovery from image focus using gray level co-occurrence matrix

NASA Astrophysics Data System (ADS)

Mahmood, Fahad; Munir, Umair; Mehmood, Fahad; Iqbal, Javaid

2018-04-01

Recovering a precise and accurate 3-D shape of the target object utilizing robust 3-D shape recovery algorithm is an ultimate objective of computer vision community. Focus measure algorithm plays an important role in this architecture which convert the color values of each pixel of the acquired 2-D image dataset into corresponding focus values. After convolving the focus measure filter with the input 2-D image dataset, a 3-D shape recovery approach is applied which will recover the depth map. In this document, we are concerned with proposing Gray Level Co-occurrence Matrix along with its statistical features for computing the focus information of the image dataset. The Gray Level Co-occurrence Matrix quantifies the texture present in the image using statistical features and then applies joint probability distributive function of the gray level pairs of the input image. Finally, we quantify the focus value of the input image using Gaussian Mixture Model. Due to its little computational complexity, sharp focus measure curve, robust to random noise sources and accuracy, it is considered as superior alternative to most of recently proposed 3-D shape recovery approaches. This algorithm is deeply investigated on real image sequences and synthetic image dataset. The efficiency of the proposed scheme is also compared with the state of art 3-D shape recovery approaches. Finally, by means of two global statistical measures, root mean square error and correlation, we claim that this approach -in spite of simplicity generates accurate results.

Effect of pore architecture on oxygen diffusion in 3D scaffolds for tissue engineering.

PubMed

Ahn, Geunseon; Park, Jeong Hun; Kang, Taeyun; Lee, Jin Woo; Kang, Hyun-Wook; Cho, Dong-Woo

2010-10-01

The aim of this study was to maximize oxygen diffusion within a three-dimensional scaffold in order to improve cell viability and proliferation. To evaluate the effect of pore architecture on oxygen diffusion, we designed a regular channel shape with uniform diameter, referred to as cylinder shaped, and a new channel shape with a channel diameter gradient, referred to as cone shaped. A numerical analysis predicted higher oxygen concentration in the cone-shaped channels than in the cylinder-shaped channels, throughout the scaffold. To confirm these numerical results, we examined cell proliferation and viability in 2D constructs and 3D scaffolds. Cell culture experiments revealed that cell proliferation and viability were superior in the constructs and scaffolds with cone-shaped channels.

Structural stability of posterior retainer design for resin-bonded prostheses: a 3D finite element study.

PubMed

Lin, Jie; Zheng, Zhiqiang; Shinya, Akikazu; Matinlinna, Jukka Pekka; Botelho, Michael George; Shinya, Akiyoshi

2015-09-01

The purpose of this in vitro study was to compare the stress distribution and natural frequency of different shape and thickness retainer designs for maxillary posterior resin-bonded prostheses using finite element (FE) method. A 3D FE model of a three unit posterior resin-bonded prosthesis analysis model was generated. Three different shaped retainer designs, viz. C-shaped (three axial surface wraparounds), D-shaped (three axial surface wraparounds with central groove) and O-shaped (360° wraparounds), and three different thicknesses, viz., 0.4, 0.8, and 1.2 mm, resin-bonded prostheses were used in this study. The resin-bonded prosthesis analysis model was imported into an FE analysis software (ANSYS 10.0, ANSYS, USA) and attribution of material properties. The nodes at the bottom surface of the roots were assigned fixed zero displacement in the three spatial dimensions. A simulated angle of 45° loading of a 100 N force was applied to the node of the pontic lingual cusp surface. The stress distributions and corresponding natural frequencies were analyzed and resolved. The C-shaped retainer for 0.4 mm thickness recorded the greatest von Mises stresses of 71.4 MPa for all three groups. C-shaped, D-shaped and O-shaped retainer presented natural frequencies 3,988, 7,754, and 10,494 Hz, respectively. D-shaped retainer and O-shaped retainer increased natural frequencies and structural rigidity over the traditional C-shaped retainer. The maximum von Mises stresses values of the remaining tooth and prosthesis decreased with greater retainer thickness. D-shaped retainer and O-shaped retainer increased natural frequencies and structural rigidity over the traditional C-shaped retainer.

Removing Shape-Preserving Transformations in Square-Root Elastic (SRE) Framework for Shape Analysis of Curves

PubMed Central

Joshi, Shantanu H.; Klassen, Eric; Srivastava, Anuj; Jermyn, Ian

2011-01-01

This paper illustrates and extends an efficient framework, called the square-root-elastic (SRE) framework, for studying shapes of closed curves, that was first introduced in [2]. This framework combines the strengths of two important ideas - elastic shape metric and path-straightening methods - for finding geodesics in shape spaces of curves. The elastic metric allows for optimal matching of features between curves while path-straightening ensures that the algorithm results in geodesic paths. This paper extends this framework by removing two important shape preserving transformations: rotations and re-parameterizations, by forming quotient spaces and constructing geodesics on these quotient spaces. These ideas are demonstrated using experiments involving 2D and 3D curves. PMID:21738385

The grasshopper problem

NASA Astrophysics Data System (ADS)

Goulko, Olga; Kent, Adrian

2017-11-01

We introduce and physically motivate the following problem in geometric combinatorics, originally inspired by analysing Bell inequalities. A grasshopper lands at a random point on a planar lawn of area 1. It then jumps once, a fixed distance d, in a random direction. What shape should the lawn be to maximize the chance that the grasshopper remains on the lawn after jumping? We show that, perhaps surprisingly, a disc-shaped lawn is not optimal for any d>0. We investigate further by introducing a spin model whose ground state corresponds to the solution of a discrete version of the grasshopper problem. Simulated annealing and parallel tempering searches are consistent with the hypothesis that, for d<π-1/2, the optimal lawn resembles a cogwheel with n cogs, where the integer n is close to π (arcsin⁡(√{π }d / 2 )) -1. We find transitions to other shapes for d ≳π-1 / 2.

Learning Weight Uncertainty with Stochastic Gradient MCMC for Shape Classification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Chunyuan; Stevens, Andrew J.; Chen, Changyou

2016-08-10

Learning the representation of shape cues in 2D & 3D objects for recognition is a fundamental task in computer vision. Deep neural networks (DNNs) have shown promising performance on this task. Due to the large variability of shapes, accurate recognition relies on good estimates of model uncertainty, ignored in traditional training of DNNs, typically learned via stochastic optimization. This paper leverages recent advances in stochastic gradient Markov Chain Monte Carlo (SG-MCMC) to learn weight uncertainty in DNNs. It yields principled Bayesian interpretations for the commonly used Dropout/DropConnect techniques and incorporates them into the SG-MCMC framework. Extensive experiments on 2D &more » 3D shape datasets and various DNN models demonstrate the superiority of the proposed approach over stochastic optimization. Our approach yields higher recognition accuracy when used in conjunction with Dropout and Batch-Normalization.« less

A new method for 3D thinning of hybrid shaped porous media using artificial intelligence. Application to trabecular bone.

PubMed

Jennane, Rachid; Aufort, Gabriel; Benhamou, Claude Laurent; Ceylan, Murat; Ozbay, Yüksel; Ucan, Osman Nuri

2012-04-01

Curve and surface thinning are widely-used skeletonization techniques for modeling objects in three dimensions. In the case of disordered porous media analysis, however, neither is really efficient since the internal geometry of the object is usually composed of both rod and plate shapes. This paper presents an alternative to compute a hybrid shape-dependent skeleton and its application to porous media. The resulting skeleton combines 2D surfaces and 1D curves to represent respectively the plate-shaped and rod-shaped parts of the object. For this purpose, a new technique based on neural networks is proposed: cascade combinations of complex wavelet transform (CWT) and complex-valued artificial neural network (CVANN). The ability of the skeleton to characterize hybrid shaped porous media is demonstrated on a trabecular bone sample. Results show that the proposed method achieves high accuracy rates about 99.78%-99.97%. Especially, CWT (2nd level)-CVANN structure converges to optimum results as high accuracy rate-minimum time consumption.

Interfacing 3D micro/nanochannels with a branch-shaped reservoir enhances fluid and mass transport

NASA Astrophysics Data System (ADS)

Kumar, Prasoon; Gandhi, Prasanna S.; Majumder, Mainak

2017-01-01

Three-dimensional (3D) micro/nanofluidic devices can accelerate progress in numerous fields such as tissue engineering, drug delivery, self-healing and cooling devices. However, efficient connections between networks of micro/nanochannels and external fluidic ports are key to successful applications of 3D micro/nanofluidic devices. Therefore, in this work, the extent of the role of reservoir geometry in interfacing with vascular (micro/nanochannel) networks, and in the enabling of connections with external fluidic ports while maintaining the compactness of devices, has been experimentally and theoretically investigated. A statistical modelling suggested that a branch-shaped reservoir demonstrates enhanced interfacing with vascular networks when compared to other regular geometries of reservoirs. Time-lapse dye flow experiments by capillary action through fabricated 3D micro/nanofluidic devices confirmed the connectivity of branch-shaped reservoirs with micro/nanochannel networks in fluidic devices. This demonstrated a ~2.2-fold enhancement of the volumetric flow rate in micro/nanofluidic networks when interfaced to branch-shaped reservoirs over rectangular reservoirs. The enhancement is due to a ~2.8-fold increase in the perimeter of the reservoirs. In addition, the mass transfer experiments exhibited a ~1.7-fold enhancement in solute flux across 3D micro/nanofluidic devices that interfaced with branch-shaped reservoirs when compared to rectangular reservoirs. The fabrication of 3D micro/nanofluidic devices and their efficient interfacing through branch-shaped reservoirs to an external fluidic port can potentially enable their use in complex applications, in which enhanced surface-to-volume interactions are desirable.

Automated Quantification and Integrative Analysis of 2D and 3D Mitochondrial Shape and Network Properties

PubMed Central

Nikolaisen, Julie; Nilsson, Linn I. H.; Pettersen, Ina K. N.; Willems, Peter H. G. M.; Lorens, James B.; Koopman, Werner J. H.; Tronstad, Karl J.

2014-01-01

Mitochondrial morphology and function are coupled in healthy cells, during pathological conditions and (adaptation to) endogenous and exogenous stress. In this sense mitochondrial shape can range from small globular compartments to complex filamentous networks, even within the same cell. Understanding how mitochondrial morphological changes (i.e. “mitochondrial dynamics”) are linked to cellular (patho) physiology is currently the subject of intense study and requires detailed quantitative information. During the last decade, various computational approaches have been developed for automated 2-dimensional (2D) analysis of mitochondrial morphology and number in microscopy images. Although these strategies are well suited for analysis of adhering cells with a flat morphology they are not applicable for thicker cells, which require a three-dimensional (3D) image acquisition and analysis procedure. Here we developed and validated an automated image analysis algorithm allowing simultaneous 3D quantification of mitochondrial morphology and network properties in human endothelial cells (HUVECs). Cells expressing a mitochondria-targeted green fluorescence protein (mitoGFP) were visualized by 3D confocal microscopy and mitochondrial morphology was quantified using both the established 2D method and the new 3D strategy. We demonstrate that both analyses can be used to characterize and discriminate between various mitochondrial morphologies and network properties. However, the results from 2D and 3D analysis were not equivalent when filamentous mitochondria in normal HUVECs were compared with circular/spherical mitochondria in metabolically stressed HUVECs treated with rotenone (ROT). 2D quantification suggested that metabolic stress induced mitochondrial fragmentation and loss of biomass. In contrast, 3D analysis revealed that the mitochondrial network structure was dissolved without affecting the amount and size of the organelles. Thus, our results demonstrate that 3D imaging and quantification are crucial for proper understanding of mitochondrial shape and topology in non-flat cells. In summary, we here present an integrative method for unbiased 3D quantification of mitochondrial shape and network properties in mammalian cells. PMID:24988307

GaAs micromachining in the 1 H2SO4:1 H2O2:8 H2O system. From anisotropy to simulation

NASA Astrophysics Data System (ADS)

Tellier, C. R.

2011-02-01

The bulk micromachining on (010), (110) and (111)A GaAs substrates in the 1 H2SO4:1 H2O2:8 H2O system is investigated. Focus is placed on anisotropy of 3D etching shapes with a special emphasis on convex and concave undercuts which are of prime importance in the wet micromachining of mechanical structures. Etched structures exhibit curved contours and more and less rounded sidewalls showing that the anisotropy is of type 2. This anisotropy can be conveniently described by a kinematic and tensorial model. Hence, a database composed of dissolution constants is further determined from experiments. A self-elaborated simulator which works with the proposed database is used to derive theoretical 3D shapes. Simulated shapes agree well with observed shapes of microstructures. The successful simulations open up two important applications for MEMS: CAD of mask patterns and meshing of simulated shapes for FEM simulation tools.

Transferring of speech movements from video to 3D face space.

PubMed

Pei, Yuru; Zha, Hongbin

2007-01-01

We present a novel method for transferring speech animation recorded in low quality videos to high resolution 3D face models. The basic idea is to synthesize the animated faces by an interpolation based on a small set of 3D key face shapes which span a 3D face space. The 3D key shapes are extracted by an unsupervised learning process in 2D video space to form a set of 2D visemes which are then mapped to the 3D face space. The learning process consists of two main phases: 1) Isomap-based nonlinear dimensionality reduction to embed the video speech movements into a low-dimensional manifold and 2) K-means clustering in the low-dimensional space to extract 2D key viseme frames. Our main contribution is that we use the Isomap-based learning method to extract intrinsic geometry of the speech video space and thus to make it possible to define the 3D key viseme shapes. To do so, we need only to capture a limited number of 3D key face models by using a general 3D scanner. Moreover, we also develop a skull movement recovery method based on simple anatomical structures to enhance 3D realism in local mouth movements. Experimental results show that our method can achieve realistic 3D animation effects with a small number of 3D key face models.

An Antenna with Good Electrical Properties and Artistic Shape for Lampshade

NASA Astrophysics Data System (ADS)

Zhou, Chang; Yu, Yang; Ji, Chen

2018-06-01

An improved transparent antenna based on transparent ceramic MgAl2O4 with artistic shape which can be used as lampshade is presented in this paper. A great peak gain and good pattern can be achieved by choosing the property shape and optimizing location of the feed of the antenna. Simulation results indicate that this antenna can achieve return loss >-15dB, peak gain >8 dBi at 2 GHz and 40% relative impedance bandwidth. Both the electrical properties and artistic shape of the antenna are realized and the lampshade which made by MgAl2O4 meets the requirement for communication, decoration and high light transmission.

Image simulation and surface reconstruction of undercut features in atomic force microscopy

NASA Astrophysics Data System (ADS)

Qian, Xiaoping; Villarrubia, John; Tian, Fenglei; Dixson, Ronald

2007-03-01

CD-AFMs (critical dimension atomic force microscopes) are instruments with servo-control of the tip in more than one direction. With appropriately "boot-shaped" or flared tips, such instruments can image vertical or even undercut features. As with any AFM, the image is a dilation of the sample shape with the tip shape. Accurate extraction of the CD requires a correction for the tip effect. Analytical methods to correct images for the tip shape have been available for some time for the traditional (vertical feedback only) AFMs, but were until recently unavailable for instruments with multi-dimensional feedback. Dahlen et al. [J. Vac. Sci. Technol. B23, pp. 2297-2303, (2005)] recently introduced a swept-volume approach, implemented for 2-dimensional (2D) feedback. It permits image simulation and sample reconstruction, techniques previously developed for the traditional instruments, to be extended for the newer tools. We have introduced [X. Qian and J. S. Villarrubia, Ultramicroscopy, in press] an alternative dexel-based method, that does the same in either 2D or 3D. This paper describes the application of this method to sample shapes of interest in semiconductor manufacturing. When the tip shape is known (e.g., by prior measurement using a tip characterizer) a 3D sample surface may be reconstructed from its 3D image. Basing the CD measurement upon such a reconstruction is shown here to remove some measurement artifacts that are not removed (or are incompletely removed) by the existing measurement procedures.

Cord serum 25-hydroxyvitamin D is not associated with cranial anthropometrics in infants up to 6 months of age. An Odense Child Cohort study.

PubMed

Egge, Sissil; Christensen, Nikolas; Lykkedegn, Sine; Jensen, Tina Kold; Christesen, Henrik Thybo

2017-11-11

Skull changes are poorly described in vitamin D insufficiency [serum 25-hydroxyvitamin D (s-25(OH)D) 25-50 nmol/L]. We aimed to investigate factors associated with cranial anthropometrics in infants, especially s-25(OH)D. In infants 2.5-6 months old from the Odense Child Cohort, associations between cord and pregnancy s-25(OH)D and anterior fontanel area (n = 765), head circumference (HC, n = 1776) and head shape (n = 1527) were investigated along with other factors. Age was corrected for preterm birth. The mean (SD) s-25(OH)D in early pregnancy was 65.97 (21.33) nmol/L; late pregnancy 78.61 (27.18) nmol/L; and cord 47.1 (21.7) nmol/L. At median (IQR) age 3.7 (2.5-5.9) months, the fontanel area was 225 (0-1690) mm 2 , and mean (SD) HC was 41.5 (1.5) cm. Asymmetric/flat head shape was present in 846 infants (55.3%). No associations were found between cord, early or late pregnancy s-25(OH)D and any cranial measure by univariate or adjusted analysis. Among significant, independent associations in multivariate analysis, fontanel area was associated inversely with gestational age (GA); HC was associated directly with GA, maternal pre-pregnancy overweight and caesarean section and inversely with smoking; and asymmetrical head shape showed a novel association with male sex: adjusted OR = 1.54 (95% CI 1.25; 1.89), p < 0.001. Other associations with asymmetrical head shape included parity 3+, gestational age and maternal age 30+ years (all protective). In conclusion, neither pregnancy nor cord s-25(OH)D was associated with fontanel size, HC or asymmetrical head shape despite a high prevalence of cord s-25(OH)D < 50 nmol/L. Lower GA was associated with larger fontanel size, lower HC and asymmetrical head shape, and boys more frequently had asymmetrical head shape, probably due to heavier heads.

Estimation of 3D shape from image orientations.

PubMed

Fleming, Roland W; Holtmann-Rice, Daniel; Bülthoff, Heinrich H

2011-12-20

One of the main functions of vision is to estimate the 3D shape of objects in our environment. Many different visual cues, such as stereopsis, motion parallax, and shading, are thought to be involved. One important cue that remains poorly understood comes from surface texture markings. When a textured surface is slanted in 3D relative to the observer, the surface patterns appear compressed in the retinal image, providing potentially important information about 3D shape. What is not known, however, is how the brain actually measures this information from the retinal image. Here, we explain how the key information could be extracted by populations of cells tuned to different orientations and spatial frequencies, like those found in the primary visual cortex. To test this theory, we created stimuli that selectively stimulate such cell populations, by "smearing" (filtering) images of 2D random noise into specific oriented patterns. We find that the resulting patterns appear vividly 3D, and that increasing the strength of the orientation signals progressively increases the sense of 3D shape, even though the filtering we apply is physically inconsistent with what would occur with a real object. This finding suggests we have isolated key mechanisms used by the brain to estimate shape from texture. Crucially, we also find that adapting the visual system's orientation detectors to orthogonal patterns causes unoriented random noise to look like a specific 3D shape. Together these findings demonstrate a crucial role of orientation detectors in the perception of 3D shape.

Surface Topography and Mechanical Strain Promote Keratocyte Phenotype and Extracellular Matrix Formation in a Biomimetic 3D Corneal Model.

PubMed

Zhang, Wei; Chen, Jialin; Backman, Ludvig J; Malm, Adam D; Danielson, Patrik

2017-03-01

The optimal functionality of the native corneal stroma is mainly dependent on the well-ordered arrangement of extracellular matrix (ECM) and the pressurized structure. In order to develop an in vitro corneal model, it is crucial to mimic the in vivo microenvironment of the cornea. In this study, the influence of surface topography and mechanical strain on keratocyte phenotype and ECM formation within a biomimetic 3D corneal model is studied. By modifying the surface topography of materials, it is found that patterned silk fibroin film with 600 grooves mm -1 optimally supports cell alignment and ECM arrangement. Furthermore, treatment with 3% dome-shaped mechanical strain, which resembles the shape and mechanics of native cornea, significantly enhances the expression of keratocyte markers as compared to flat-shaped strain. Accordingly, a biomimetic 3D corneal model, in the form of a collagen-modified, silk fibroin-patterned construct subjected to 3% dome-shaped strain, is created. Compared to traditional 2D cultures, it supports a significantly higher expression of keratocyte and ECM markers, and in conclusion better maintains keratocyte phenotype, alignment, and fusiform cell shape. Therefore, the novel biomimetic 3D corneal model developed in this study serves as a useful in vitro 3D culture model to improve current 2D cultures for corneal studies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints.

PubMed

Awale, Mahendra; Jin, Xian; Reymond, Jean-Louis

2015-01-01

Tools to explore large compound databases in search for analogs of query molecules provide a strategically important support in drug discovery to help identify available analogs of any given reference or hit compound by ligand based virtual screening (LBVS). We recently showed that large databases can be formatted for very fast searching with various 2D-fingerprints using the city-block distance as similarity measure, in particular a 2D-atom pair fingerprint (APfp) and the related category extended atom pair fingerprint (Xfp) which efficiently encode molecular shape and pharmacophores, but do not perceive stereochemistry. Here we investigated related 3D-atom pair fingerprints to enable rapid stereoselective searches in the ZINC database (23.2 million 3D structures). Molecular fingerprints counting atom pairs at increasing through-space distance intervals were designed using either all atoms (16-bit 3DAPfp) or different atom categories (80-bit 3DXfp). These 3D-fingerprints retrieved molecular shape and pharmacophore analogs (defined by OpenEye ROCS scoring functions) of 110,000 compounds from the Cambridge Structural Database with equal or better accuracy than the 2D-fingerprints APfp and Xfp, and showed comparable performance in recovering actives from decoys in the DUD database. LBVS by 3DXfp or 3DAPfp similarity was stereoselective and gave very different analogs when starting from different diastereomers of the same chiral drug. Results were also different from LBVS with the parent 2D-fingerprints Xfp or APfp. 3D- and 2D-fingerprints also gave very different results in LBVS of folded molecules where through-space distances between atom pairs are much shorter than topological distances. 3DAPfp and 3DXfp are suitable for stereoselective searches for shape and pharmacophore analogs of query molecules in large databases. Web-browsers for searching ZINC by 3DAPfp and 3DXfp similarity are accessible at www.gdb.unibe.ch and should provide useful assistance to drug discovery projects. Graphical abstractAtom pair fingerprints based on through-space distances (3DAPfp) provide better shape encoding than atom pair fingerprints based on topological distances (APfp) as measured by the recovery of ROCS shape analogs by fp similarity.

Soft tissue nasal asymmetry as an indicator of orofacial cleft predisposition.

PubMed

Zhang, Charles; Miller, Steven F; Roosenboom, Jasmien; Wehby, George L; Moreno Uribe, Lina M; Hecht, Jacqueline T; Deleyiannis, Frederic W B; Christensen, Kaare; Marazita, Mary L; Weinberg, Seth M

2018-06-01

The biological relatives of offspring with nonsyndromic orofacial clefts have been shown to exhibit distinctive facial features, including excess asymmetry, which are hypothesized to indicate the presence of genetic risk factors. The significance of excess soft tissue nasal asymmetry in at-risk relatives is unclear and was examined in the present study. Our sample included 164 unaffected parents from families with a history of orofacial clefting and 243 adult controls. Geometric morphometric methods were used to analyze the coordinates of 15 nasal landmarks collected from three-dimensional facial surface images. Following generalized Procrustes analysis, Procrustes ANOVA and MANOVA tests were applied to determine the type and magnitude of nasal asymmetry present in each group. Group differences in mean nasal asymmetry were also assessed via permutation testing. We found that nasal asymmetry in both parents and controls was directional in nature, although the magnitude of the asymmetry was greater in parents. This was confirmed with permutation testing, where the mean nasal asymmetry was significantly different (p < .0001) between parents and controls. The asymmetry was greatest for midline structures and the nostrils. When subsets of parents were subsequently analyzed and compared (parents with bilateral vs. unilateral offspring; parents with left vs. right unilateral offspring), each group showed a similar pattern of asymmetry and could not be distinguished statistically. Thus, the side of the unilateral cleft (right vs. left) in offspring was not associated with the direction of the nasal asymmetry in parents. © 2018 Wiley Periodicals, Inc.

Efficient local representations for three-dimensional palmprint recognition

NASA Astrophysics Data System (ADS)

Yang, Bing; Wang, Xiaohua; Yao, Jinliang; Yang, Xin; Zhu, Wenhua

2013-10-01

Palmprints have been broadly used for personal authentication because they are highly accurate and incur low cost. Most previous works have focused on two-dimensional (2-D) palmprint recognition in the past decade. Unfortunately, 2-D palmprint recognition systems lose the shape information when capturing palmprint images. Moreover, such 2-D palmprint images can be easily forged or affected by noise. Hence, three-dimensional (3-D) palmprint recognition has been regarded as a promising way to further improve the performance of palmprint recognition systems. We have developed a simple, but efficient method for 3-D palmprint recognition by using local features. We first utilize shape index representation to describe the geometry of local regions in 3-D palmprint data. Then, we extract local binary pattern and Gabor wavelet features from the shape index image. The two types of complementary features are finally fused at a score level for further improvements. The experimental results on the Hong Kong Polytechnic 3-D palmprint database, which contains 8000 samples from 400 palms, illustrate the effectiveness of the proposed method.

Restoring warped document images through 3D shape modeling.

PubMed

Tan, Chew Lim; Zhang, Li; Zhang, Zheng; Xia, Tao

2006-02-01

Scanning a document page from a thick bound volume often results in two kinds of distortions in the scanned image, i.e., shade along the "spine" of the book and warping in the shade area. In this paper, we propose an efficient restoration method based on the discovery of the 3D shape of a book surface from the shading information in a scanned document image. From a technical point of view, this shape from shading (SFS) problem in real-world environments is characterized by 1) a proximal and moving light source, 2) Lambertian reflection, 3) nonuniform albedo distribution, and 4) document skew. Taking all these factors into account, we first build practical models (consisting of a 3D geometric model and a 3D optical model) for the practical scanning conditions to reconstruct the 3D shape of the book surface. We next restore the scanned document image using this shape based on deshading and dewarping models. Finally, we evaluate the restoration results by comparing our estimated surface shape with the real shape as well as the OCR performance on original and restored document images. The results show that the geometric and photometric distortions are mostly removed and the OCR results are improved markedly.

Review and comparison of non-conventional imaging systems for three-dimensional digitization of transparent objects

NASA Astrophysics Data System (ADS)

Mériaudeau, Fabrice; Rantoson, Rindra; Fofi, David; Stolz, Christophe

2012-04-01

Fashion and design greatly influence the conception of manufactured products which now exhibit complex forms and shapes. Two-dimensional quality control procedures (e.g., shape, textures, colors, and 2D geometry) are progressively being replaced by 3D inspection methods (e.g., 3D geometry, colors, and texture on the 3D shape) therefore requiring a digitization of the object surface. Three dimensional surface acquisition is a topic which has been studied to a large extent, and a significant number of techniques for acquiring 3D shapes has been proposed, leading to a wide range of commercial solutions available on the market. These systems cover a wide range from micro-scale objects such as shape from focus and shape from defocus techniques, to several meter sized objects (time of flight technique). Nevertheless, the use of such systems still encounters difficulties when dealing with non-diffuse (non Lambertian) surfaces as is the case for transparent, semi-transparent, or highly reflective materials (e.g., glass, crystals, plastics, and shiny metals). We review and compare various systems and approaches which were recently developed for 3D digitization of transparent objects.

A comparison of cranial fluctuating asymmetry between the two sexes in a Joseon Dynasty population of Korea.

PubMed

Jung, Hyunwoo; Woo, Eun Jin; Pak, Sunyoung

Cranial fluctuating asymmetry (FA) has been used to examine developmental stress levels in various populations. In bioarchaeological studies, developmental stress can be an important factor for inferring standard of living in a population. However, the crania of a Joseon Dynasty population have only been studied in terms of its morphological characteristics. In this regard, the cranial FA of the two sexes from a Joseon Dynasty population of Korea were compared here for examining their aspects of living conditions in relation to developmental stress and socio-cultural factors. In this study, 77 individuals (39 males and 38 females) who belong to the 15th to the early-20th centuries from Seoul and Gyeonggi province in Korea were investigated. Nineteen three-dimensional landmarks on the vault and basicranium were collected using MicroScribe G2X. The coordinate data were aligned into a common coordinate plane by Procrustes least-squares superimposition. Procrustes ANOVA was adopted to evaluate FA at a population level. The FA of males and females were compared with t-test using SPSS 18. There was statistically insignificant difference in FA between the two sexes in the Joseon Dynasty population. The result was interpreted to reflect both relatively high developmental stress and sex-related discrimination in the population. It was postulated that relatively high developmental stress could increase difference in FA between the two sexes in the prenatal term compared to the postnatal term because sex-related discrimination cannot be practiced before birth and males have lower stress resistance than females. Then, the difference between the two sexes in the cranial FA could be decreased during postnatal development related to sex-related discrimination, resulting in insignificant FA difference of the two sexes in spite of high developmental stress of the Joseon Dynasty population. The results will be useful for comparing and reconstructing living conditions of ancient Korean populations.

3D Simulations of Void collapse in Energetic Materials

NASA Astrophysics Data System (ADS)

Rai, Nirmal Kumar; Udaykumar, H. S.

2017-06-01

Voids present in the microstructure of heterogeneous energetic materials effect the sensitivity towards ignition. It is established that the morphology of voids can play a significant role in sensitivity enhancement of energetic materials. Depending on the void shape, sensitivity can be either increased or decreased under given loading conditions. In the past, effects of different void shapes i.e. triangular, ellipse, cylindrical etc. on the sensitivity of energetic materials have been analyzed. However, most of these studies are performed in 2D and are limited under the plain strain assumption. Axisymmetric studies have also been performed in the past to incorporate the 3D effects, however axisymmetric modeling is limited to only certain geometries i.e. sphere. This work analyzes the effects of various void shapes in three dimensions on the ignition behavior of HMX. Various void shapes are analyzed including spherical, prolate and oblate speheroid oriented at different orientations, etc. Three dimensional void collapse simulations are performed on a single void to quantify the effects void morphology on initiation. A Cartesian grid based Eulerian solver SCIMITAR3D is used to perform the void collapse simulations. Various aspects of void morphology i.e. size, thickness of voids, elongation, orientation etc. are considered to obtain a comprehensive analysis. Also, 2D plane strain calculations are compared with the three dimensional analysis to evaluate the salient differences between 2D and 3D modeling.

Multi-shape active composites by 3D printing of digital shape memory polymers

NASA Astrophysics Data System (ADS)

Wu, Jiangtao; Yuan, Chao; Ding, Zhen; Isakov, Michael; Mao, Yiqi; Wang, Tiejun; Dunn, Martin L.; Qi, H. Jerry

2016-04-01

Recent research using 3D printing to create active structures has added an exciting new dimension to 3D printing technology. After being printed, these active, often composite, materials can change their shape over time; this has been termed as 4D printing. In this paper, we demonstrate the design and manufacture of active composites that can take multiple shapes, depending on the environmental temperature. This is achieved by 3D printing layered composite structures with multiple families of shape memory polymer (SMP) fibers - digital SMPs - with different glass transition temperatures (Tg) to control the transformation of the structure. After a simple single-step thermomechanical programming process, the fiber families can be sequentially activated to bend when the temperature is increased. By tuning the volume fraction of the fibers, bending deformation can be controlled. We develop a theoretical model to predict the deformation behavior for better understanding the phenomena and aiding the design. We also design and print several flat 2D structures that can be programmed to fold and open themselves when subjected to heat. With the advantages of an easy fabrication process and the controllable multi-shape memory effect, the printed SMP composites have a great potential in 4D printing applications.

Multi-shape active composites by 3D printing of digital shape memory polymers.

PubMed

Wu, Jiangtao; Yuan, Chao; Ding, Zhen; Isakov, Michael; Mao, Yiqi; Wang, Tiejun; Dunn, Martin L; Qi, H Jerry

2016-04-13

Recent research using 3D printing to create active structures has added an exciting new dimension to 3D printing technology. After being printed, these active, often composite, materials can change their shape over time; this has been termed as 4D printing. In this paper, we demonstrate the design and manufacture of active composites that can take multiple shapes, depending on the environmental temperature. This is achieved by 3D printing layered composite structures with multiple families of shape memory polymer (SMP) fibers - digital SMPs - with different glass transition temperatures (Tg) to control the transformation of the structure. After a simple single-step thermomechanical programming process, the fiber families can be sequentially activated to bend when the temperature is increased. By tuning the volume fraction of the fibers, bending deformation can be controlled. We develop a theoretical model to predict the deformation behavior for better understanding the phenomena and aiding the design. We also design and print several flat 2D structures that can be programmed to fold and open themselves when subjected to heat. With the advantages of an easy fabrication process and the controllable multi-shape memory effect, the printed SMP composites have a great potential in 4D printing applications.

Multi-shape active composites by 3D printing of digital shape memory polymers

PubMed Central

Wu, Jiangtao; Yuan, Chao; Ding, Zhen; Isakov, Michael; Mao, Yiqi; Wang, Tiejun; Dunn, Martin L.; Qi, H. Jerry

2016-01-01

Recent research using 3D printing to create active structures has added an exciting new dimension to 3D printing technology. After being printed, these active, often composite, materials can change their shape over time; this has been termed as 4D printing. In this paper, we demonstrate the design and manufacture of active composites that can take multiple shapes, depending on the environmental temperature. This is achieved by 3D printing layered composite structures with multiple families of shape memory polymer (SMP) fibers – digital SMPs - with different glass transition temperatures (Tg) to control the transformation of the structure. After a simple single-step thermomechanical programming process, the fiber families can be sequentially activated to bend when the temperature is increased. By tuning the volume fraction of the fibers, bending deformation can be controlled. We develop a theoretical model to predict the deformation behavior for better understanding the phenomena and aiding the design. We also design and print several flat 2D structures that can be programmed to fold and open themselves when subjected to heat. With the advantages of an easy fabrication process and the controllable multi-shape memory effect, the printed SMP composites have a great potential in 4D printing applications. PMID:27071543

Volumetric three-dimensional intravascular ultrasound visualization using shape-based nonlinear interpolation

PubMed Central

2013-01-01

Background Intravascular ultrasound (IVUS) is a standard imaging modality for identification of plaque formation in the coronary and peripheral arteries. Volumetric three-dimensional (3D) IVUS visualization provides a powerful tool to overcome the limited comprehensive information of 2D IVUS in terms of complex spatial distribution of arterial morphology and acoustic backscatter information. Conventional 3D IVUS techniques provide sub-optimal visualization of arterial morphology or lack acoustic information concerning arterial structure due in part to low quality of image data and the use of pixel-based IVUS image reconstruction algorithms. In the present study, we describe a novel volumetric 3D IVUS reconstruction algorithm to utilize IVUS signal data and a shape-based nonlinear interpolation. Methods We developed an algorithm to convert a series of IVUS signal data into a fully volumetric 3D visualization. Intermediary slices between original 2D IVUS slices were generated utilizing the natural cubic spline interpolation to consider the nonlinearity of both vascular structure geometry and acoustic backscatter in the arterial wall. We evaluated differences in image quality between the conventional pixel-based interpolation and the shape-based nonlinear interpolation methods using both virtual vascular phantom data and in vivo IVUS data of a porcine femoral artery. Volumetric 3D IVUS images of the arterial segment reconstructed using the two interpolation methods were compared. Results In vitro validation and in vivo comparative studies with the conventional pixel-based interpolation method demonstrated more robustness of the shape-based nonlinear interpolation algorithm in determining intermediary 2D IVUS slices. Our shape-based nonlinear interpolation demonstrated improved volumetric 3D visualization of the in vivo arterial structure and more realistic acoustic backscatter distribution compared to the conventional pixel-based interpolation method. Conclusions This novel 3D IVUS visualization strategy has the potential to improve ultrasound imaging of vascular structure information, particularly atheroma determination. Improved volumetric 3D visualization with accurate acoustic backscatter information can help with ultrasound molecular imaging of atheroma component distribution. PMID:23651569

Kinematics of flagellar swimming in Euglena gracilis: Helical trajectories and flagellar shapes.

PubMed

Rossi, Massimiliano; Cicconofri, Giancarlo; Beran, Alfred; Noselli, Giovanni; DeSimone, Antonio

2017-12-12

The flagellar swimming of euglenids, which are propelled by a single anterior flagellum, is characterized by a generalized helical motion. The 3D nature of this swimming motion, which lacks some of the symmetries enjoyed by more common model systems, and the complex flagellar beating shapes that power it make its quantitative description challenging. In this work, we provide a quantitative, 3D, highly resolved reconstruction of the swimming trajectories and flagellar shapes of specimens of Euglena gracilis We achieved this task by using high-speed 2D image recordings taken with a conventional inverted microscope combined with a precise characterization of the helical motion of the cell body to lift the 2D data to 3D trajectories. The propulsion mechanism is discussed. Our results constitute a basis for future biophysical research on a relatively unexplored type of eukaryotic flagellar movement. Copyright © 2017 the Author(s). Published by PNAS.

3D shape recovery from image focus using Gabor features

NASA Astrophysics Data System (ADS)

Mahmood, Fahad; Mahmood, Jawad; Zeb, Ayesha; Iqbal, Javaid

2018-04-01

Recovering an accurate and precise depth map from a set of acquired 2-D image dataset of the target object each having different focus information is an ultimate goal of 3-D shape recovery. Focus measure algorithm plays an important role in this architecture as it converts the corresponding color value information into focus information which will be then utilized for recovering depth map. This article introduces Gabor features as focus measure approach for recovering depth map from a set of 2-D images. Frequency and orientation representation of Gabor filter features is similar to human visual system and normally applied for texture representation. Due to its little computational complexity, sharp focus measure curve, robust to random noise sources and accuracy, it is considered as superior alternative to most of recently proposed 3-D shape recovery approaches. This algorithm is deeply investigated on real image sequences and synthetic image dataset. The efficiency of the proposed scheme is also compared with the state of art 3-D shape recovery approaches. Finally, by means of two global statistical measures, root mean square error and correlation, we claim that this approach, in spite of simplicity, generates accurate results.

Implicit Boundary Integral Methods for the Helmholtz Equation in Exterior Domains

DTIC Science & Technology

2016-06-01

1 2 Figure 3.3: (Left) The “Kite shape. Right: The bean shape. The interface is the zero set of φ(x, y, z) = 9(1.6x+ ( y 1.6 )2)2 + ( y 1.5 )2 + ( z...1.5 )2 − 10. 3.4 Scattering in three dimensions by a “ Bean ” shape We test on a non-convex shape in 3D as shown in figure 3.3, the bean shape. The...solutions computed by EIBIM and IBIM using different mesh sizes. The scattering surface is the bean shape shown in Figure (3.3). k = 1, 0 = √ ∆x. Evaluated

Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis.

PubMed

Smola, Matthew J; Rice, Greggory M; Busan, Steven; Siegfried, Nathan A; Weeks, Kevin M

2015-11-01

Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistries exploit small electrophilic reagents that react with 2'-hydroxyl groups to interrogate RNA structure at single-nucleotide resolution. Mutational profiling (MaP) identifies modified residues by using reverse transcriptase to misread a SHAPE-modified nucleotide and then counting the resulting mutations by massively parallel sequencing. The SHAPE-MaP approach measures the structure of large and transcriptome-wide systems as accurately as can be done for simple model RNAs. This protocol describes the experimental steps, implemented over 3 d, that are required to perform SHAPE probing and to construct multiplexed SHAPE-MaP libraries suitable for deep sequencing. Automated processing of MaP sequencing data is accomplished using two software packages. ShapeMapper converts raw sequencing files into mutational profiles, creates SHAPE reactivity plots and provides useful troubleshooting information. SuperFold uses these data to model RNA secondary structures, identify regions with well-defined structures and visualize probable and alternative helices, often in under 1 d. SHAPE-MaP can be used to make nucleotide-resolution biophysical measurements of individual RNA motifs, rare components of complex RNA ensembles and entire transcriptomes.

A Deformable Generic 3D Model of Haptoral Anchor of Monogenean

PubMed Central

Teo, Bee Guan; Dhillon, Sarinder Kaur; Lim, Lee Hong Susan

2013-01-01

In this paper, a digital 3D model which allows for visualisation in three dimensions and interactive manipulation is explored as a tool to help us understand the structural morphology and elucidate the functions of morphological structures of fragile microorganisms which defy live studies. We developed a deformable generic 3D model of haptoral anchor of dactylogyridean monogeneans that can subsequently be deformed into different desired anchor shapes by using direct manipulation deformation technique. We used point primitives to construct the rectangular building blocks to develop our deformable 3D model. Point primitives are manually marked on a 2D illustration of an anchor on a Cartesian graph paper and a set of Cartesian coordinates for each point primitive is manually extracted from the graph paper. A Python script is then written in Blender to construct 3D rectangular building blocks based on the Cartesian coordinates. The rectangular building blocks are stacked on top or by the side of each other following their respective Cartesian coordinates of point primitive. More point primitives are added at the sites in the 3D model where more structural variations are likely to occur, in order to generate complex anchor structures. We used Catmull-Clark subdivision surface modifier to smoothen the surface and edge of the generic 3D model to obtain a smoother and more natural 3D shape and antialiasing option to reduce the jagged edges of the 3D model. This deformable generic 3D model can be deformed into different desired 3D anchor shapes through direct manipulation deformation technique by aligning the vertices (pilot points) of the newly developed deformable generic 3D model onto the 2D illustrations of the desired shapes and moving the vertices until the desire 3D shapes are formed. In this generic 3D model all the vertices present are deployed for displacement during deformation. PMID:24204903

A deformable generic 3D model of haptoral anchor of Monogenean.

PubMed

Teo, Bee Guan; Dhillon, Sarinder Kaur; Lim, Lee Hong Susan

2013-01-01

In this paper, a digital 3D model which allows for visualisation in three dimensions and interactive manipulation is explored as a tool to help us understand the structural morphology and elucidate the functions of morphological structures of fragile microorganisms which defy live studies. We developed a deformable generic 3D model of haptoral anchor of dactylogyridean monogeneans that can subsequently be deformed into different desired anchor shapes by using direct manipulation deformation technique. We used point primitives to construct the rectangular building blocks to develop our deformable 3D model. Point primitives are manually marked on a 2D illustration of an anchor on a Cartesian graph paper and a set of Cartesian coordinates for each point primitive is manually extracted from the graph paper. A Python script is then written in Blender to construct 3D rectangular building blocks based on the Cartesian coordinates. The rectangular building blocks are stacked on top or by the side of each other following their respective Cartesian coordinates of point primitive. More point primitives are added at the sites in the 3D model where more structural variations are likely to occur, in order to generate complex anchor structures. We used Catmull-Clark subdivision surface modifier to smoothen the surface and edge of the generic 3D model to obtain a smoother and more natural 3D shape and antialiasing option to reduce the jagged edges of the 3D model. This deformable generic 3D model can be deformed into different desired 3D anchor shapes through direct manipulation deformation technique by aligning the vertices (pilot points) of the newly developed deformable generic 3D model onto the 2D illustrations of the desired shapes and moving the vertices until the desire 3D shapes are formed. In this generic 3D model all the vertices present are deployed for displacement during deformation.

3D numerical simulation of free surface shape during the crystal growth of floating zone (FZ) silicon

NASA Astrophysics Data System (ADS)

Han, Xue-Feng; Liu, Xin; Nakano, Satoshi; Harada, Hirofumi; Miyamura, Yoshiji; Kakimoto, Koichi

2018-02-01

In FZ growth processes, the stability of the free surface is important in the production of single crystal silicon with high quality. To investigate the shape of the free surface in the FZ silicon crystal growth, a 3D numerical model that included gas and liquid phases was developed. In this present study, 3D Young-Laplacian equations have been solved using the Volume of Fluid (VOF) Model. Using this new model, we predicted the 3D shape of the free surface in FZ silicon crystal growth. The effect of magnetic pressure on shape of free surface has been considered. In particular, the free surface of the eccentric growth model, which could not be previously solved using the 2D Young-Laplacian equations, was solved using the VOF model. The calculation results are validated by the experimental results.

Structure of Csd3 from Helicobacter pylori, a cell shape-determining metallopeptidase

DOE Office of Scientific and Technical Information (OSTI.GOV)

An, Doo Ri; Kim, Hyoun Sook; Seoul National University, Seoul 151 742

2015-03-01

H. pylori Csd3 (HP0506), together with other peptidoglycan hydrolases, plays an important role in determining cell shape. Its crystal structure in the latent state is reported. Helicobacter pylori is associated with various gastrointestinal diseases such as gastritis, ulcers and gastric cancer. Its colonization of the human gastric mucosa requires high motility, which depends on its helical cell shape. Seven cell shape-determining genes (csd1, csd2, csd3/hdpA, ccmA, csd4, csd5 and csd6) have been identified in H. pylori. Their proteins play key roles in determining the cell shape through modifications of the cell-wall peptidoglycan by the alteration of cross-linking or by themore » trimming of peptidoglycan muropeptides. Among them, Csd3 (also known as HdpA) is a bifunctional enzyme. Its d, d-endopeptidase activity cleaves the d-Ala{sup 4}-mDAP{sup 3} peptide bond between cross-linked muramyl tetrapeptides and pentapeptides. It is also a d, d-carboxypeptidase that cleaves off the terminal d-Ala{sup 5} from the muramyl pentapeptide. Here, the crystal structure of this protein has been determined, revealing the organization of its three domains in a latent and inactive state. The N-terminal domain 1 and the core of domain 2 share the same fold despite a very low level of sequence identity, and their surface-charge distributions are different. The C-terminal LytM domain contains the catalytic site with a Zn{sup 2+} ion, like the similar domains of other M23 metallopeptidases. Domain 1 occludes the active site of the LytM domain. The core of domain 2 is held against the LytM domain by the C-terminal tail region that protrudes from the LytM domain.« less

Cell shape characterization and classification with discrete Fourier transforms and self-organizing maps.

PubMed

Kriegel, Fabian L; Köhler, Ralf; Bayat-Sarmadi, Jannike; Bayerl, Simon; Hauser, Anja E; Niesner, Raluca; Luch, Andreas; Cseresnyes, Zoltan

2018-03-01

Cells in their natural environment often exhibit complex kinetic behavior and radical adjustments of their shapes. This enables them to accommodate to short- and long-term changes in their surroundings under physiological and pathological conditions. Intravital multi-photon microscopy is a powerful tool to record this complex behavior. Traditionally, cell behavior is characterized by tracking the cells' movements, which yields numerous parameters describing the spatiotemporal characteristics of cells. Cells can be classified according to their tracking behavior using all or a subset of these kinetic parameters. This categorization can be supported by the a priori knowledge of experts. While such an approach provides an excellent starting point for analyzing complex intravital imaging data, faster methods are required for automated and unbiased characterization. In addition to their kinetic behavior, the 3D shape of these cells also provide essential clues about the cells' status and functionality. New approaches that include the study of cell shapes as well may also allow the discovery of correlations amongst the track- and shape-describing parameters. In the current study, we examine the applicability of a set of Fourier components produced by Discrete Fourier Transform (DFT) as a tool for more efficient and less biased classification of complex cell shapes. By carrying out a number of 3D-to-2D projections of surface-rendered cells, the applied method reduces the more complex 3D shape characterization to a series of 2D DFTs. The resulting shape factors are used to train a Self-Organizing Map (SOM), which provides an unbiased estimate for the best clustering of the data, thereby characterizing groups of cells according to their shape. We propose and demonstrate that such shape characterization is a powerful addition to, or a replacement for kinetic analysis. This would make it especially useful in situations where live kinetic imaging is less practical or not possible at all. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

Aging and the haptic perception of 3D surface shape.

PubMed

Norman, J Farley; Kappers, Astrid M L; Beers, Amanda M; Scott, A Kate; Norman, Hideko F; Koenderink, Jan J

2011-04-01

Two experiments evaluated the ability of older and younger adults to perceive the three-dimensional (3D) shape of object surfaces from active touch (haptics). The ages of the older adults ranged from 64 to 84 years, while those of the younger adults ranged from 18 to 27 years. In Experiment 1, the participants haptically judged the shape of large (20 cm diameter) surfaces with an entire hand. In contrast, in Experiment 2, the participants explored the shape of small (5 cm diameter) surfaces with a single finger. The haptic surfaces varied in shape index (Koenderink, Solid shape, 1990; Koenderink, Image and Vision Computing, 10, 557-564, 1992) from -1.0 to +1.0 in steps of 0.25. For both types of surfaces (large and small), the participants were able to judge surface shape reliably. The older participants' judgments of surface shape were just as accurate and precise as those of the younger participants. The results of the current study demonstrate that while older adults do possess reductions in tactile sensitivity and acuity, they nevertheless can effectively perceive 3D surface shape from haptic exploration.

Preparation and characterization of Ba0.2Sr0.2La0.6MnO3 nanoparticles and investigation of size & shape effect on microwave absorption

NASA Astrophysics Data System (ADS)

Peymanfar, Reza; Javanshir, Shahrzad

2017-06-01

In this paper, the design and characterization of a radar absorbing material (RAM) was investigated at microwave frequency. Ba0.2Sr0.2La0.6MnO3 magnetic nanoparticles was synthesized thru a facile hydrothermal method in the presence of polymethyl methacrylate (PMMA) and the possibility of shape and size-controlled synthesis of nanoparticles (NPs) over the range 15-50 Nm was also explored. Afterward, the effect of shape and size of the synthesized Ba0.2Sr0.2La0.6MnO3 NPs on microwave absorption properties was investigated in KU-band. The crystal structures and morphology of as-synthesized nanoparticles were characterized and confirmed by FESEM, XRD, VSM, FTIR analysis. The RAM samples were prepared by dispersion of magnetic NPs in silicone rubber in an ultrasonic bath. The maximum reflection loss (RL) values NPs were 12.04 dB at 14.82 GHz and a broad absorption band (over 1.22 GHz) with RL values <-10 dB are obtained and the maximum reflection loss (RL) values of decrease and shaped NPs were 22.36 dB at 14.78 GHz and a broad absorption band (over 2.67 GHz) with RL values <-10 dB are obtained. The results indicated that the particle size and shape play a major role on the absorption properties of the composites in the 12.4-18 GHz frequency range. It is observed that microwave absorption properties increased with the decrease in average particle size of NPs.

Thermodynamics of Nucleic Acid ‘Shape Readout’ by an Aminosugar†

PubMed Central

Xi, Hongjuan; Davis, Erik; Ranjan, Nihar; Xue, Liang; Hyde-Volpe, David; Arya, Dev P.

2012-01-01

Recognition of nucleic acids is important for our understanding of nucleic acid structure as well as for our understanding of nucleic acid-protein interactions. In addition to the direct readout mechanisms of nucleic acids such as H-bonding, shape recognition of nucleic acids is being increasingly recognized to play an equally important role in DNA recognition. Competition Dialysis, UV, Flourescent Intercalator displacement (FID), Computational Docking, and calorimetry studies were conducted to study the interaction of neomycin with a variety of nucleic acid conformations (shapes). At pH 5.5, these results suggest: (1) Neomycin binds three RNA structures (16S A site rRNA, poly(rA)•poly(rA), and poly(rA)•poly(rU)) with high affinities, Ka~107M−1. (2) The binding of neomycin to A-form GC-rich oligomer d(A2G15C15T2)2 has comparable affinity to RNA structures. (3) The binding of neomycin to DNA•RNA hybrids shows a three-fold variance attributable to their structural differences (poly(dA) •poly(rU), Ka=9.4×106M−1 and poly(rA)•poly(dT), Ka=3.1×106M−1). (4) The interaction of neomycin with DNA triplex poly(dA)•2poly(dT) yields a binding affinity of Ka=2.4×105M−1. (5) Poly(dA-dT)2 showed the lowest association constant for all nucleic acids studied (Ka=<105). (6) Neomycin binds to G-quadruplexes with Ka~104-105M−1. (7) Computational studies show that the decrease in major groove width in the B to A transition correlates with increasing neomycin affinity. Neomycin’s affinity for various nucleic acid structures can be ranked as follows, RNAs and GC-rich d(A2G15C15T2)2 structures > poly(dA)•poly(rU) > poly(rA)•poly(dT) > T•A-T triplex , G-quadruplexes, B-form AT-rich or GC-rich DNA sequences. The results illustrate the first example of a small molecule based ‘shape readout’ of different nucleic acid conformations. PMID:21863895

A Review of Discrete Element Method (DEM) Particle Shapes and Size Distributions for Lunar Soil

NASA Technical Reports Server (NTRS)

Lane, John E.; Metzger, Philip T.; Wilkinson, R. Allen

2010-01-01

As part of ongoing efforts to develop models of lunar soil mechanics, this report reviews two topics that are important to discrete element method (DEM) modeling the behavior of soils (such as lunar soils): (1) methods of modeling particle shapes and (2) analytical representations of particle size distribution. The choice of particle shape complexity is driven primarily by opposing tradeoffs with total number of particles, computer memory, and total simulation computer processing time. The choice is also dependent on available DEM software capabilities. For example, PFC2D/PFC3D and EDEM support clustering of spheres; MIMES incorporates superquadric particle shapes; and BLOKS3D provides polyhedra shapes. Most commercial and custom DEM software supports some type of complex particle shape beyond the standard sphere. Convex polyhedra, clusters of spheres and single parametric particle shapes such as the ellipsoid, polyellipsoid, and superquadric, are all motivated by the desire to introduce asymmetry into the particle shape, as well as edges and corners, in order to better simulate actual granular particle shapes and behavior. An empirical particle size distribution (PSD) formula is shown to fit desert sand data from Bagnold. Particle size data of JSC-1a obtained from a fine particle analyzer at the NASA Kennedy Space Center is also fitted to a similar empirical PSD function.

Excess electron is trapped in a large single molecular cage C60F60.

PubMed

Wang, Yin-Feng; Li, Zhi-Ru; Wu, Di; Sun, Chia-Chung; Gu, Feng-Long

2010-01-15

A new kind of solvated electron systems, sphere-shaped e(-)@C60F60 (I(h)) and capsule-shaped e(-)@C60F60 (D6h), in contrast to the endohedral complex M@C60, is represented at the B3LYP/6-31G(d) + dBF (diffusive basis functions) density functional theory. It is proven, by examining the singly occupied molecular orbital (SOMO) and the spin density map of e(-)@C60F60, that the excess electron is indeed encapsulated inside the C60F60 cage. The shape of the electron cloud in SOMO matches with the shape of C60F60 cage. These cage-like single molecular solvated electrons have considerably large vertical electron detachment energies VDE of 4.95 (I(h)) and 4.67 eV (D6h) at B3LYP/6-31+G(3df) + dBF level compared to the VDE of 3.2 eV for an electron in bulk water (Coe et al., Int Rev Phys Chem 2001, 20, 33) and that of 3.66 eV for e(-)@C20F20 (Irikura, J Phys Chem A 2008, 112, 983), which shows their higher stability. The VDE of the sphere-shaped e(-)@C60F60 (I(h)) is greater than that of the capsule-shaped e(-)@C60F60 (D6h), indicating that the excess electron prefers to reside in the cage with the higher symmetry to form the more stable solvated electron. It is also noticed that the cage size [7.994 (I(h)), 5.714 and 9.978 A (D6h) in diameter] is much larger than that (2.826 A) of (H2O)20- dodecahedral cluster (Khan, Chem Phys Lett 2005, 401, 85). Copyright 2009 Wiley Periodicals, Inc.

ShapeRotator: An R tool for standardized rigid rotations of articulated three-dimensional structures with application for geometric morphometrics.

PubMed

Vidal-García, Marta; Bandara, Lashi; Keogh, J Scott

2018-05-01

The quantification of complex morphological patterns typically involves comprehensive shape and size analyses, usually obtained by gathering morphological data from all the structures that capture the phenotypic diversity of an organism or object. Articulated structures are a critical component of overall phenotypic diversity, but data gathered from these structures are difficult to incorporate into modern analyses because of the complexities associated with jointly quantifying 3D shape in multiple structures. While there are existing methods for analyzing shape variation in articulated structures in two-dimensional (2D) space, these methods do not work in 3D, a rapidly growing area of capability and research. Here, we describe a simple geometric rigid rotation approach that removes the effect of random translation and rotation, enabling the morphological analysis of 3D articulated structures. Our method is based on Cartesian coordinates in 3D space, so it can be applied to any morphometric problem that also uses 3D coordinates (e.g., spherical harmonics). We demonstrate the method by applying it to a landmark-based dataset for analyzing shape variation using geometric morphometrics. We have developed an R tool (ShapeRotator) so that the method can be easily implemented in the commonly used R package geomorph and MorphoJ software. This method will be a valuable tool for 3D morphological analyses in articulated structures by allowing an exhaustive examination of shape and size diversity.

1D vs. 2D shape selectivity in the crystallization-driven self-assembly of polylactide block copolymers.

PubMed

Inam, Maria; Cambridge, Graeme; Pitto-Barry, Anaïs; Laker, Zachary P L; Wilson, Neil R; Mathers, Robert T; Dove, Andrew P; O'Reilly, Rachel K

2017-06-01

2D materials such as graphene, LAPONITE® clays or molybdenum disulfide nanosheets are of extremely high interest to the materials community as a result of their high surface area and controllable surface properties. While several methods to access 2D inorganic materials are known, the investigation of 2D organic nanomaterials is less well developed on account of the lack of ready synthetic accessibility. Crystallization-driven self-assembly (CDSA) has become a powerful method to access a wide range of complex but precisely-defined nanostructures. The preparation of 2D structures, however, particularly those aimed towards biomedical applications, is limited, with few offering biocompatible and biodegradable characteristics as well as control over self-assembly in two dimensions. Herein, in contrast to conventional self-assembly rules, we show that the solubility of polylactide (PLLA)-based amphiphiles in alcohols results in unprecedented shape selectivity based on unimer solubility. We use log  P oct analysis to drive solvent selection for the formation of large uniform 2D diamond-shaped platelets, up to several microns in size, using long, soluble coronal blocks. By contrast, less soluble PLLA-containing block copolymers yield cylindrical micelles and mixed morphologies. The methods developed in this work provide a simple and consistently reproducible protocol for the preparation of well-defined 2D organic nanomaterials, whose size and morphology are expected to facilitate potential applications in drug delivery, tissue engineering and in nanocomposites.

Identification of different shapes, colors and sizes of standard oral dosage forms in diabetes type 2 patients-A pilot study.

PubMed

Stegemann, Sven; Riedl, Regina; Sourij, Harald

2017-01-30

The clear identification of drug products by the patients is essential for a safe and effective medication management. In order to understand the impact of shape, size and color on medication identification a study was performed in subjects with type 2 diabetes mellitus (T2D). Ten model drugs differentiated by shape, size and color were evaluated using a mixed method of medication schedule preparation by the participants followed by a semi-structured interview. Detection times were fastest for the large round tablet shape and the bi-chromatic forms. Larger size was easier to identify than the smaller sizes except for the bi-chromatic forms. The shape was the major source of errors, followed by the size and the color dimension. The results from this study suggests that color as a single dimension are perceived more effectively by subjects with T2D compared to shape and size, which requires a more demanding processing of three dimension and is dependent on the perspective. Copyright © 2016 Elsevier B.V. All rights reserved.

Morphological decomposition of 2-D binary shapes into convex polygons: a heuristic algorithm.

PubMed

Xu, J

2001-01-01

In many morphological shape decomposition algorithms, either a shape can only be decomposed into shape components of extremely simple forms or a time consuming search process is employed to determine a decomposition. In this paper, we present a morphological shape decomposition algorithm that decomposes a two-dimensional (2-D) binary shape into a collection of convex polygonal components. A single convex polygonal approximation for a given image is first identified. This first component is determined incrementally by selecting a sequence of basic shape primitives. These shape primitives are chosen based on shape information extracted from the given shape at different scale levels. Additional shape components are identified recursively from the difference image between the given image and the first component. Simple operations are used to repair certain concavities caused by the set difference operation. The resulting hierarchical structure provides descriptions for the given shape at different detail levels. The experiments show that the decomposition results produced by the algorithm seem to be in good agreement with the natural structures of the given shapes. The computational cost of the algorithm is significantly lower than that of an earlier search-based convex decomposition algorithm. Compared to nonconvex decomposition algorithms, our algorithm allows accurate approximations for the given shapes at low coding costs.

Superior adsorption and photoinduced carries transfer behaviors of dandelion-shaped Bi2S3@MoS2: experiments and theory

PubMed Central

Li, Mengjiao; Wang, Junyong; Zhang, Peng; Deng, Qinglin; Zhang, Jinzhong; Jiang, Kai; Hu, Zhigao; Chu, Junhao

2017-01-01

The enhanced light-harvesting capacity and effective separation of photogenerated carriers in fantastic hierarchical heterostructures enjoy striking attention for potential applications in the field of solar cells and photocatalysis. A three-dimensional (3D) dandelion-shaped hierarchical Bi2S3 microsphere compactly decorated with wing-shaped few layered MoS2 lamella (D-BM) was fabricated via a facile hydrothermal self-assembly process. Especially, polyethylene glycol (PEG) has been proven as the vital template to form D-BM microsphere. Importantly, the as-prepared D-BM microsphere presents pH-dependent superior adsorption behavior and remarkable visible light photocatalytic activity for degradation of organic dyestuffs (Rhodamine B/RhB and Methylene blue/MB), far exceeding those for the pure Bi2S3 and MoS2. It is understandable that D-BM with high surface area possesses more active sites and promotes light utilization due to the unique porous structure with outspread wings. Besides, based on the experiments and theoretical calculations, the staggered type II band alignment of D-BM permits the charge injection from Bi2S3 to MoS2, subsequently accelerates the separation and restrains the recombination of carriers, leading to excellent photocatalytic activity, as well as the photoconductance and photoresponse performance (with Ilight/Idark ratio 567). PMID:28211893

Aging and visual 3-D shape recognition from motion.

PubMed

Norman, J Farley; Adkins, Olivia C; Dowell, Catherine J; Hoyng, Stevie C; Shain, Lindsey M; Pedersen, Lauren E; Kinnard, Jonathan D; Higginbotham, Alexia J; Gilliam, Ashley N

2017-11-01

Two experiments were conducted to evaluate the ability of younger and older adults to recognize 3-D object shape from patterns of optical motion. In Experiment 1, participants were required to identify dotted surfaces that rotated in depth (i.e., surface structure portrayed using the kinetic depth effect). The task difficulty was manipulated by limiting the surface point lifetimes within the stimulus apparent motion sequences. In Experiment 2, the participants identified solid, naturally shaped objects (replicas of bell peppers, Capsicum annuum) that were defined by occlusion boundary contours, patterns of specular highlights, or combined optical patterns containing both boundary contours and specular highlights. Significant and adverse effects of increased age were found in both experiments. Despite the fact that previous research has found that increases in age do not reduce solid shape discrimination, our current results indicated that the same conclusion does not hold for shape identification. We demonstrated that aging results in a reduction in the ability to visually recognize 3-D shape independent of how the 3-D structure is defined (motions of isolated points, deformations of smooth optical fields containing specular highlights, etc.).

SABRE: ligand/structure-based virtual screening approach using consensus molecular-shape pattern recognition.

PubMed

Wei, Ning-Ning; Hamza, Adel

2014-01-27

We present an efficient and rational ligand/structure shape-based virtual screening approach combining our previous ligand shape-based similarity SABRE (shape-approach-based routines enhanced) and the 3D shape of the receptor binding site. Our approach exploits the pharmacological preferences of a number of known active ligands to take advantage of the structural diversities and chemical similarities, using a linear combination of weighted molecular shape density. Furthermore, the algorithm generates a consensus molecular-shape pattern recognition that is used to filter and place the candidate structure into the binding pocket. The descriptor pool used to construct the consensus molecular-shape pattern consists of four dimensional (4D) fingerprints generated from the distribution of conformer states available to a molecule and the 3D shapes of a set of active ligands computed using SABRE software. The virtual screening efficiency of SABRE was validated using the Database of Useful Decoys (DUD) and the filtered version (WOMBAT) of 10 DUD targets. The ligand/structure shape-based similarity SABRE algorithm outperforms several other widely used virtual screening methods which uses the data fusion of multiscreening tools (2D and 3D fingerprints) and demonstrates a superior early retrieval rate of active compounds (EF(0.1%) = 69.0% and EF(1%) = 98.7%) from a large size of ligand database (∼95,000 structures). Therefore, our developed similarity approach can be of particular use for identifying active compounds that are similar to reference molecules and predicting activity against other targets (chemogenomics). An academic license of the SABRE program is available on request.

Universal inverse design of surfaces with thin nematic elastomer sheets.

PubMed

Aharoni, Hillel; Xia, Yu; Zhang, Xinyue; Kamien, Randall D; Yang, Shu

2018-06-21

Programmable shape-shifting materials can take different physical forms to achieve multifunctionality in a dynamic and controllable manner. Although morphing a shape from 2D to 3D via programmed inhomogeneous local deformations has been demonstrated in various ways, the inverse problem-finding how to program a sheet in order for it to take an arbitrary desired 3D shape-is much harder yet critical to realize specific functions. Here, we address this inverse problem in thin liquid crystal elastomer (LCE) sheets, where the shape is preprogrammed by precise and local control of the molecular orientation of the liquid crystal monomers. We show how blueprints for arbitrary surface geometries can be generated using approximate numerical methods and how local extrinsic curvatures can be generated to assist in properly converting these geometries into shapes. Backed by faithfully alignable and rapidly lockable LCE chemistry, we precisely embed our designs in LCE sheets using advanced top-down microfabrication techniques. We thus successfully produce flat sheets that, upon thermal activation, take an arbitrary desired shape, such as a face. The general design principles presented here for creating an arbitrary 3D shape will allow for exploration of unmet needs in flexible electronics, metamaterials, aerospace and medical devices, and more.

Shape forming by thermal expansion mismatch and shape memory locking in polymer/elastomer laminates

NASA Astrophysics Data System (ADS)

Yuan, Chao; Ding, Zhen; Wang, T. J.; Dunn, Martin L.; Qi, H. Jerry

2017-10-01

This paper studies a novel method to fabricate three-dimensional (3D) structure from 2D thermo-responsive shape memory polymer (SMP)/elastomer bilayer laminate. In this method, the shape change is actuated by the thermal mismatch strain between the SMP and the elastomer layers upon heating. However, the glass transition behavior of the SMP locks the material into a new 3D shape that is stable even upon cooling. Therefore, the second shape becomes a new permanent shape of the laminate. A theoretical model that accounts for the temperature-dependent thermomechanical behavior of the SMP material and thermal mismatch strain between the two layers is developed to better understand the underlying physics. Model predictions and experiments show good agreement and indicate that the theoretical model can well predict the bending behavior of the bilayer laminate. The model is then used in the optimal design of geometrical configuration and material selection. The latter also illustrates the requirement of thermomechanical behaviors of the SMP to lock the shape. Based on the fundamental understandings, several self-folding structures are demonstrated by the bilayer laminate design.

Differential conductance and defect states in the heavy-fermion superconductor CeCoIn 5

DOE PAGES

John S. Van Dyke; Davis, James C.; Morr, Dirk K.

2016-01-22

We demonstrate that the electronic band structure extracted from quasiparticle interference spectroscopy [Nat. Phys. 9, 468 (2013)] and the theoretically computed form of the superconducting gaps [Proc. Natl. Acad. Sci. USA 111, 11663 (2014)] can be used to understand the dI/dV line shape measured in the normal and superconducting state of CeCoIn5 [Nat. Phys. 9, 474 (2013)]. In particular, the dI/dV line shape, and the spatial structure of defect-induced impurity states, reflects the existence of multiple superconducting gaps of d x2–y2 symmetry. As a result, these results strongly support a recently proposed microscopic origin of the unconventional superconducting state.

Estimation of Time Dependent Properties from Surface Pressure in Open Cavities

DTIC Science & Technology

2008-02-01

static pressure of the cavity. The stagnation and static pressures are measured separately with Druck Model DPI 145 pressure transducers (with a quoted...interacting with the ZNMF actuator jets, the 2D shape of the vortical structures transform to a 3D shape with spanwise vortical structures. These...Therefore, the pressure gradient in the d direction is dd ° 3d Substituting Equation (5.3) into Equation (5.5) results in ^l = PJk(e^-Re^)/c^ (5.6

Two- and three-dimensional folding of thin film single-crystalline silicon for photovoltaic power applications

PubMed Central

Guo, Xiaoying; Li, Huan; Yeop Ahn, Bok; Duoss, Eric B.; Hsia, K. Jimmy; Lewis, Jennifer A.; Nuzzo, Ralph G.

2009-01-01

Fabrication of 3D electronic structures in the micrometer-to-millimeter range is extremely challenging due to the inherently 2D nature of most conventional wafer-based fabrication methods. Self-assembly, and the related method of self-folding of planar patterned membranes, provide a promising means to solve this problem. Here, we investigate self-assembly processes driven by wetting interactions to shape the contour of a functional, nonplanar photovoltaic (PV) device. A mechanics model based on the theory of thin plates is developed to identify the critical conditions for self-folding of different 2D geometrical shapes. This strategy is demonstrated for specifically designed millimeter-scale silicon objects, which are self-assembled into spherical, and other 3D shapes and integrated into fully functional light-trapping PV devices. The resulting 3D devices offer a promising way to efficiently harvest solar energy in thin cells using concentrator microarrays that function without active light tracking systems. PMID:19934059

Two- and three-dimensional folding of thin film single-crystalline silicon for photovoltaic power applications.

PubMed

Guo, Xiaoying; Li, Huan; Ahn, Bok Yeop; Duoss, Eric B; Hsia, K Jimmy; Lewis, Jennifer A; Nuzzo, Ralph G

2009-12-01

Fabrication of 3D electronic structures in the micrometer-to-millimeter range is extremely challenging due to the inherently 2D nature of most conventional wafer-based fabrication methods. Self-assembly, and the related method of self-folding of planar patterned membranes, provide a promising means to solve this problem. Here, we investigate self-assembly processes driven by wetting interactions to shape the contour of a functional, nonplanar photovoltaic (PV) device. A mechanics model based on the theory of thin plates is developed to identify the critical conditions for self-folding of different 2D geometrical shapes. This strategy is demonstrated for specifically designed millimeter-scale silicon objects, which are self-assembled into spherical, and other 3D shapes and integrated into fully functional light-trapping PV devices. The resulting 3D devices offer a promising way to efficiently harvest solar energy in thin cells using concentrator microarrays that function without active light tracking systems.

Three-dimensional simulations of void collapse in energetic materials

NASA Astrophysics Data System (ADS)

Rai, Nirmal Kumar; Udaykumar, H. S.

2018-03-01

The collapse of voids in porous energetic materials leads to hot-spot formation and reaction initiation. This work advances the current knowledge of the dynamics of void collapse and hot-spot formation using 3D reactive void collapse simulations in HMX. Four different void shapes, i.e., sphere, cylinder, plate, and ellipsoid, are studied. For all four shapes, collapse generates complex three-dimensional (3D) baroclinic vortical structures. The hot spots are collocated with regions of intense vorticity. The differences in the vortical structures for the different void shapes are shown to significantly impact the relative sensitivity of the voids. Voids of high surface area generate hot spots of greater intensity; intricate, highly contorted vortical structures lead to hot spots of corresponding tortuosity and therefore enhanced growth rates of reaction fronts. In addition, all 3D voids are shown to be more sensitive than their two-dimensional (2D) counterparts. The results provide physical insights into hot-spot formation and growth and point to the limitations of 2D analyses of hot-spot formation.

The compressed breast during mammography and breast tomosynthesis: in vivo shape characterization and modeling

NASA Astrophysics Data System (ADS)

Rodríguez-Ruiz, Alejandro; Agasthya, Greeshma A.; Sechopoulos, Ioannis

2017-09-01

To characterize and develop a patient-based 3D model of the compressed breast undergoing mammography and breast tomosynthesis. During this IRB-approved, HIPAA-compliant study, 50 women were recruited to undergo 3D breast surface imaging with structured light (SL) during breast compression, along with simultaneous acquisition of a tomosynthesis image. A pair of SL systems were used to acquire 3D surface images by projecting 24 different patterns onto the compressed breast and capturing their reflection off the breast surface in approximately 12-16 s. The 3D surface was characterized and modeled via principal component analysis. The resulting surface model was combined with a previously developed 2D model of projected compressed breast shapes to generate a full 3D model. Data from ten patients were discarded due to technical problems during image acquisition. The maximum breast thickness (found at the chest-wall) had an average value of 56 mm, and decreased 13% towards the nipple (breast tilt angle of 5.2°). The portion of the breast not in contact with the compression paddle or the support table extended on average 17 mm, 18% of the chest-wall to nipple distance. The outermost point along the breast surface lies below the midline of the total thickness. A complete 3D model of compressed breast shapes was created and implemented as a software application available for download, capable of generating new random realistic 3D shapes of breasts undergoing compression. Accurate characterization and modeling of the breast curvature and shape was achieved and will be used for various image processing and clinical tasks.

Crystallization of micrometer-sized particles with molecular contours.

PubMed

Song, Pengcheng; Olmsted, Brian K; Chaikin, Paul; Ward, Michael D

2013-11-12

The crystallization of micrometer-sized particles with shapes mimicking those of tetrabenzoheptacene (TBH) and 1,2:5,6-dibenzanthracene (DBT), both flat polyacenes, in an electric field results in the formation of ordered 2D packings that mimic the plane group symmetries in their respective molecular crystal equivalents. Whereas the particles packed in low-density disordered arrangements under a gravitational gradient, dielectrophoresis (under an ac electric field) produced ordered high-density packings with readily identifiable plane group symmetry. The ordered colloidal assemblies were stable for hours, with the packing density decreasing slowly but with recognizable symmetry for up to 12 h for the TBH-shaped particles and up to 4 h for the DBT-shaped particles. This unexpected stability is attributed to jamming behavior associated with interlocking of the dogbone-shaped (TBH) and Z-block (DBT) particles, contrasting with the more rapid reduction of packing density and loss of hexagonal symmetry for disk-shaped particles upon removal of the electric field. The TBH-shaped and DBT-shaped particles assemble into the p2 plane group, which corresponds to the densest particle packing among the possible close-packed plane groups for these particle symmetries. The p2 symmetry observed for the TBH-shaped and DBT-shaped colloid crystal emulates the p2 symmetry of the (010) layers in their respective molecular crystals, which crystallize in monoclinic lattices. Notably, DBT-shaped particles also form ordered domains with pgg symmetry, replicating the plane group symmetry of the (100) layer in the orthorhombic polymorph of DBT. These observations illustrate that the 2D ordering of colloid particles can mimic the packing of molecules with similar shapes, demonstrating that packing can transcend length scales from the molecular to the colloidal.

Early differential sensitivity of evoked-potentials to local and global shape during the perception of three-dimensional objects.

PubMed

Leek, E Charles; Roberts, Mark; Oliver, Zoe J; Cristino, Filipe; Pegna, Alan J

2016-08-01

Here we investigated the time course underlying differential processing of local and global shape information during the perception of complex three-dimensional (3D) objects. Observers made shape matching judgments about pairs of sequentially presented multi-part novel objects. Event-related potentials (ERPs) were used to measure perceptual sensitivity to 3D shape differences in terms of local part structure and global shape configuration - based on predictions derived from hierarchical structural description models of object recognition. There were three types of different object trials in which stimulus pairs (1) shared local parts but differed in global shape configuration; (2) contained different local parts but shared global configuration or (3) shared neither local parts nor global configuration. Analyses of the ERP data showed differential amplitude modulation as a function of shape similarity as early as the N1 component between 146-215ms post-stimulus onset. These negative amplitude deflections were more similar between objects sharing global shape configuration than local part structure. Differentiation among all stimulus types was reflected in N2 amplitude modulations between 276-330ms. sLORETA inverse solutions showed stronger involvement of left occipitotemporal areas during the N1 for object discrimination weighted towards local part structure. The results suggest that the perception of 3D object shape involves parallel processing of information at local and global scales. This processing is characterised by relatively slow derivation of 'fine-grained' local shape structure, and fast derivation of 'coarse-grained' global shape configuration. We propose that the rapid early derivation of global shape attributes underlies the observed patterns of N1 amplitude modulations. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Age- and sex-specific thorax finite element model development and simulation.

PubMed

Schoell, Samantha L; Weaver, Ashley A; Vavalle, Nicholas A; Stitzel, Joel D

2015-01-01

The shape, size, bone density, and cortical thickness of the thoracic skeleton vary significantly with age and sex, which can affect the injury tolerance, especially in at-risk populations such as the elderly. Computational modeling has emerged as a powerful and versatile tool to assess injury risk. However, current computational models only represent certain ages and sexes in the population. The purpose of this study was to morph an existing finite element (FE) model of the thorax to depict thorax morphology for males and females of ages 30 and 70 years old (YO) and to investigate the effect on injury risk. Age- and sex-specific FE models were developed using thin-plate spline interpolation. In order to execute the thin-plate spline interpolation, homologous landmarks on the reference, target, and FE model are required. An image segmentation and registration algorithm was used to collect homologous rib and sternum landmark data from males and females aged 0-100 years. The Generalized Procrustes Analysis was applied to the homologous landmark data to quantify age- and sex-specific isolated shape changes in the thorax. The Global Human Body Models Consortium (GHBMC) 50th percentile male occupant model was morphed to create age- and sex-specific thoracic shape change models (scaled to a 50th percentile male size). To evaluate the thoracic response, 2 loading cases (frontal hub impact and lateral impact) were simulated to assess the importance of geometric and material property changes with age and sex. Due to the geometric and material property changes with age and sex, there were observed differences in the response of the thorax in both the frontal and lateral impacts. Material property changes alone had little to no effect on the maximum thoracic force or the maximum percent compression. With age, the thorax becomes stiffer due to superior rotation of the ribs, which can result in increased bone strain that can increase the risk of fracture. For the 70-YO models, the simulations predicted a higher number of rib fractures in comparison to the 30-YO models. The male models experienced more superior rotation of the ribs in comparison to the female models, which resulted in a higher number of rib fractures for the males. In this study, age- and sex-specific thoracic models were developed and the biomechanical response was studied using frontal and lateral impact simulations. The development of these age- and sex-specific FE models of the thorax will lead to an improved understanding of the complex relationship between thoracic geometry, age, sex, and injury risk.

The effect of age upon the perception of 3-D shape from motion.

PubMed

Norman, J Farley; Cheeseman, Jacob R; Pyles, Jessica; Baxter, Michael W; Thomason, Kelsey E; Calloway, Autum B

2013-12-18

Two experiments evaluated the ability of 50 older, middle-aged, and younger adults to discriminate the 3-dimensional (3-D) shape of curved surfaces defined by optical motion. In Experiment 1, temporal correspondence was disrupted by limiting the lifetimes of the moving surface points. In order to discriminate 3-D surface shape reliably, the younger and middle-aged adults needed a surface point lifetime of approximately 4 views (in the apparent motion sequences). In contrast, the older adults needed a much longer surface point lifetime of approximately 9 views in order to reliably perform the same task. In Experiment 2, the negative effect of age upon 3-D shape discrimination from motion was replicated. In this experiment, however, the participants' abilities to discriminate grating orientation and speed were also assessed. Edden et al. (2009) have recently demonstrated that behavioral grating orientation discrimination correlates with GABA (gamma aminobutyric acid) concentration in human visual cortex. Our results demonstrate that the negative effect of age upon 3-D shape perception from motion is not caused by impairments in the ability to perceive motion per se, but does correlate significantly with grating orientation discrimination. This result suggests that the age-related decline in 3-D shape discrimination from motion is related to decline in GABA concentration in visual cortex. Copyright © 2013 Elsevier B.V. All rights reserved.

3D shape measurements with a single interferometric sensor for in-situ lathe monitoring

NASA Astrophysics Data System (ADS)

Kuschmierz, R.; Huang, Y.; Czarske, J.; Metschke, S.; Löffler, F.; Fischer, A.

2015-05-01

Temperature drifts, tool deterioration, unknown vibrations as well as spindle play are major effects which decrease the achievable precision of computerized numerically controlled (CNC) lathes and lead to shape deviations between the processed work pieces. Since currently no measurement system exist for fast, precise and in-situ 3d shape monitoring with keyhole access, much effort has to be made to simulate and compensate these effects. Therefore we introduce an optical interferometric sensor for absolute 3d shape measurements, which was integrated into a working lathe. According to the spindle rotational speed, a measurement rate of 2,500 Hz was achieved. In-situ absolute shape, surface profile and vibration measurements are presented. While thermal drifts of the sensor led to errors of several mµm for the absolute shape, reference measurements with a coordinate machine show, that the surface profile could be measured with an uncertainty below one micron. Additionally, the spindle play of 0.8 µm was measured with the sensor.

Dependence of the shape of graphene nanobubbles on trapped substance

NASA Astrophysics Data System (ADS)

Ghorbanfekr-Kalashami, H.; Vasu, K. S.; Nair, R. R.; Peeters, François M.; Neek-Amal, M.

2017-06-01

Van der Waals (vdW) interaction between two-dimensional crystals (2D) can trap substances in high pressurized (of order 1 GPa) on nanobubbles. Increasing the adhesion between the 2D crystals further enhances the pressure and can lead to a phase transition of the trapped material. We found that the shape of the nanobubble can depend critically on the properties of the trapped substance. In the absence of any residual strain in the top 2D crystal, flat nanobubbles can be formed by trapped long hydrocarbons (that is, hexadecane). For large nanobubbles with radius 130 nm, our atomic force microscopy measurements show nanobubbles filled with hydrocarbons (water) have a cylindrical symmetry (asymmetric) shape which is in good agreement with our molecular dynamics simulations. This study provides insights into the effects of the specific material and the vdW pressure on the microscopic details of graphene bubbles.

Dependence of the shape of graphene nanobubbles on trapped substance.

PubMed

Ghorbanfekr-Kalashami, H; Vasu, K S; Nair, R R; Peeters, François M; Neek-Amal, M

2017-06-16

Van der Waals (vdW) interaction between two-dimensional crystals (2D) can trap substances in high pressurized (of order 1 GPa) on nanobubbles. Increasing the adhesion between the 2D crystals further enhances the pressure and can lead to a phase transition of the trapped material. We found that the shape of the nanobubble can depend critically on the properties of the trapped substance. In the absence of any residual strain in the top 2D crystal, flat nanobubbles can be formed by trapped long hydrocarbons (that is, hexadecane). For large nanobubbles with radius 130 nm, our atomic force microscopy measurements show nanobubbles filled with hydrocarbons (water) have a cylindrical symmetry (asymmetric) shape which is in good agreement with our molecular dynamics simulations. This study provides insights into the effects of the specific material and the vdW pressure on the microscopic details of graphene bubbles.

Dependence of the shape of graphene nanobubbles on trapped substance

PubMed Central

Ghorbanfekr-Kalashami, H.; Vasu, K. S.; Nair, R. R.; Peeters, François M.; Neek-Amal, M.

2017-01-01

Van der Waals (vdW) interaction between two-dimensional crystals (2D) can trap substances in high pressurized (of order 1 GPa) on nanobubbles. Increasing the adhesion between the 2D crystals further enhances the pressure and can lead to a phase transition of the trapped material. We found that the shape of the nanobubble can depend critically on the properties of the trapped substance. In the absence of any residual strain in the top 2D crystal, flat nanobubbles can be formed by trapped long hydrocarbons (that is, hexadecane). For large nanobubbles with radius 130 nm, our atomic force microscopy measurements show nanobubbles filled with hydrocarbons (water) have a cylindrical symmetry (asymmetric) shape which is in good agreement with our molecular dynamics simulations. This study provides insights into the effects of the specific material and the vdW pressure on the microscopic details of graphene bubbles. PMID:28621311

2D IR Spectroscopy using Four-Wave Mixing, Pulse Shaping, and IR Upconversion: A Quantitative Comparison

PubMed Central

Rock, William; Li, Yun-Liang; Pagano, Philip; Cheatum, Christopher M.

2013-01-01

Recent technological advances have led to major changes in the apparatuses used to collect 2D IR spectra. Pulse shaping offers several advantages including rapid data collection, inherent phase stability, and phase cycling capabilities. Visible array detection via upconversion allows the use of visible detectors that are cheaper, faster, more sensitive, and less noisy than IR detectors. However, despite these advantages, many researchers are reluctant to implement these technologies. Here we present a quantitative study of the S/N of 2D IR spectra collected with a traditional four-wave mixing (FWM) apparatus, with a pulse shaping apparatus, and with visible detection via upconversion to address the question of whether or not weak chromophores at low concentrations are still accessible with such an apparatus. We find that the enhanced averaging capability of the pulse shaping apparatus enables the detection of small signals that would be challenging to measure even with the traditional FWM apparatus, and we demonstrate this ability on a sample of cyanylated dihydrofolate reductase (DHFR). PMID:23687988

Implementation and Validation of 3-D Ice Accretion Measurement Methodology

NASA Technical Reports Server (NTRS)

Lee, Sam; Broeren, Andy P.; Kreeger, Richard E.; Potapczuk, Mark; Utt, Lloyd

2014-01-01

A research program has been implemented to develop and validate the use of a commercial 3-D laser scanning system to record ice accretion geometry in the NASA Icing Research Tunnel. A main component of the program was the geometric assessment of the 3- D laser scanning system on a 2-D (straight wing) and a 3-D (swept wing) airfoil geometries. This exercise consisted of comparison of scanned ice accretion to castings of the same ice accretion. The scan data were also used to create rapid prototype artificial ice shapes that were scanned and compared to the original ice accretion. The results from geometric comparisons on the straight wing showed that the ice shape models generated through the scan/rapid prototype process compared reasonably well with the cast shapes. Similar results were obtained with the geometric comparisons on the swept wing. It was difficult to precisely compare the scans of the cast shapes to the original ice accretion scans because the cast shapes appear to have shrunk during the mold/casting process by as much as 0.10-inch. However the comparison of the local ice-shape features were possible and produced better results. The rapid prototype manufacturing process was shown to reproduce the original ice accretion scan normally within 0.01-inch.

An interactive local flattening operator to support digital investigations on artwork surfaces.

PubMed

Pietroni, Nico; Massimiliano, Corsini; Cignoni, Paolo; Scopigno, Roberto

2011-12-01

Analyzing either high-frequency shape detail or any other 2D fields (scalar or vector) embedded over a 3D geometry is a complex task, since detaching the detail from the overall shape can be tricky. An alternative approach is to move to the 2D space, resolving shape reasoning to easier image processing techniques. In this paper we propose a novel framework for the analysis of 2D information distributed over 3D geometry, based on a locally smooth parametrization technique that allows us to treat local 3D data in terms of image content. The proposed approach has been implemented as a sketch-based system that allows to design with a few gestures a set of (possibly overlapping) parameterizations of rectangular portions of the surface. We demonstrate that, due to the locality of the parametrization, the distortion is under an acceptable threshold, while discontinuities can be avoided since the parametrized geometry is always homeomorphic to a disk. We show the effectiveness of the proposed technique to solve specific Cultural Heritage (CH) tasks: the analysis of chisel marks over the surface of a unfinished sculpture and the local comparison of multiple photographs mapped over the surface of an artwork. For this very difficult task, we believe that our framework and the corresponding tool are the first steps toward a computer-based shape reasoning system, able to support CH scholars with a medium they are more used to. © 2011 IEEE

Shape Comparison Between 0.4–2.0 and 20–60 lm Cement Particles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holzer, L.; Flatt, R; Erdogan, S

Portland cement powder, ground from much larger clinker particles, has a particle size distribution from about 0.1 to 100 {micro}m. An important question is then: does particle shape depend on particle size? For the same cement, X-ray computed tomography has been used to examine the 3-D shape of particles in the 20-60 {micro}m sieve range, and focused ion beam nanotomography has been used to examine the 3-D shape of cement particles found in the 0.4-2.0 {micro}m sieve range. By comparing various kinds of computed particle shape data for each size class, the conclusion is made that, within experimental uncertainty, bothmore » size classes are prolate, but the smaller size class particles, 0.4-2.0 {micro}m, tend to be somewhat more prolate than the 20-60 {micro}m size class. The practical effect of this shape difference on the set-point was assessed using the Virtual Cement and Concrete Testing Laboratory to simulate the hydration of five cement powders. Results indicate that nonspherical aspect ratio is more important in determining the set-point than are the actual shape details.« less

The terminal velocity of volcanic particles with shape obtained from 3D X-ray microtomography

NASA Astrophysics Data System (ADS)

Dioguardi, Fabio; Mele, Daniela; Dellino, Pierfrancesco; Dürig, Tobias

2017-01-01

New experiments of falling volcanic particles were performed in order to define terminal velocity models applicable in a wide range of Reynolds number Re. Experiments were carried out with fluids of various viscosities and with particles that cover a wide range of size, density and shape. Particle shape, which strongly influences fluid drag, was measured in 3D by High-resolution X-ray microtomography, by which sphericity Φ3D and fractal dimension D3D were obtained. They are easier to measure and less operator dependent than the 2D shape parameters used in previous papers. Drag laws that make use of the new 3D parameters were obtained by fitting particle data to the experiments, and single-equation terminal velocity models were derived. They work well both at high and low Re (3 × 10- 2 < Re < 104), while earlier formulations made use of different equations at different ranges of Re. The new drag laws are well suited for the modelling of particle transportation both in the eruptive column, where coarse and fine particles are present, and also in the distal part of the umbrella region, where fine ash is involved in the large-scale domains of atmospheric circulation. A table of the typical values of Φ3D and D3D of particles from known plinian, subplinian and ash plume eruptions is presented. Graphs of terminal velocity as a function of grain size are finally proposed as tools to help volcanologists and atmosphere scientists to model particle transportation of explosive eruptions.

Two-Dimensional Nanomaterials for Biomedical Applications: Emerging Trends and Future Prospects.

PubMed

Chimene, David; Alge, Daniel L; Gaharwar, Akhilesh K

2015-12-02

Two-dimensional (2D) nanomaterials are ultrathin nanomaterials with a high degree of anisotropy and chemical functionality. Research on 2D nanomaterials is still in its infancy, with the majority of research focusing on elucidating unique material characteristics and few reports focusing on biomedical applications of 2D nanomaterials. Nevertheless, recent rapid advances in 2D nanomaterials have raised important and exciting questions about their interactions with biological moieties. 2D nanoparticles such as carbon-based 2D materials, silicate clays, transition metal dichalcogenides (TMDs), and transition metal oxides (TMOs) provide enhanced physical, chemical, and biological functionality owing to their uniform shapes, high surface-to-volume ratios, and surface charge. Here, we focus on state-of-the-art biomedical applications of 2D nanomaterials as well as recent developments that are shaping this emerging field. Specifically, we describe the unique characteristics that make 2D nanoparticles so valuable, as well as the biocompatibility framework that has been investigated so far. Finally, to both capture the growing trend of 2D nanomaterials for biomedical applications and to identify promising new research directions, we provide a critical evaluation of potential applications of recently developed 2D nanomaterials. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nanofibers-based nanoweb promise superhydrophobic polyaniline: from star-shaped to leaf-shaped structures.

PubMed

Fan, Haosen; Wang, Hao; Guo, Jing; Zhao, Ning; Xu, Jian

2013-11-01

Star-shaped and leaf-shaped polyaniline (PANI) hierarchical structures with interlaced nanofibers on the surface were successfully prepared by chemical polymerization of aniline in the presence of lithium triflate (LT). Chemical structure and composition of the star-like PANI obtained were characterized by FTIR and UV-vis spectra. PANI 2D architectures can be tailored from star-shaped to leaf-shaped structures by change the concentration of LT. The synthesized star-like and leaf-like polyaniline show good superhydrophobicity with water contact angles of both above 150° due to the combination of the rough nanoweb structure and the low surface tension of fluorinated chain of dopant. This method is a facile and applicable strategy for a large-scale fabrication of 2D PANI micro/nanostructures. Many potential applications such as self-cleaning and antifouling coating can be expected based on the superhydrophobic PANI micro/nanostructures. Crown Copyright © 2013. Published by Elsevier Inc. All rights reserved.

Rapid Software-Based Design and Optical Transient Liquid Molding of Microparticles.

PubMed

Wu, Chueh-Yu; Owsley, Keegan; Di Carlo, Dino

2015-12-22

Microparticles with complex 3D shape and composition are produced using a novel fabrication method, optical transient liquid molding, in which a 2D light pattern exposes a photopolymer precursor stream shaped along the flow axis by software-aided inertial flow engineering. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Three dimensional shape measurement of wear particle by iterative volume intersection

NASA Astrophysics Data System (ADS)

Wu, Hongkun; Li, Ruowei; Liu, Shilong; Rahman, Md Arifur; Liu, Sanchi; Kwok, Ngaiming; Peng, Zhongxiao

2018-04-01

The morphology of wear particle is a fundamental indicator where wear oriented machine health can be assessed. Previous research proved that thorough measurement of the particle shape allows more reliable explanation of the occurred wear mechanism. However, most of current particle measurement techniques are focused on extraction of the two-dimensional (2-D) morphology, while other critical particle features including volume and thickness are not available. As a result, a three-dimensional (3-D) shape measurement method is developed to enable a more comprehensive particle feature description. The developed method is implemented in three steps: (1) particle profiles in multiple views are captured via a camera mounted above a micro fluid channel; (2) a preliminary reconstruction is accomplished by the shape-from-silhouette approach with the collected particle contours; (3) an iterative re-projection process follows to obtain the final 3-D measurement by minimizing the difference between the original and the re-projected contours. Results from real data are presented, demonstrating the feasibility of the proposed method.

The Limits of Shape Recognition following Late Emergence from Blindness.

PubMed

McKyton, Ayelet; Ben-Zion, Itay; Doron, Ravid; Zohary, Ehud

2015-09-21

Visual object recognition develops during the first years of life. But what if one is deprived of vision during early post-natal development? Shape information is extracted using both low-level cues (e.g., intensity- or color-based contours) and more complex algorithms that are largely based on inference assumptions (e.g., illumination is from above, objects are often partially occluded). Previous studies, testing visual acuity using a 2D shape-identification task (Lea symbols), indicate that contour-based shape recognition can improve with visual experience, even after years of visual deprivation from birth. We hypothesized that this may generalize to other low-level cues (shape, size, and color), but not to mid-level functions (e.g., 3D shape from shading) that might require prior visual knowledge. To that end, we studied a unique group of subjects in Ethiopia that suffered from an early manifestation of dense bilateral cataracts and were surgically treated only years later. Our results suggest that the newly sighted rapidly acquire the ability to recognize an odd element within an array, on the basis of color, size, or shape differences. However, they are generally unable to find the odd shape on the basis of illusory contours, shading, or occlusion relationships. Little recovery of these mid-level functions is seen within 1 year post-operation. We find that visual performance using low-level cues is relatively robust to prolonged deprivation from birth. However, the use of pictorial depth cues to infer 3D structure from the 2D retinal image is highly susceptible to early and prolonged visual deprivation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Identifying asteroid families >2 Gyrs-old

NASA Astrophysics Data System (ADS)

Bolin, Bryce T.; Morbidelli, Alessandro; Delbo, Marco; Walsh, Kevin J.

2017-10-01

There are only a few known Main Belt (MB) asteroid families with ages >2 Gyr. The lack of ancient families may be due to a bias in current techniques used to identify families. Ancient asteroid family fragments disperse in their orbital elements (a,e,i), due to secular resonances and the Yarkovsky effect (YE) making them difficult to identify. We have developed a new technique that is insensitive to the resonant spreading of fragments in e and i by searching for V-shaped correlations between family members in a vs 1/Diameter space. Our V-shape technique is demonstrated on known families and used to discover a 4 Gyr-old family linking most dark asteroids in the inner MB previously not included in any known family. In addition, the 4 Gyr-old family reveals asteroids with D >35 km that are do not belong to any asteroid family implying that they originally accreted from the protoplanetary disk.The V-shape detection tool is also a powerful analysis tool by finding the boundary of an asteroid family and fitting for its shape. Following the proposed relationship between thermal inertia (TI) with D, we find that asteroids YE drift rate might have a more complex size dependence than previous thought, leading to a curved family boundary in a vs 1/D space. The V-shape tool is capable of detecting this on synthetic families and was deployed on >30 families located throughout the MB to find this effect and quantify the YE size-dependent drift rate. We find that there is no correlation between family age and V-shape curvature. In addition, the V-shape curvature decreases for asteroid families with larger a suggesting that the relationship between TI and D is weaker in the outer MB.By examining families <20 Myrs-old, we can use this tool to separate family shape that is due to the initial ejection velocity and that which is due to the YE drift rate. V-shapes which do not contain any spreading due to YE preserve their initial ejection velocity. We constrain the initial initial velocity of young families by measuring the curvature of their fragments' V-shape in a vs 1/D space. We find that the majority of <20 Myr-old asteroid families have initial velocity fields scaling with 1/D supporting impact experiments.

Aerial 3D display by use of a 3D-shaped screen with aerial imaging by retro-reflection (AIRR)

NASA Astrophysics Data System (ADS)

Kurokawa, Nao; Ito, Shusei; Yamamoto, Hirotsugu

2017-06-01

The purpose of this paper is to realize an aerial 3D display. We design optical system that employs a projector below a retro-reflector and a 3D-shaped screen. A floating 3D image is formed with aerial imaging by retro-reflection (AIRR). Our proposed system is composed of a 3D-shaped screen, a projector, a quarter-wave retarder, a retro-reflector, and a reflective polarizer. Because AIRR forms aerial images that are plane-symmetric of the light sources regarding the reflective polarizer, the shape of the 3D screen is inverted from a desired aerial 3D image. In order to expand viewing angle, the 3D-shaped screen is surrounded by a retro-reflector. In order to separate the aerial image from reflected lights on the retro- reflector surface, the retro-reflector is tilted by 30 degrees. A projector is located below the retro-reflector at the same height of the 3D-shaped screen. The optical axis of the projector is orthogonal to the 3D-shaped screen. Scattered light on the 3D-shaped screen forms the aerial 3D image. In order to demonstrate the proposed optical design, a corner-cube-shaped screen is used for the 3D-shaped screen. Thus, the aerial 3D image is a cube that is floating above the reflective polarizer. For example, an aerial green cube is formed by projecting a calculated image on the 3D-shaped screen. The green cube image is digitally inverted in depth by our developed software. Thus, we have succeeded in forming aerial 3D image with our designed optical system.

3D scanning and 3D printing as innovative technologies for fabricating personalized topical drug delivery systems.

PubMed

Goyanes, Alvaro; Det-Amornrat, Usanee; Wang, Jie; Basit, Abdul W; Gaisford, Simon

2016-07-28

Acne is a multifactorial inflammatory skin disease with high prevalence. In this work, the potential of 3D printing to produce flexible personalised-shape anti-acne drug (salicylic acid) loaded devices was demonstrated by two different 3D printing (3DP) technologies: Fused Deposition Modelling (FDM) and stereolithography (SLA). 3D scanning technology was used to obtain a 3D model of a nose adapted to the morphology of an individual. In FDM 3DP, commercially produced Flex EcoPLA™ (FPLA) and polycaprolactone (PCL) filaments were loaded with salicylic acid by hot melt extrusion (HME) (theoretical drug loading - 2% w/w) and used as feedstock material for 3D printing. Drug loading in the FPLA-salicylic acid and PCL-salicylic acid 3D printed patches was 0.4% w/w and 1.2% w/w respectively, indicating significant thermal degradation of drug during HME and 3D printing. Diffusion testing in Franz cells using a synthetic membrane revealed that the drug loaded printed samples released <187μg/cm(2) within 3h. FPLA-salicylic acid filament was successfully printed as a nose-shape mask by FDM 3DP, but the PCL-salicylic acid filament was not. In the SLA printing process, the drug was dissolved in different mixtures of poly(ethylene glycol) diacrylate (PEGDA) and poly(ethylene glycol) (PEG) that were solidified by the action of a laser beam. SLA printing led to 3D printed devices (nose-shape) with higher resolution and higher drug loading (1.9% w/w) than FDM, with no drug degradation. The results of drug diffusion tests revealed that drug diffusion was faster than with the FDM devices, 229 and 291μg/cm(2) within 3h for the two formulations evaluated. In this study, SLA printing was the more appropriate 3D printing technology to manufacture anti-acne devices with salicylic acid. The combination of 3D scanning and 3D printing has the potential to offer solutions to produce personalised drug loaded devices, adapted in shape and size to individual patients. Copyright © 2016 Elsevier B.V. All rights reserved.

Evaluating a 2D image-based computerized approach for measuring riverine pebble roundness

NASA Astrophysics Data System (ADS)

Cassel, Mathieu; Piégay, Hervé; Lavé, Jérôme; Vaudor, Lise; Hadmoko Sri, Danang; Wibiwo Budi, Sandy; Lavigne, Franck

2018-06-01

The geometrical characteristics of pebbles are important features to study transport pathways, sedimentary history, depositional environments, abrasion processes or to target sediment sources. Both the shape and roundness of pebbles can be described by a still growing number of metrics in 2D and 3D or by visual charts. Despite new developments, existing tools remain proprietary and no pebble roundness toolbox has been available widely within the scientific community. The toolbox developed by Roussillon et al. (2009) automatically computes the size, shape and roundness indexes of pebbles from their 2D maximal projection plans. Using a digital camera, this toolbox operates using 2D pictures taken of pebbles placed on a one square meter red board, allowing data collection to be quickly and efficiently acquired at a large scale. Now that the toolbox is freely available for download,

A combined morphometric analysis of foot form and its association with sex, stature, and body mass.

PubMed

Domjanic, Jacqueline; Seidler, Horst; Mitteroecker, Philipp

2015-08-01

Morphometric analysis of footprints is a classic means for orthopedic diagnosis. In forensics and physical anthropology, it is commonly used for the estimation of stature and body mass. We studied individual variation and sexual dimorphism of foot dimensions and footprint shape by a combination of classic foot measurements and geometric morphometric methods. Left and right feet of 134 healthy adult males and females were scanned twice with a 3D optical laser scanner, and stature as well as body mass were recorded. Foot length and width were measured on the 3D scans. The 2D footprints were extracted as the plantar-most 2 mm of the 3D scans and measured with 85 landmarks and semilandmarks. Both foot size and footprint shape are sexually dimorphic and relate to stature and body mass. While dimorphism in foot length largely results from dimorphism in stature, dimorphism in footprint shape partly owes to the dimorphism in BMI. Stature could be estimated well based on foot length (R(2)  = 0.76), whereas body mass was more closely related to foot width (R(2)  = 0.62). Sex could be estimated correctly for 95% of the individuals based on a combination of foot width and length. Geometric morphometrics proved to be an effective tool for the detailed analysis of footprint shape. However, for the estimation of stature, body mass, and sex, shape variables did not considerably improve estimates based on foot length and width. © 2015 Wiley Periodicals, Inc.

Computer-assisted shape descriptors for skull morphology in craniosynostosis.

PubMed

Shim, Kyu Won; Lee, Min Jin; Lee, Myung Chul; Park, Eun Kyung; Kim, Dong Seok; Hong, Helen; Kim, Yong Oock

2016-03-01

Our aim was to develop a novel method for characterizing common skull deformities with high sensitivity and specificity, based on two-dimensional (2D) shape descriptors in computed tomography (CT) images. Between 2003 and 2014, 44 normal subjects and 39 infants with craniosynostosis (sagittal, 29; bicoronal, 10) enrolled for analysis. Mean age overall was 16 months (range, 1-120 months), with a male:female ratio of 56:29. Two reference planes, sagittal (S-plane: through top of lateral ventricle) and coronal (C-plane: at maximum dimension of fourth ventricle), were utilized to formulate three 2D shape descriptors (cranial index [CI], cranial radius index [CR], and cranial extreme spot index [CES]), which were then applied to S- and C-plane target images of both groups. In infants with sagittal craniosynostosis, CI in S-plane (S-CI) usually was <1.0 (mean, 0.78; range, 0.67-0.95), with CR consistently at 3 and a characteristic CES pattern of two discrete hot spots oriented diagonally. In the bicoronal craniosynostosis subset, CI was >1.0 (mean 1.11; range, 1.04-1.25), with CR at -3 and a CES pattern of four discrete diagonally oriented hot spots. Scatter plots underscored the highly intuitive joint performance of CI and CES in distinguishing normal and deformed states. Altogether, these novel 2D shape descriptors enabled effective discrimination of sagittal and bicoronal skull deformities. Newly developed 2D shape descriptors for cranial CT imaging enabled recognition of common skull deformities with statistical significance, perhaps providing impetus for automated CT-based diagnosis of craniosynostosis.

Shape tailoring to enhance and tune the properties of graphene nanomechanical resonators

NASA Astrophysics Data System (ADS)

Miller, David; Alemán, Benjamín

2017-06-01

The shape of a nanomechanical resonator profoundly affects its mechanical properties and determines its suitability for various applications, such as ultra-sensitive mass and force detection. Despite the promise of 2D nanomechanical systems in such applications, full control over the shape of suspended 2D materials, such as graphene, has not been achieved. We present an effective, single-step method to shape pre-suspended graphene into nanomechanical resonators with arbitrary geometries leading to enhanced properties in comparison to conventional drumheads. Our technique employs focused ion beam milling and achieves feature sizes ranging from a few tens of nanometers to several microns, while obtaining near perfect yield. We compare the mechanical properties of the shaped devices to unmodified drumheads, and find that low-tension, singly-clamped graphene cantilevers display a 20 fold increase in the mechanical quality factor (Q) with a factor 100 reduction in the mechanical damping. Importantly, we achieve these results while simultaneously removing mass, which enables state-of-the-art force sensitivity for a graphene mechanical resonator at room temperature. Our approach opens up a unique, currently inaccessible regime in graphene nanomechanics, one characterized by low strain, low frequency, small mass, and high Q, and facilitates tailoring of non-linearity and damping in mechanical structures composed of graphene and other 2D crystals.

Synchrotron radiation microtomography of Taylor bubbles in capillary two-phase flow

NASA Astrophysics Data System (ADS)

Boden, Stephan; dos Santos Rolo, Tomy; Baumbach, Tilo; Hampel, Uwe

2014-07-01

We report on a study to measure the three-dimensional shape of Taylor bubbles in capillaries using synchrotron radiation in conjunction with ultrafast radiographic imaging. Moving Taylor bubbles in 2-mm round and square capillaries were radiographically scanned with an ultrahigh frame rate of up to 36,000 fps and 5.6-µm pixel separation. Consecutive images were properly processed to yield 2D transmission radiographs of high contrast-to-noise ratio. Application of 3D tomographic image reconstruction disclosed the 3D bubble shape. The results provide a reference data base for development of sophisticated interface resolving CFD computations.

Evaluation of the physico-chemical, rheological and sensory characteristics of commercially available Frankfurters in Spain and consumer preferences.

PubMed

González-Viñas, M A; Caballero, A B; Gallego, I; García Ruiz, A

2004-08-01

The physico-chemical, rheological and sensory characteristics of different commercially available Frankfurters were studied. Samples presented values of A(w) and pH from 0.954 to 0.972 and 5.88 to 6.43, respectively. Greater differences were observed in parameters such as fat and salt content, with values ranging from 10.83% to 21.92% and 1.85% to 3.01%, respectively. With regard to total nitrogen, all samples presented values close to 2%. Free-choice profiling and generalised procrustes analysis of the sensory data permitted differentiation between samples and provided information about the attributes responsible for the observed differences. All the frankfurters scored in the moderate range for overall acceptability. Consumers identified reasons for purchasing frankfurters when evaluating the product's packaging. The most important criterion for consumers when purchasing frankfurters was the appetising aspect of the product in the packaging's illustration.

Stereo Viewing Modulates Three-Dimensional Shape Processing During Object Recognition: A High-Density ERP Study

PubMed Central

2017-01-01

The role of stereo disparity in the recognition of 3-dimensional (3D) object shape remains an unresolved issue for theoretical models of the human visual system. We examined this issue using high-density (128 channel) recordings of event-related potentials (ERPs). A recognition memory task was used in which observers were trained to recognize a subset of complex, multipart, 3D novel objects under conditions of either (bi-) monocular or stereo viewing. In a subsequent test phase they discriminated previously trained targets from untrained distractor objects that shared either local parts, 3D spatial configuration, or neither dimension, across both previously seen and novel viewpoints. The behavioral data showed a stereo advantage for target recognition at untrained viewpoints. ERPs showed early differential amplitude modulations to shape similarity defined by local part structure and global 3D spatial configuration. This occurred initially during an N1 component around 145–190 ms poststimulus onset, and then subsequently during an N2/P3 component around 260–385 ms poststimulus onset. For mono viewing, amplitude modulation during the N1 was greatest between targets and distracters with different local parts for trained views only. For stereo viewing, amplitude modulation during the N2/P3 was greatest between targets and distracters with different global 3D spatial configurations and generalized across trained and untrained views. The results show that image classification is modulated by stereo information about the local part, and global 3D spatial configuration of object shape. The findings challenge current theoretical models that do not attribute functional significance to stereo input during the computation of 3D object shape. PMID:29022728

Loss of 3-D shape constancy in interior spaces: the basis of the Ames-room illusion.

PubMed

Dorward, F M; Day, R H

1997-01-01

The apparently rectangular form of the irregularly shaped Ames room is explained in terms of a loss of interior 3-D shape constancy consequent on viewing the room with one eye through a small specifically positioned aperture. In the absence of retinal disparity and motion parallax the appearance of the room is held to shift markedly toward the rectangular dimensions of its retinal image. Three experiments designed to test this explanation with a miniature (one-tenth size) version of the Ames room No 1 with the matched 2-D shape of the back wall and as an index of interior 3-D shape are reported. The experiments showed that interior constancy was almost fully restored with binocular viewing of the room (experiment 1). The effect with a 'skeletal' version of the room was about the same as that with the conventional version and was clearly evident when the back wall or its frame version was presented alone (experiment 2), and it varied according to whether the interior perspective corresponded with that of the Ames or a rectangular room (experiment 3). Experiment 3 also showed that a rectangular room is significantly distorted when the interior perspective accords with that of the Ames room. These outcomes are construed as supporting the loss-of-constancy explanation and as showing that the Ames-room effect is one of a class of illusions attributable to the absence of stimulus correlates that normally sustain visual shape constancy.

Three-dimensional quantitative analysis of healthy foot shape: a proof of concept study.

PubMed

Stanković, Kristina; Booth, Brian G; Danckaers, Femke; Burg, Fien; Vermaelen, Philippe; Duerinck, Saartje; Sijbers, Jan; Huysmans, Toon

2018-01-01

Foot morphology has received increasing attention from both biomechanics researches and footwear manufacturers. Usually, the morphology of the foot is quantified by 2D footprints. However, footprint quantification ignores the foot's vertical dimension and hence, does not allow accurate quantification of complex 3D foot shape. The shape variation of healthy 3D feet in a population of 31 adult women and 31 adult men who live in Belgium was studied using geometric morphometric methods. The effect of different factors such as sex, age, shoe size, frequency of sport activity, Body Mass Index (BMI), foot asymmetry, and foot loading on foot shape was investigated. Correlation between these factors and foot shape was examined using multivariate linear regression. The complex nature of a foot's 3D shape leads to high variability in healthy populations. After normalizing for scale, the major axes of variation in foot morphology are (in order of decreasing variance): arch height, combined ball width and inter-toe distance, global foot width, hallux bone orientation (valgus-varus), foot type (e.g. Egyptian, Greek), and midfoot width. These first six modes of variation capture 92.59% of the total shape variation. Higher BMI results in increased ankle width, Achilles tendon width, heel width and a thicker forefoot along the dorsoplantar axis. Age was found to be associated with heel width, Achilles tendon width, toe height and hallux orientation. A bigger shoe size was found to be associated with a narrow Achilles tendon, a hallux varus, a narrow heel, heel expansion along the posterior direction, and a lower arch compared to smaller shoe size. Sex was found to be associated with differences in ankle width, Achilles tendon width, and heel width. Frequency of sport activity was associated with Achilles tendon width and toe height. A detailed analysis of the 3D foot shape, allowed by geometric morphometrics, provides insights in foot variations in three dimensions that can not be obtained from 2D footprints. These insights could be applied in various scientific disciplines, including orthotics and shoe design.

Shape analysis of corpus callosum in autism subtype using planar conformal mapping

NASA Astrophysics Data System (ADS)

He, Qing; Duan, Ye; Yin, Xiaotian; Gu, Xianfeng; Karsch, Kevin; Miles, Judith

2009-02-01

A number of studies have documented that autism has a neurobiological basis, but the anatomical extent of these neurobiological abnormalities is largely unknown. In this study, we aimed at analyzing highly localized shape abnormalities of the corpus callosum in a homogeneous group of autism children. Thirty patients with essential autism and twenty-four controls participated in this study. 2D contours of the corpus callosum were extracted from MR images by a semiautomatic segmentation method, and the 3D model was constructed by stacking the contours. The resulting 3D model had two openings at the ends, thus a new conformal parameterization for high genus surfaces was applied in our shape analysis work, which mapped each surface onto a planar domain. Surface matching among different individual meshes was achieved by re-triangulating each mesh according to a template surface. Statistical shape analysis was used to compare the 3D shapes point by point between patients with autism and their controls. The results revealed significant abnormalities in the anterior most and anterior body in essential autism group.

Dense 3D Face Alignment from 2D Video for Real-Time Use

PubMed Central

Jeni, László A.; Cohn, Jeffrey F.; Kanade, Takeo

2018-01-01

To enable real-time, person-independent 3D registration from 2D video, we developed a 3D cascade regression approach in which facial landmarks remain invariant across pose over a range of approximately 60 degrees. From a single 2D image of a person’s face, a dense 3D shape is registered in real time for each frame. The algorithm utilizes a fast cascade regression framework trained on high-resolution 3D face-scans of posed and spontaneous emotion expression. The algorithm first estimates the location of a dense set of landmarks and their visibility, then reconstructs face shapes by fitting a part-based 3D model. Because no assumptions are required about illumination or surface properties, the method can be applied to a wide range of imaging conditions that include 2D video and uncalibrated multi-view video. The method has been validated in a battery of experiments that evaluate its precision of 3D reconstruction, extension to multi-view reconstruction, temporal integration for videos and 3D head-pose estimation. Experimental findings strongly support the validity of real-time, 3D registration and reconstruction from 2D video. The software is available online at http://zface.org. PMID:29731533

Shape Universality Classes in the Random Sequential Adsorption of Nonspherical Particles

NASA Astrophysics Data System (ADS)

Baule, Adrian

2017-07-01

Random sequential adsorption (RSA) of particles of a particular shape is used in a large variety of contexts to model particle aggregation and jamming. A key feature of these models is the observed algebraic time dependence of the asymptotic jamming coverage ˜t-ν as t →∞ . However, the exact value of the exponent ν is not known apart from the simplest case of the RSA of monodisperse spheres adsorbed on a line (Renyi's seminal "car parking problem"), where ν =1 can be derived analytically. Empirical simulation studies have conjectured on a case-by-case basis that for general nonspherical particles, ν =1 /(d +d ˜ ), where d denotes the dimension of the domain, and d ˜ the number of orientational degrees of freedom of a particle. Here, we solve this long-standing problem analytically for the d =1 case—the "Paris car parking problem." We prove, in particular, that the scaling exponent depends on the particle shape, contrary to the original conjecture and, remarkably, falls into two universality classes: (i) ν =1 /(1 +d ˜ /2 ) for shapes with a smooth contact distance, e.g., ellipsoids, and (ii) ν =1 /(1 +d ˜ ) for shapes with a singular contact distance, e.g., spherocylinders and polyhedra. The exact solution explains, in particular, why many empirically observed scalings fall in between these two limits.

Shape Tracking of a Dexterous Continuum Manipulator Utilizing Two Large Deflection Shape Sensors

PubMed Central

Farvardin, Amirhossein; Grupp, Robert; Murphy, Ryan J.; Taylor, Russell H.; Iordachita, Iulian

2016-01-01

Dexterous continuum manipulators (DCMs) can largely increase the reachable region and steerability for minimally and less invasive surgery. Many such procedures require the DCM to be capable of producing large deflections. The real-time control of the DCM shape requires sensors that accurately detect and report large deflections. We propose a novel, large deflection, shape sensor to track the shape of a 35 mm DCM designed for a less invasive treatment of osteolysis. Two shape sensors, each with three fiber Bragg grating sensing nodes is embedded within the DCM, and the sensors’ distal ends fixed to the DCM. The DCM centerline is computed using the centerlines of each sensor curve. An experimental platform was built and different groups of experiments were carried out, including free bending and three cases of bending with obstacles. For each experiment, the DCM drive cable was pulled with a precise linear slide stage, the DCM centerline was calculated, and a 2D camera image was captured for verification. The reconstructed shape created with the shape sensors is compared with the ground truth generated by executing a 2D–3D registration between the camera image and 3D DCM model. Results show that the distal tip tracking accuracy is 0.40 ± 0.30 mm for the free bending and 0.61 ± 0.15 mm, 0.93 ± 0.05 mm and 0.23 ± 0.10 mm for three cases of bending with obstacles. The data suggest FBG arrays can accurately characterize the shape of large-deflection DCMs. PMID:27761103

The relationship between three-dimensional knee MRI bone shape and total knee replacement—a case control study: data from the Osteoarthritis Initiative

PubMed Central

Barr, Andrew J.; Dube, Bright; Hensor, Elizabeth M. A.; Kingsbury, Sarah R.; Peat, George; Bowes, Mike A.; Sharples, Linda D.

2016-01-01

Objective. There is growing understanding of the importance of bone in OA. Our aim was to determine the relationship between 3D MRI bone shape and total knee replacement (TKR). Methods. A nested case-control study within the Osteoarthritis Initiative cohort identified case knees with confirmed TKR for OA and controls that were matched using propensity scores. Active appearance modelling quantification of the bone shape of all knee bones identified vectors between knees having or not having OA. Vectors were scaled such that −1 and +1 represented the mean non-OA and mean OA shapes. Results. Compared to controls (n = 310), TKR cases (n = 310) had a more positive mean baseline 3D bone shape vector, indicating more advanced structural OA, for the femur [mean 0.98 vs −0.11; difference (95% CI) 1.10 (0.88, 1.31)], tibia [mean 0.86 vs −0.07; difference (95% CI) 0.94 (0.72, 1.16)] and patella [mean 0.95 vs 0.03; difference (95% CI) 0.92 (0.65, 1.20)]. Odds ratios (95% CI) for TKR per normalized unit of 3D bone shape vector for the femur, tibia and patella were: 1.85 (1.59, 2.16), 1.64 (1.42, 1.89) and 1.36 (1.22, 1.50), respectively, all P < 0.001. After including Kellgren–Lawrence grade in a multivariable analysis, only the femur 3D shape vector remained significantly associated with TKR [odds ratio 1.24 (1.02, 1.51)]. Conclusion. 3D bone shape was associated with the endpoint of this study, TKR, with femoral shape being most associated. This study contributes to the validation of quantitative MRI bone biomarkers for OA structure-modification trials. PMID:27185958

CAT & MAUS: A novel system for true dynamic motion measurement of underlying bony structures with compensation for soft tissue movement.

PubMed

Jia, Rui; Monk, Paul; Murray, David; Noble, J Alison; Mellon, Stephen

2017-09-06

Optoelectronic motion capture systems are widely employed to measure the movement of human joints. However, there can be a significant discrepancy between the data obtained by a motion capture system (MCS) and the actual movement of underlying bony structures, which is attributed to soft tissue artefact. In this paper, a computer-aided tracking and motion analysis with ultrasound (CAT & MAUS) system with an augmented globally optimal registration algorithm is presented to dynamically track the underlying bony structure during movement. The augmented registration part of CAT & MAUS was validated with a high system accuracy of 80%. The Euclidean distance between the marker-based bony landmark and the bony landmark tracked by CAT & MAUS was calculated to quantify the measurement error of an MCS caused by soft tissue artefact during movement. The average Euclidean distance between the target bony landmark measured by each of the CAT & MAUS system and the MCS alone varied from 8.32mm to 16.87mm in gait. This indicates the discrepancy between the MCS measured bony landmark and the actual underlying bony landmark. Moreover, Procrustes analysis was applied to demonstrate that CAT & MAUS reduces the deformation of the body segment shape modeled by markers during motion. The augmented CAT & MAUS system shows its potential to dynamically detect and locate actual underlying bony landmarks, which reduces the MCS measurement error caused by soft tissue artefact during movement. Copyright © 2017 Elsevier Ltd. All rights reserved.

Orientation estimation of anatomical structures in medical images for object recognition

NASA Astrophysics Data System (ADS)

Bağci, Ulaş; Udupa, Jayaram K.; Chen, Xinjian

2011-03-01

Recognition of anatomical structures is an important step in model based medical image segmentation. It provides pose estimation of objects and information about "where" roughly the objects are in the image and distinguishing them from other object-like entities. In,1 we presented a general method of model-based multi-object recognition to assist in segmentation (delineation) tasks. It exploits the pose relationship that can be encoded, via the concept of ball scale (b-scale), between the binary training objects and their associated grey images. The goal was to place the model, in a single shot, close to the right pose (position, orientation, and scale) in a given image so that the model boundaries fall in the close vicinity of object boundaries in the image. Unlike position and scale parameters, we observe that orientation parameters require more attention when estimating the pose of the model as even small differences in orientation parameters can lead to inappropriate recognition. Motivated from the non-Euclidean nature of the pose information, we propose in this paper the use of non-Euclidean metrics to estimate orientation of the anatomical structures for more accurate recognition and segmentation. We statistically analyze and evaluate the following metrics for orientation estimation: Euclidean, Log-Euclidean, Root-Euclidean, Procrustes Size-and-Shape, and mean Hermitian metrics. The results show that mean Hermitian and Cholesky decomposition metrics provide more accurate orientation estimates than other Euclidean and non-Euclidean metrics.

Multivectored Superficial Muscular Aponeurotic System Suspension for Facial Paralysis.

PubMed

Leach, Garrison; Kurnik, Nicole; Joganic, Jessica; Joganic, Edward

2017-06-01

Facial paralysis is a devastating condition that may cause severe cosmetic and functional deformities. In this study we describe our technique for superficial muscular aponeurotic system (SMAS) suspension using barbed suture and compare the vectors of suspension in relation to the underlying musculature. This study also quantifies the improvements in postoperative symmetry using traditional anthropologic landmarks. The efficacy of this procedure for improving facial paralysis was determined by comparing anthropometric indices and using Procrustes distance between 4 groupings of homologous landmarks plotted on each patient's preoperative and postoperative photos. Geometric morphometrics was used to evaluate change in facial shape and improvement in symmetry postoperatively.To analyze the vector of suspension in relation to the underlying musculature, specific anthropologic landmarks were used to calculate the vector of the musculature in 3 facial hemispheres from cadaveric controls against the vector of repair in our patients. Ten patients were included in our study. Subjectively, great improvement in functional status was achieved. Geometric morphometric analysis demonstrated a statistically significant improvement in facial symmetry. Cadaveric dissection demonstrated that the suture should be placed in the SMAS in vectors parallel to the underlying musculature to achieve these results. There were no complications in our study to date. In conclusion, multivectored SMAS suture suspension is an effective method for restoring static suspension of the face after facial paralysis. This method has the benefit of producing quick, reliable results with improved function, low cost, and low morbidity.

SmaggIce 2D Version 1.8: Software Toolkit Developed for Aerodynamic Simulation Over Iced Airfoils

NASA Technical Reports Server (NTRS)

Choo, Yung K.; Vickerman, Mary B.

2005-01-01

SmaggIce 2D version 1.8 is a software toolkit developed at the NASA Glenn Research Center that consists of tools for modeling the geometry of and generating the grids for clean and iced airfoils. Plans call for the completed SmaggIce 2D version 2.0 to streamline the entire aerodynamic simulation process--the characterization and modeling of ice shapes, grid generation, and flow simulation--and to be closely coupled with the public-domain application flow solver, WIND. Grid generated using version 1.8, however, can be used by other flow solvers. SmaggIce 2D will help researchers and engineers study the effects of ice accretion on airfoil performance, which is difficult to do with existing software tools because of complex ice shapes. Using SmaggIce 2D, when fully developed, to simulate flow over an iced airfoil will help to reduce the cost of performing flight and wind-tunnel tests for certifying aircraft in natural and simulated icing conditions.

Divided attention limits perception of 3-D object shapes

PubMed Central

Scharff, Alec; Palmer, John; Moore, Cathleen M.

2013-01-01

Can one perceive multiple object shapes at once? We tested two benchmark models of object shape perception under divided attention: an unlimited-capacity and a fixed-capacity model. Under unlimited-capacity models, shapes are analyzed independently and in parallel. Under fixed-capacity models, shapes are processed at a fixed rate (as in a serial model). To distinguish these models, we compared conditions in which observers were presented with simultaneous or sequential presentations of a fixed number of objects (The extended simultaneous-sequential method: Scharff, Palmer, & Moore, 2011a, 2011b). We used novel physical objects as stimuli, minimizing the role of semantic categorization in the task. Observers searched for a specific object among similar objects. We ensured that non-shape stimulus properties such as color and texture could not be used to complete the task. Unpredictable viewing angles were used to preclude image-matching strategies. The results rejected unlimited-capacity models for object shape perception and were consistent with the predictions of a fixed-capacity model. In contrast, a task that required observers to recognize 2-D shapes with predictable viewing angles yielded an unlimited capacity result. Further experiments ruled out alternative explanations for the capacity limit, leading us to conclude that there is a fixed-capacity limit on the ability to perceive 3-D object shapes. PMID:23404158

Transport and Retention of Colloids in Porous Media: Does Shape Really Matter?

EPA Science Inventory

The effect of particle shape on its transport and retention in porous media was evaluated by stretching carboxylate-modified fluorescent polystyrene spheres into rod shapes with aspect ratios of 2:1 and 4:1. Quartz crystal microbalance with dissipation experiments (QCM-D) were c...

40 CFR 720.3 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... specific shape or design during manufacture, (2) which has end use function(s) dependent in whole or in part upon its shape or design during end use, and (3) which has either no change of chemical... particles are not considered articles regardless of shape or design. (d) Byproduct means a chemical...

40 CFR 720.3 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... specific shape or design during manufacture, (2) which has end use function(s) dependent in whole or in part upon its shape or design during end use, and (3) which has either no change of chemical... particles are not considered articles regardless of shape or design. (d) Byproduct means a chemical...

40 CFR 720.3 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... specific shape or design during manufacture, (2) which has end use function(s) dependent in whole or in part upon its shape or design during end use, and (3) which has either no change of chemical... particles are not considered articles regardless of shape or design. (d) Byproduct means a chemical...

Midsagittal Brain Shape Correlation with Intelligence and Cognitive Performance

ERIC Educational Resources Information Center

Bruner, Emiliano; Martin-Loeches, Manuel; Burgaleta, Miguel; Colom, Roberto

2011-01-01

Brain shape might influence cognitive performance because of the relationships between functions, spatial organization, and differential volumetric development of cortical areas. Here we analyze the relationships between midsagittal brain shape variation and a set of basic psychological measures. Coordinates in 2D from 102 MRI-scanned young adult…

Optimization of the beam shaping assembly in the D-D neutron generators-based BNCT using the response matrix method.

PubMed

Kasesaz, Y; Khalafi, H; Rahmani, F

2013-12-01

Optimization of the Beam Shaping Assembly (BSA) has been performed using the MCNP4C Monte Carlo code to shape the 2.45 MeV neutrons that are produced in the D-D neutron generator. Optimal design of the BSA has been chosen by considering in-air figures of merit (FOM) which consists of 70 cm Fluental as a moderator, 30 cm Pb as a reflector, 2mm (6)Li as a thermal neutron filter and 2mm Pb as a gamma filter. The neutron beam can be evaluated by in-phantom parameters, from which therapeutic gain can be derived. Direct evaluation of both set of FOMs (in-air and in-phantom) is very time consuming. In this paper a Response Matrix (RM) method has been suggested to reduce the computing time. This method is based on considering the neutron spectrum at the beam exit and calculating contribution of various dose components in phantom to calculate the Response Matrix. Results show good agreement between direct calculation and the RM method. Copyright © 2013 Elsevier Ltd. All rights reserved.

Autodetachment dynamics of acrylonitrile anion revealed by 2D electron impact spectra

NASA Astrophysics Data System (ADS)

Regeta, Khrystyna; Allan, Michael

2014-04-01

We have measured the elastic and vibrationally inelastic differential cross sections in acrylonitrile at the scattering angle of 135°. We have found out that the bands at 2.9 and 4.4 eV are shape resonances, while sharp structures in the region 0 -0.5 eV are either boomerang structure of a shape resonance or vibrational Feshbach resonances. We gain detailed view of the autodetachment dynamics from a 2D spectrum where cross section is plotted against the incident energy and the energy loss.

Direct EIT reconstructions of complex admittivities on a chest-shaped domain in 2-D.

PubMed

Hamilton, Sarah J; Mueller, Jennifer L

2013-04-01

Electrical impedance tomography (EIT) is a medical imaging technique in which current is applied on electrodes on the surface of the body, the resulting voltage is measured, and an inverse problem is solved to recover the conductivity and/or permittivity in the interior. Images are then formed from the reconstructed conductivity and permittivity distributions. In the 2-D geometry, EIT is clinically useful for chest imaging. In this work, an implementation of a D-bar method for complex admittivities on a general 2-D domain is presented. In particular, reconstructions are computed on a chest-shaped domain for several realistic phantoms including a simulated pneumothorax, hyperinflation, and pleural effusion. The method demonstrates robustness in the presence of noise. Reconstructions from trigonometric and pairwise current injection patterns are included.

Three-Dimensional Biologically Relevant Spectrum (BRS-3D): Shape Similarity Profile Based on PDB Ligands as Molecular Descriptors.

PubMed

Hu, Ben; Kuang, Zheng-Kun; Feng, Shi-Yu; Wang, Dong; He, Song-Bing; Kong, De-Xin

2016-11-17

The crystallized ligands in the Protein Data Bank (PDB) can be treated as the inverse shapes of the active sites of corresponding proteins. Therefore, the shape similarity between a molecule and PDB ligands indicated the possibility of the molecule to bind with the targets. In this paper, we proposed a shape similarity profile that can be used as a molecular descriptor for ligand-based virtual screening. First, through three-dimensional (3D) structural clustering, 300 diverse ligands were extracted from the druggable protein-ligand database, sc-PDB. Then, each of the molecules under scrutiny was flexibly superimposed onto the 300 ligands. Superimpositions were scored by shape overlap and property similarity, producing a 300 dimensional similarity array termed the "Three-Dimensional Biologically Relevant Spectrum (BRS-3D)". Finally, quantitative or discriminant models were developed with the 300 dimensional descriptor using machine learning methods (support vector machine). The effectiveness of this approach was evaluated using 42 benchmark data sets from the G protein-coupled receptor (GPCR) ligand library and the GPCR decoy database (GLL/GDD). We compared the performance of BRS-3D with other 2D and 3D state-of-the-art molecular descriptors. The results showed that models built with BRS-3D performed best for most GLL/GDD data sets. We also applied BRS-3D in histone deacetylase 1 inhibitors screening and GPCR subtype selectivity prediction. The advantages and disadvantages of this approach are discussed.

Case study of 3D fingerprints applications

PubMed Central

Liu, Feng; Liang, Jinrong; Shen, Linlin; Yang, Meng; Zhang, David; Lai, Zhihui

2017-01-01

Human fingers are 3D objects. More information will be provided if three dimensional (3D) fingerprints are available compared with two dimensional (2D) fingerprints. Thus, this paper firstly collected 3D finger point cloud data by Structured-light Illumination method. Additional features from 3D fingerprint images are then studied and extracted. The applications of these features are finally discussed. A series of experiments are conducted to demonstrate the helpfulness of 3D information to fingerprint recognition. Results show that a quick alignment can be easily implemented under the guidance of 3D finger shape feature even though this feature does not work for fingerprint recognition directly. The newly defined distinctive 3D shape ridge feature can be used for personal authentication with Equal Error Rate (EER) of ~8.3%. Also, it is helpful to remove false core point. Furthermore, a promising of EER ~1.3% is realized by combining this feature with 2D features for fingerprint recognition which indicates the prospect of 3D fingerprint recognition. PMID:28399141

Case study of 3D fingerprints applications.

PubMed

Liu, Feng; Liang, Jinrong; Shen, Linlin; Yang, Meng; Zhang, David; Lai, Zhihui

2017-01-01

Human fingers are 3D objects. More information will be provided if three dimensional (3D) fingerprints are available compared with two dimensional (2D) fingerprints. Thus, this paper firstly collected 3D finger point cloud data by Structured-light Illumination method. Additional features from 3D fingerprint images are then studied and extracted. The applications of these features are finally discussed. A series of experiments are conducted to demonstrate the helpfulness of 3D information to fingerprint recognition. Results show that a quick alignment can be easily implemented under the guidance of 3D finger shape feature even though this feature does not work for fingerprint recognition directly. The newly defined distinctive 3D shape ridge feature can be used for personal authentication with Equal Error Rate (EER) of ~8.3%. Also, it is helpful to remove false core point. Furthermore, a promising of EER ~1.3% is realized by combining this feature with 2D features for fingerprint recognition which indicates the prospect of 3D fingerprint recognition.

Laser Imprint Reduction with a Short Shaping Laser Pulse Incident Upon a Foam-Plastic Target

DTIC Science & Technology

2002-12-01

Corporation, McLean, VA 22150, and Physics Department, Nuclear Research Center Negev , P. O. Box 9001, Beer Sheva, Israel Alexander L. Velikovich and...plasma oscillate rather than grow. Density tailoring seems to improve radiative performance of Z-pinch plasma radiation sources: For example, the cross...efficiency of the density profile shaping described above for laser imprint mitigation. We now use the the FAST2D hydrocode in a 2-D mode. The radiation

Lead-oriented synthesis: Investigation of organolithium-mediated routes to 3-D scaffolds and 3-D shape analysis of a virtual lead-like library.

PubMed

Lüthy, Monique; Wheldon, Mary C; Haji-Cheteh, Chehasnah; Atobe, Masakazu; Bond, Paul S; O'Brien, Peter; Hubbard, Roderick E; Fairlamb, Ian J S

2015-06-01

Synthetic routes to six 3-D scaffolds containing piperazine, pyrrolidine and piperidine cores have been developed. The synthetic methodology focused on the use of N-Boc α-lithiation-trapping chemistry. Notably, suitably protected and/or functionalised medicinal chemistry building blocks were synthesised via concise, connective methodology. This represents a rare example of lead-oriented synthesis. A virtual library of 190 compounds was then enumerated from the six scaffolds. Of these, 92 compounds (48%) fit the lead-like criteria of: (i) -1⩽AlogP⩽3; (ii) 14⩽number of heavy atoms⩽26; (iii) total polar surface area⩾50Å(2). The 3-D shapes of the 190 compounds were analysed using a triangular plot of normalised principal moments of inertia (PMI). From this, 46 compounds were identified which had lead-like properties and possessed 3-D shapes in under-represented areas of pharmaceutical space. Thus, the PMI analysis of the 190 member virtual library showed that whilst scaffolds which may appear on paper to be 3-D in shape, only 24% of the compounds actually had 3-D structures in the more interesting areas of 3-D drug space. Copyright © 2015 Elsevier Ltd. All rights reserved.

Classification of Bacillus and Brevibacillus species using rapid analysis of lipids by mass spectrometry.

PubMed

AlMasoud, Najla; Xu, Yun; Trivedi, Drupad K; Salivo, Simona; Abban, Tom; Rattray, Nicholas J W; Szula, Ewa; AlRabiah, Haitham; Sayqal, Ali; Goodacre, Royston

2016-11-01

Bacillus are aerobic spore-forming bacteria that are known to lead to specific diseases, such as anthrax and food poisoning. This study focuses on the characterization of these bacteria by the detection of lipids extracted from 33 well-characterized strains from the Bacillus and Brevibacillus genera, with the aim to discriminate between the different species. For the purpose of analysing the lipids extracted from these bacterial samples, two rapid physicochemical techniques were used: matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) and liquid chromatography in conjunction with mass spectrometry (LC-MS). The findings of this investigation confirmed that MALDI-TOF-MS could be used to identify different bacterial lipids and, in combination with appropriate chemometrics, allowed for the discrimination between these different bacterial species, which was supported by LC-MS. The average correct classification rates for the seven species of bacteria were 62.23 and 77.03 % based on MALDI-TOF-MS and LC-MS data, respectively. The Procrustes distance for the two datasets was 0.0699, indicating that the results from the two techniques were very similar. In addition, we also compared these bacterial lipid MALDI-TOF-MS profiles to protein profiles also collected by MALDI-TOF-MS on the same bacteria (Procrustes distance, 0.1006). The level of discrimination between lipids and proteins was equivalent, and this further indicated the potential of MALDI-TOF-MS analysis as a rapid, robust and reliable method for the classification of bacteria based on different bacterial chemical components. Graphical abstract MALDI-MS has been successfully developed for the characterization of bacteria at the subspecies level using lipids and benchmarked against HPLC.

Identification of geometric faces in hand-sketched 3D objects containing curved lines

NASA Astrophysics Data System (ADS)

El-Sayed, Ahmed M.; Wahdan, A. A.; Youssif, Aliaa A. A.

2017-07-01

The reconstruction of 3D objects from 2D line drawings is regarded as one of the key topics in the field of computer vision. The ongoing research is mainly focusing on the reconstruction of 3D objects that are mapped only from 2D straight lines, and that are symmetric in nature. Commonly, this approach only produces basic and simple shapes that are mostly flat or rather polygonized in nature, which is normally attributed to inability to handle curves. To overcome the above-mentioned limitations, a technique capable of handling non-symmetric drawings that encompass curves is considered. This paper discusses a novel technique that can be used to reconstruct 3D objects containing curved lines. In addition, it highlights an application that has been developed in accordance with the suggested technique that can convert a freehand sketch to a 3D shape using a mobile phone.

Peak clustering in two-dimensional gas chromatography with mass spectrometric detection based on theoretical calculation of two-dimensional peak shapes: the 2DAid approach.

PubMed

van Stee, Leo L P; Brinkman, Udo A Th

2011-10-28

A method is presented to facilitate the non-target analysis of data obtained in temperature-programmed comprehensive two-dimensional (2D) gas chromatography coupled to time-of-flight mass spectrometry (GC×GC-ToF-MS). One main difficulty of GC×GC data analysis is that each peak is usually modulated several times and therefore appears as a series of peaks (or peaklets) in the one-dimensionally recorded data. The proposed method, 2DAid, uses basic chromatographic laws to calculate the theoretical shape of a 2D peak (a cluster of peaklets originating from the same analyte) in order to define the area in which the peaklets of each individual compound can be expected to show up. Based on analyte-identity information obtained by means of mass spectral library searching, the individual peaklets are then combined into a single 2D peak. The method is applied, amongst others, to a complex mixture containing 362 analytes. It is demonstrated that the 2D peak shapes can be accurately predicted and that clustering and further processing can reduce the final peak list to a manageable size. Copyright © 2011 Elsevier B.V. All rights reserved.

Slow-rotation dynamic SPECT with a temporal second derivative constraint.

PubMed

Humphries, T; Celler, A; Trummer, M

2011-08-01

Dynamic tracer behavior in the human body arises as a result of continuous physiological processes. Hence, the change in tracer concentration within a region of interest (ROI) should follow a smooth curve. The authors propose a modification to an existing slow-rotation dynamic SPECT reconstruction algorithm (dSPECT) with the goal of improving the smoothness of time activity curves (TACs) and other properties of the reconstructed image. The new method, denoted d2EM, imposes a constraint on the second derivative (concavity) of the TAC in every voxel of the reconstructed image, allowing it to change sign at most once. Further constraints are enforced to prevent other nonphysical behaviors from arising. The new method is compared with dSPECT using digital phantom simulations and experimental dynamic 99mTc -DTPA renal SPECT data, to assess any improvement in image quality. In both phantom simulations and healthy volunteer experiments, the d2EM method provides smoother TACs than dSPECT, with more consistent shapes in regions with dynamic behavior. Magnitudes of TACs within an ROI still vary noticeably in both dSPECT and d2EM images, but also in images produced using an OSEM approach that reconstructs each time frame individually, based on much more complete projection data. TACs produced by averaging over a region are similar using either method, even for small ROIs. Results for experimental renal data show expected behavior in images produced by both methods, with d2EM providing somewhat smoother mean TACs and more consistent TAC shapes. The d2EM method is successful in improving the smoothness of time activity curves obtained from the reconstruction, as well as improving consistency of TAC shapes within ROIs.

A cone-shaped 3D carbon nanotube probe for neural recording.

PubMed

Su, Huan-Chieh; Lin, Chia-Min; Yen, Shiang-Jie; Chen, Yung-Chan; Chen, Chang-Hsiao; Yeh, Shih-Rung; Fang, Weileun; Chen, Hsin; Yao, Da-Jeng; Chang, Yen-Chung; Yew, Tri-Rung

2010-09-15

A novel cone-shaped 3D carbon nanotube (CNT) probe is proposed as an electrode for applications in neural recording. The electrode consists of CNTs synthesized on the cone-shaped Si (cs-Si) tip by catalytic thermal chemical vapor deposition (CVD). This probe exhibits a larger CNT surface area with the same footprint area and higher spatial resolution of neural recording compared to planar-type CNT electrodes. An approach to improve CNT characteristics by O(2) plasma treatment to modify the CNT surface will be also presented. Electrochemical characterization of O(2) plasma-treated 3D CNT (OT-CNT) probes revealed low impedance per unit area (∼64.5 Ω mm(-2)) at 1 kHz and high specific capacitance per unit area (∼2.5 mF cm(-2)). Furthermore, the OT-CNT probes were employed to record the neural signals of a crayfish nerve cord. Our findings suggest that OT-CNT probes have potential advantages as high spatial resolution and superb electrochemical properties which are suitable for neural recording applications. Copyright 2010 Elsevier B.V. All rights reserved.

A 2-D MEMS scanning mirror based on dynamic mixed mode excitation of a piezoelectric PZT thin film S-shaped actuator.

PubMed

Koh, Kah How; Kobayashi, Takeshi; Lee, Chengkuo

2011-07-18

A novel dynamic excitation of an S-shaped PZT piezoelectric actuator, which is conceptualized by having two superimposed AC voltages, is characterized in this paper through the evaluation of the 2-D scanning characteristics of an integrated silicon micromirror. The device is micromachined from a SOI wafer with a 5 μm thick Si device layer and multilayers of Pt/Ti/PZT//Pt/Ti deposited as electrode and actuation materials. A large mirror (1.65 mm x 2mm) and an S-shaped PZT actuator are formed after the backside release process. Three modes of operation are investigated: bending, torsional and mixed. The resonant frequencies obtained for bending and torsional modes are 27Hz and 70Hz respectively. The maximum measured optical deflection angles obtained at 3Vpp are ± 38.9° and ± 2.1° respectively for bending and torsional modes. Various 2-D Lissajous patterns are demonstrated by superimposing two ac sinusoidal electrical signals of different frequencies (27 Hz and 70 Hz) into one signal to be used to actuate the mirror.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Dengwang; Wang, Jie; Kapp, Daniel S.

Purpose: The aim of this work is to develop a robust algorithm for accurate segmentation of liver with special attention paid to the problems with fuzzy edges and tumor. Methods: 200 CT images were collected from radiotherapy treatment planning system. 150 datasets are selected as the panel data for shape dictionary and parameters estimation. The remaining 50 datasets were used as test images. In our study liver segmentation was formulated as optimization process of implicit function. The liver region was optimized via local and global optimization during iterations. Our method consists five steps: 1)The livers from the panel data weremore » segmented manually by physicians, and then We estimated the parameters of GMM (Gaussian mixture model) and MRF (Markov random field). Shape dictionary was built by utilizing the 3D liver shapes. 2)The outlines of chest and abdomen were located according to rib structure in the input images, and the liver region was initialized based on GMM. 3)The liver shape for each 2D slice was adjusted using MRF within the neighborhood of liver edge for local optimization. 4)The 3D liver shape was corrected by employing SSR (sparse shape representation) based on liver shape dictionary for global optimization. Furthermore, H-PSO(Hybrid Particle Swarm Optimization) was employed to solve the SSR equation. 5)The corrected 3D liver was divided into 2D slices as input data of the third step. The iteration was repeated within the local optimization and global optimization until it satisfied the suspension conditions (maximum iterations and changing rate). Results: The experiments indicated that our method performed well even for the CT images with fuzzy edge and tumors. Comparing with physician delineated results, the segmentation accuracy with the 50 test datasets (VOE, volume overlap percentage) was on average 91%–95%. Conclusion: The proposed automatic segmentation method provides a sensible technique for segmentation of CT images. This work is supported by NIH/NIBIB (1R01-EB016777), National Natural Science Foundation of China (No.61471226 and No.61201441), Research funding from Shandong Province (No.BS2012DX038 and No.J12LN23), and Research funding from Jinan City (No.201401221 and No.20120109)« less

Designing a Bio-responsive Robot from DNA Origami

PubMed Central

Ben-Ishay, Eldad; Abu-Horowitz, Almogit; Bachelet, Ido

2013-01-01

Nucleic acids are astonishingly versatile. In addition to their natural role as storage medium for biological information1, they can be utilized in parallel computing2,3 , recognize and bind molecular or cellular targets4,5 , catalyze chemical reactions6,7 , and generate calculated responses in a biological system8,9. Importantly, nucleic acids can be programmed to self-assemble into 2D and 3D structures10-12, enabling the integration of all these remarkable features in a single robot linking the sensing of biological cues to a preset response in order to exert a desired effect. Creating shapes from nucleic acids was first proposed by Seeman13, and several variations on this theme have since been realized using various techniques11,12,14,15 . However, the most significant is perhaps the one proposed by Rothemund, termed scaffolded DNA origami16. In this technique, the folding of a long (>7,000 bases) single-stranded DNA 'scaffold' is directed to a desired shape by hundreds of short complementary strands termed 'staples'. Folding is carried out by temperature annealing ramp. This technique was successfully demonstrated in the creation of a diverse array of 2D shapes with remarkable precision and robustness. DNA origami was later extended to 3D as well17,18 . The current paper will focus on the caDNAno 2.0 software19 developed by Douglas and colleagues. caDNAno is a robust, user-friendly CAD tool enabling the design of 2D and 3D DNA origami shapes with versatile features. The design process relies on a systematic and accurate abstraction scheme for DNA structures, making it relatively straightforward and efficient. In this paper we demonstrate the design of a DNA origami nanorobot that has been recently described20. This robot is 'robotic' in the sense that it links sensing to actuation, in order to perform a task. We explain how various sensing schemes can be integrated into the structure, and how this can be relayed to a desired effect. Finally we use Cando21 to simulate the mechanical properties of the designed shape. The concept we discuss can be adapted to multiple tasks and settings. PMID:23893007

Pulse Propagation Effects in Optical 2D Fourier-Transform Spectroscopy: Theory.

PubMed

Spencer, Austin P; Li, Hebin; Cundiff, Steven T; Jonas, David M

2015-04-30

A solution to Maxwell's equations in the three-dimensional frequency domain is used to calculate rephasing two-dimensional Fourier transform (2DFT) spectra of the D2 line of atomic rubidium vapor in argon buffer gas. Experimental distortions from the spatial propagation of pulses through the sample are simulated in 2DFT spectra calculated for the homogeneous Bloch line shape model. Spectral features that appear at optical densities of up to 3 are investigated. As optical density increases, absorptive and dispersive distortions start with peak shape broadening, progress to peak splitting, and ultimately result in a previously unexplored coherent transient twisting of the split peaks. In contrast to the low optical density limit, where the 2D peak shape for the Bloch model depends only on the total dephasing time, these distortions of the 2D peak shape at finite optical density vary with the waiting time and the excited state lifetime through coherent transient effects. Experiment-specific conditions are explored, demonstrating the effects of varying beam overlap within the sample and of pseudo-time domain filtering. For beam overlap starting at the sample entrance, decreasing the length of beam overlap reduces the line width along the ωτ axis but also reduces signal intensity. A pseudo-time domain filter, where signal prior to the center of the last excitation pulse is excluded from the FID-referenced 2D signal, reduces propagation distortions along the ωt axis. It is demonstrated that 2DFT rephasing spectra cannot take advantage of an excitation-detection transformation that can eliminate propagation distortions in 2DFT relaxation spectra. Finally, the high optical density experimental 2DFT spectrum of rubidium vapor in argon buffer gas [J. Phys. Chem. A 2013, 117, 6279-6287] is quantitatively compared, in line width, in depth of peak splitting, and in coherent transient peak twisting, to a simulation with optical density higher than that reported.

Rectification of the chordal axis transform and a new criterion for shape decomposition.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prasad, Lakshman

2004-01-01

In an earlier work we proposed the chordal axis transform (CAT) as a more useful alternative to the medial axis transform (MAT) for obtaining skeletons of discrete shapes. Since then, the CAT has benefited various applications in 2D and 3D shape analysis. In this paper, we revisit the CAT to address its deficiencies that are an artifact of the underlying constrained Delaunay triangulation (CDT). We introduce a valuation on the internal edges of a discrete shape's CDT based on a concept of approximate co-circularity. This valuation provides a basis for suppression of the role of certain edges in the constructionmore » of the CAT skeleton. The result is a rectified CAT skeleton that has smoother branches as well as branch points of varying degrees, unlike the original CAT skeleton whose branches exhibit oscillations in tapered sections of shapes and allows only degree 3 branch points. Additionally, the valuation leads to a new criterion for parsing shapes into visually salient parts that closely resemble the empirical decompositions of shapes by human subjects as recorded in experiments by M. Singh, G. Seyranian, and D. Hoffinan.« less

Measuring the 2D baryon acoustic oscillation signal of galaxies in WiggleZ: cosmological constraints.

PubMed

Hinton, Samuel R; Kazin, Eyal; Davis, Tamara M; Blake, Chris; Brough, Sarah; Colless, Matthew; Couch, Warrick J; Drinkwater, Michael J; Glazebrook, Karl; Jurek, Russell J; Parkinson, David; Pimbblet, Kevin A; Poole, Gregory B; Pracy, Michael; Woods, David

2017-02-01

We present results from the 2D anisotropic baryon acoustic oscillation (BAO) signal present in the final data set from the WiggleZ Dark Energy Survey. We analyse the WiggleZ data in two ways: first using the full shape of the 2D correlation function and secondly focusing only on the position of the BAO peak in the reconstructed data set. When fitting for the full shape of the 2D correlation function we use a multipole expansion to compare with theory. When we use the reconstructed data we marginalize over the shape and just measure the position of the BAO peak, analysing the data in wedges separating the signal along the line of sight from that parallel to the line of sight. We verify our method with mock data and find the results to be free of bias or systematic offsets. We also redo the pre-reconstruction angle-averaged (1D) WiggleZ BAO analysis with an improved covariance and present an updated result. The final results are presented in the form of Ω c   h 2 , H ( z ), and D A ( z ) for three redshift bins with effective redshifts z = 0.44, 0.60, and 0.73. Within these bins and methodologies, we recover constraints between 5 and 22 per cent error. Our cosmological constraints are consistent with flat ΛCDM cosmology and agree with results from the Baryon Oscillation Spectroscopic Survey.

Short-term visual deprivation, tactile acuity, and haptic solid shape discrimination.

PubMed

Crabtree, Charles E; Norman, J Farley

2014-01-01

Previous psychophysical studies have reported conflicting results concerning the effects of short-term visual deprivation upon tactile acuity. Some studies have found that 45 to 90 minutes of total light deprivation produce significant improvements in participants' tactile acuity as measured with a grating orientation discrimination task. In contrast, a single 2011 study found no such improvement while attempting to replicate these earlier findings. A primary goal of the current experiment was to resolve this discrepancy in the literature by evaluating the effects of a 90-minute period of total light deprivation upon tactile grating orientation discrimination. We also evaluated the potential effect of short-term deprivation upon haptic 3-D shape discrimination using a set of naturally-shaped solid objects. According to previous research, short-term deprivation enhances performance in a tactile 2-D shape discrimination task - perhaps a similar improvement also occurs for haptic 3-D shape discrimination. The results of the current investigation demonstrate that not only does short-term visual deprivation not enhance tactile acuity, it additionally has no effect upon haptic 3-D shape discrimination. While visual deprivation had no effect in our study, there was a significant effect of experience and learning for the grating orientation task - the participants' tactile acuity improved over time, independent of whether they had, or had not, experienced visual deprivation.

2D deblending using the multi-scale shaping scheme

NASA Astrophysics Data System (ADS)

Li, Qun; Ban, Xingan; Gong, Renbin; Li, Jinnuo; Ge, Qiang; Zu, Shaohuan

2018-01-01

Deblending can be posed as an inversion problem, which is ill-posed and requires constraint to obtain unique and stable solution. In blended record, signal is coherent, whereas interference is incoherent in some domains (e.g., common receiver domain and common offset domain). Due to the different sparsity, coefficients of signal and interference locate in different curvelet scale domains and have different amplitudes. Take into account the two differences, we propose a 2D multi-scale shaping scheme to constrain the sparsity to separate the blended record. In the domain where signal concentrates, the multi-scale scheme passes all the coefficients representing signal, while, in the domain where interference focuses, the multi-scale scheme suppresses the coefficients representing interference. Because the interference is suppressed evidently at each iteration, the constraint of multi-scale shaping operator in all scale domains are weak to guarantee the convergence of algorithm. We evaluate the performance of the multi-scale shaping scheme and the traditional global shaping scheme by using two synthetic and one field data examples.

Systematic study and comparison of photonic nanojets produced by dielectric microparticles in 2D- and 3D-spatial configurations

NASA Astrophysics Data System (ADS)

Geints, Yu E.; Zemlyanov, A. A.; Minin, O. V.; Minin, I. V.

2018-06-01

We present the systematic study of key characteristics (field intensity enhancement, spatial extents) of the 2D- and 3D-photonic nanojets (PNJs) produced by geometrically-regular micron-sized dielectric particles illuminated by a plane laser wave. By means of the finite-difference time-domain calculations, we highlight the differences and similarities between PNJs in these two spatial configurations for curved- (sphere, circular cylinder) and rectangle-shaped scatterers (cube, square bar). Our findings can be useful, for example, for the design of particle-based high-resolution imaging because the spatial resolution by such systems might be further controlled by the optimization of refractive index contrast and geometrical shape of the particle-lens.

Design and implementation of low profile antenna for dual-band applications using rotated e-shaped conductor-backed plane.

PubMed

Jalali, Mahdi; Sedghi, Tohid; Shafei, Shahin

2014-01-01

A novel configuration of a printed monopole antenna with a very compact size for satisfying WLAN operations at the 5.2/5.8 GHz and also for X-band operations at the 10 GHz has been proposed. The antenna includes a simple square-shaped patch as the radiator, the rotated U-shaped conductor back plane element with embedded strip on it, and the partial rectangular ground surface. By using the rotated U-shaped conductor-backed plane with proper values, good impedance matching and improvement in bandwidth can be achieved, at the lower and upper bands. The impedance bandwidth for S11 < -10 dB is about 1.15 GHz for 5 GHz band and 5.3 GHz for X-band. The measured peak gains are about 1.9 dBi at WLAN-band and 4.2 dBi at X-band. The experimental results represent that the realized antenna with good omnidirectional radiation characteristics, enough impedance bandwidth, and reasonable gains can be appropriate for various applications of the future developed technologies and handheld devices.

PubChem3D: Shape compatibility filtering using molecular shape quadrupoles

PubMed Central

2011-01-01

Background PubChem provides a 3-D neighboring relationship, which involves finding the maximal shape overlap between two static compound 3-D conformations, a computationally intensive step. It is highly desirable to avoid this overlap computation, especially if it can be determined with certainty that a conformer pair cannot meet the criteria to be a 3-D neighbor. As such, PubChem employs a series of pre-filters, based on the concept of volume, to remove approximately 65% of all conformer neighbor pairs prior to shape overlap optimization. Given that molecular volume, a somewhat vague concept, is rather effective, it leads one to wonder: can the existing PubChem 3-D neighboring relationship, which consists of billions of shape similar conformer pairs from tens of millions of unique small molecules, be used to identify additional shape descriptor relationships? Or, put more specifically, can one place an upper bound on shape similarity using other "fuzzy" shape-like concepts like length, width, and height? Results Using a basis set of 4.18 billion 3-D neighbor pairs identified from single conformer per compound neighboring of 17.1 million molecules, shape descriptors were computed for all conformers. These steric shape descriptors included several forms of molecular volume and shape quadrupoles, which essentially embody the length, width, and height of a conformer. For a given 3-D neighbor conformer pair, the volume and each quadrupole component (Qx, Qy, and Qz) were binned and their frequency of occurrence was examined. Per molecular volume type, this effectively produced three different maps, one per quadrupole component (Qx, Qy, and Qz), of allowed values for the similarity metric, shape Tanimoto (ST) ≥ 0.8. The efficiency of these relationships (in terms of true positive, true negative, false positive and false negative) as a function of ST threshold was determined in a test run of 13.2 billion conformer pairs not previously considered by the 3-D neighbor set. At an ST ≥ 0.8, a filtering efficiency of 40.4% of true negatives was achieved with only 32 false negatives out of 24 million true positives, when applying the separate Qx, Qy, and Qz maps in a series (Qxyz). This efficiency increased linearly as a function of ST threshold in the range 0.8-0.99. The Qx filter was consistently the most efficient followed by Qy and then by Qz. Use of a monopole volume showed the best overall performance, followed by the self-overlap volume and then by the analytic volume. Application of the monopole-based Qxyz filter in a "real world" test of 3-D neighboring of 4,218 chemicals of biomedical interest against 26.1 million molecules in PubChem reduced the total CPU cost of neighboring by between 24-38% and, if used as the initial filter, removed from consideration 48.3% of all conformer pairs at almost negligible computational overhead. Conclusion Basic shape descriptors, such as those embodied by size, length, width, and height, can be highly effective in identifying shape incompatible compound conformer pairs. When performing a 3-D search using a shape similarity cut-off, computation can be avoided by identifying conformer pairs that cannot meet the result criteria. Applying this methodology as a filter for PubChem 3-D neighboring computation, an improvement of 31% was realized, increasing the average conformer pair throughput from 154,000 to 202,000 per second per CPU core. PMID:21774809

Unique Zigzag-Shaped Buckling Zn2C Monolayer with Strain-Tunable Band Gap and Negative Poisson Ratio.

PubMed

Meng, Lingbiao; Zhang, Yingjuan; Zhou, Minjie; Zhang, Jicheng; Zhou, Xiuwen; Ni, Shuang; Wu, Weidong

2018-02-19

Designing new materials with reduced dimensionality and distinguished properties has continuously attracted intense interest for materials innovation. Here we report a novel two-dimensional (2D) Zn 2 C monolayer nanomaterial with exceptional structure and properties by means of first-principles calculations. This new Zn 2 C monolayer is composed of quasi-tetrahedral tetracoordinate carbon and quasi-linear bicoordinate zinc, featuring a peculiar zigzag-shaped buckling configuration. The unique coordinate topology endows this natural 2D semiconducting monolayer with strongly strain tunable band gap and unusual negative Poisson ratios. The monolayer has good dynamic and thermal stabilities and is also the lowest-energy structure of 2D space indicated by the particle-swarm optimization (PSO) method, implying its synthetic feasibility. With these intriguing properties the material may find applications in nanoelectronics and micromechanics.

Stretchable surfaces with programmable 3D texture morphing for synthetic camouflaging skins

NASA Astrophysics Data System (ADS)

Pikul, J. H.; Li, S.; Bai, H.; Hanlon, R. T.; Cohen, I.; Shepherd, R. F.

2017-10-01

Technologies that use stretchable materials are increasingly important, yet we are unable to control how they stretch with much more sophistication than inflating balloons. Nature, however, demonstrates remarkable control of stretchable surfaces; for example, cephalopods can project hierarchical structures from their skin in milliseconds for a wide range of textural camouflage. Inspired by cephalopod muscular morphology, we developed synthetic tissue groupings that allowed programmable transformation of two-dimensional (2D) stretchable surfaces into target 3D shapes. The synthetic tissue groupings consisted of elastomeric membranes embedded with inextensible textile mesh that inflated to within 10% of their target shapes by using a simple fabrication method and modeling approach. These stretchable surfaces transform from flat sheets to 3D textures that imitate natural stone and plant shapes and camouflage into their background environments.

Cube search, revisited.

PubMed

Zhang, Xuetao; Huang, Jie; Yigit-Elliott, Serap; Rosenholtz, Ruth

2015-03-16

Observers can quickly search among shaded cubes for one lit from a unique direction. However, replace the cubes with similar 2-D patterns that do not appear to have a 3-D shape, and search difficulty increases. These results have challenged models of visual search and attention. We demonstrate that cube search displays differ from those with "equivalent" 2-D search items in terms of the informativeness of fairly low-level image statistics. This informativeness predicts peripheral discriminability of target-present from target-absent patches, which in turn predicts visual search performance, across a wide range of conditions. Comparing model performance on a number of classic search tasks, cube search does not appear unexpectedly easy. Easy cube search, per se, does not provide evidence for preattentive computation of 3-D scene properties. However, search asymmetries derived from rotating and/or flipping the cube search displays cannot be explained by the information in our current set of image statistics. This may merely suggest a need to modify the model's set of 2-D image statistics. Alternatively, it may be difficult cube search that provides evidence for preattentive computation of 3-D scene properties. By attributing 2-D luminance variations to a shaded 3-D shape, 3-D scene understanding may slow search for 2-D features of the target. © 2015 ARVO.

Cube search, revisited

PubMed Central

Zhang, Xuetao; Huang, Jie; Yigit-Elliott, Serap; Rosenholtz, Ruth

2015-01-01

Observers can quickly search among shaded cubes for one lit from a unique direction. However, replace the cubes with similar 2-D patterns that do not appear to have a 3-D shape, and search difficulty increases. These results have challenged models of visual search and attention. We demonstrate that cube search displays differ from those with “equivalent” 2-D search items in terms of the informativeness of fairly low-level image statistics. This informativeness predicts peripheral discriminability of target-present from target-absent patches, which in turn predicts visual search performance, across a wide range of conditions. Comparing model performance on a number of classic search tasks, cube search does not appear unexpectedly easy. Easy cube search, per se, does not provide evidence for preattentive computation of 3-D scene properties. However, search asymmetries derived from rotating and/or flipping the cube search displays cannot be explained by the information in our current set of image statistics. This may merely suggest a need to modify the model's set of 2-D image statistics. Alternatively, it may be difficult cube search that provides evidence for preattentive computation of 3-D scene properties. By attributing 2-D luminance variations to a shaded 3-D shape, 3-D scene understanding may slow search for 2-D features of the target. PMID:25780063

Photoionization of atomic barium subshells in the 4 d threshold region using the relativistic multiconfiguration Tamm-Dancoff approximation

NASA Astrophysics Data System (ADS)

Ganesan, Aarthi; Deshmukh, P. C.; Manson, S. T.

2017-03-01

Photoionization cross sections and photoelectron angular distribution asymmetry parameters are calculated for the 4 d10, 5 s2, 5 p6 , and 6 s2 subshells of atomic barium as a test of the relativistic multiconfiguration Tamm-Dancoff (RMCTD) method. The shape resonance present in the near-threshold region of the 4 d subshell is studied in detail in the 4 d photoionization along with the 5 s , 5 p , and 6 s subshells in the region of the 4 d thresholds, as the 4 d shape resonance strongly influences these subshells in its vicinity. The results are compared with available experiment and other many-body theoretical results in an effort to assess the capabilities of the RMCTD methodology. The electron correlations addressed in the RMCTD method give relatively good agreement with the experimental data, indicating that the important many-body correlations are included correctly.

Retrieving spin textures on curved magnetic thin films with full-field soft X-ray microscopies

DOE PAGES

Streubel, Robert; Kronast, Florian; Fischer, Peter; ...

2015-07-03

X-ray tomography is a well-established technique to characterize 3D structures in material sciences and biology; its magnetic analogue—magnetic X-ray tomography—is yet to be developed. We demonstrate the visualization and reconstruction of magnetic domain structures in a 3D curved magnetic thin films with tubular shape by means of full-field soft X-ray microscopies. In the 3D arrangement of the magnetization is retrieved from a set of 2D projections by analysing the evolution of the magnetic contrast with varying projection angle. By using reconstruction algorithms to analyse the angular evolution of 2D projections provides quantitative information about domain patterns and magnetic coupling phenomenamore » between windings of azimuthally and radially magnetized tubular objects. In conclusion, the present approach represents a first milestone towards visualizing magnetization textures of 3D curved thin films with virtually arbitrary shape.« less

Retrieving spin textures on curved magnetic thin films with full-field soft X-ray microscopies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Streubel, Robert; Kronast, Florian; Fischer, Peter

X-ray tomography is a well-established technique to characterize 3D structures in material sciences and biology; its magnetic analogue—magnetic X-ray tomography—is yet to be developed. We demonstrate the visualization and reconstruction of magnetic domain structures in a 3D curved magnetic thin films with tubular shape by means of full-field soft X-ray microscopies. In the 3D arrangement of the magnetization is retrieved from a set of 2D projections by analysing the evolution of the magnetic contrast with varying projection angle. By using reconstruction algorithms to analyse the angular evolution of 2D projections provides quantitative information about domain patterns and magnetic coupling phenomenamore » between windings of azimuthally and radially magnetized tubular objects. In conclusion, the present approach represents a first milestone towards visualizing magnetization textures of 3D curved thin films with virtually arbitrary shape.« less

3D surface reconstruction and visualization of the Drosophila wing imaginal disc at cellular resolution

NASA Astrophysics Data System (ADS)

Bai, Linge; Widmann, Thomas; Jülicher, Frank; Dahmann, Christian; Breen, David

2013-01-01

Quantifying and visualizing the shape of developing biological tissues provide information about the morphogenetic processes in multicellular organisms. The size and shape of biological tissues depend on the number, size, shape, and arrangement of the constituting cells. To better understand the mechanisms that guide tissues into their final shape, it is important to investigate the cellular arrangement within tissues. Here we present a data processing pipeline to generate 3D volumetric surface models of epithelial tissues, as well as geometric descriptions of the tissues' apical cell cross-sections. The data processing pipeline includes image acquisition, editing, processing and analysis, 2D cell mesh generation, 3D contourbased surface reconstruction, cell mesh projection, followed by geometric calculations and color-based visualization of morphological parameters. In their first utilization we have applied these procedures to construct a 3D volumetric surface model at cellular resolution of the wing imaginal disc of Drosophila melanogaster. The ultimate goal of the reported effort is to produce tools for the creation of detailed 3D geometric models of the individual cells in epithelial tissues. To date, 3D volumetric surface models of the whole wing imaginal disc have been created, and the apicolateral cell boundaries have been identified, allowing for the calculation and visualization of cell parameters, e.g. apical cross-sectional area of cells. The calculation and visualization of morphological parameters show position-dependent patterns of cell shape in the wing imaginal disc. Our procedures should offer a general data processing pipeline for the construction of 3D volumetric surface models of a wide variety of epithelial tissues.

Understanding consumer attitudes toward food technologies in Canada.

PubMed

Henson, Spencer; Annou, Mamane; Cranfield, John; Ryks, Joanne

2008-12-01

This article reports a study on consumer attitudes to 21 food and nonfood technologies in Canada. The study involves repertory grid interviews with 36 food consumers, the data from which are analyzed using generalized Procrustes analysis. Results highlight the role of perceived risk and perceived benefit in determining the acceptability of the technologies, with individual technologies lying along a continuum between the two. For technology as a whole and the 21 specific technologies, the perceived risk and perceived benefit constructs were the dominant determinants of consumer acceptability. While perceptions of perceived risk and perceived benefit differed between individual respondents, there were very limited consistent relations with a range of sociodemographic variables.

151. Bromocriptine Challenge Affects Working Memory Processing in Humans Depending on DRD2-Related Genes

PubMed Central

Pergola, Giulio; Selvaggi, Pierluigi; Gelao, Barbara; Di Carlo, Pasquale; Nettis, Maria Antonietta; Amico, Graziella; Felici, Valentina; Fazio, Leonardo; Rampino, Antonio; Sambataro, Fabio; Blasi, Giuseppe; Bertolino, Alessandro

2017-01-01

Abstract Background: Dopamine D2 receptors (D2R) contribute to the inverted-U shaped relationship between dopamine dorsolateral prefrontal cortex (DLPFC) and working memory (WM). Genetic variation in DRD2 coding for D2Rs modulates D2 signaling, but other genes in its pathway may be involved. In a previous work, using gene co-expression networks we identified 84 partner genes coregulated with DRD2 and eight single nucleotide polymorphisms (SNPs) predicting coexpression of the whole gene set in the human DLPFC [1]. These SNPs combined into a polygenic coexpression index (PCI) predicted WM performance and DLPFC activity in two independent samples of living healthy humans [1]. Here, we asked whether response to D2R targeting drugs is associated with this PCI. Thus, we investigated the interaction between WM behavioral/brain response to the D2R agonist Bromocriptine (BRO) and the PCI. [1] Pergola G, Di Carlo P, et al. (In press). Translational Psychiatry. Methods: Fifty healthy volunteers entered a double-blind, crossover, randomized, placebo-controlled fMRI study with BRO 1.25 mg and performed the N-Back WM task during the fMRI scanning session. We computed the PCI for all participants and investigated its association with WM-related behavior and brain activity using general linear models. Results: A PCI by drug interaction was significant on both DLPFC signal (right BA46, 242 voxels, F(1, 48) = 24; right BA9, 177 voxels, F(1, 48) = 19; P < .05 cluster-level FWE corrected) and behavioral scores, F(1, 46) = 4.6, P = .045, using a U-shaped quadratic model. The U-shaped relationship between the PCI and WM processing found on placebo was reversed on BRO. Furthermore, the increase in behavioral performance on BRO correlated with a decrease in BA46 activity, t(48) = −2.0, P = .049). Conclusion: The combined effect of multiple alleles on DRD2 coexpression covaried with drug response such that different allelic patterns were associated with similar responses, as in the inverted U-shaped model of WM. Thus, multiple genes and multiple allelic patterns are implicated in the inverted U-shaped dopamine/WM relationship. This relationship is reversed when individuals are administered BRO, suggesting that brain and behavioral response to this pharmacological challenge depends on a pleiotropic individual genetic background. Hence, pharmacogenomics in schizophrenia should take into account allelic patterns associated with molecular phenomena such as gene expression to predict drug response.

Shape matters: Cr(VI) removal using iron nanoparticle impregnated 1-D vs 2-D carbon nanohybrids prepared by ultrasonic spray pyrolysis

NASA Astrophysics Data System (ADS)

Masud, Arvid; Cui, Yanbin; Atkinson, John D.; Aich, Nirupam

2018-03-01

Iron nanoparticles (Fe NPs) are used for treating water contaminated with metals or organic compounds. One-dimensional (1-D) carbon nanotubes (CNTs) and two-dimensional (2-D) graphenes act as useful nanocarbon (NC) supports for Fe NPs by resisting aggregation and enhancing adsorption and redox activity. However, no study showed how shape difference between tubular CNT and planar graphene structures dictates the physicochemical properties and pollutant removal potential of their iron-based nanohybrids. In this work, ultrasonic spray pyrolysis was used to continuously prepare Fe-CNT and Fe-rGO nanohybrids. Both NC shape and Fe/NC ratio influenced Fe NP size, loading, and oxidation states. High Fe content (precursor Fe/NC mass ratio = 2) resulted Fe NPs with diameters of 30.97 ± 7.00 and 24.11 ± 4.42 nm for Fe-CNT and Fe-rGO, respectively; however, low Fe content (Fe/NC = 0.2) provided more uniformly dispersed Fe NPs of 15.65 ± 3.06 and 9.67 ± 1.49 nm, respectively, while unsupported Fe NPs were 285.71 ± 132.42 nm. The USP-derived nanohybrids, for the first time, were used for removal of pollutant, i.e., chromium (Cr(VI)) from aqueous media. Both CNT and rGO provided synergistic effects to significantly enhance Fe NPs' ability to remove Cr(VI); the effect was more pronounced in Fe-rGO than Fe-CNT and also for low Fe content in both cases. Fe-rGO with low Fe/NC ratio and smallest Fe NPs provided the highest Cr(VI) removal capacity (25 mg/g), which was a multifold improvement over bare Fe NPs and other synthesized nanohybrids (range 7-14 mg/g). Overall, 2-D rGO improved contaminant removal capacity of the nanohybrids more than 1-D CNT indicating towards shape effect of NC supports. [Figure not available: see fulltext.

Resonances in the reaction ortho- and para- D2 + H at temperatures below 10 K

NASA Astrophysics Data System (ADS)

Simbotin, I.; Côté, R.

2016-05-01

In a previous study we reported cross sections for the reaction H2 + D in the temperature regime 10-6 < T < 10 K, and found pronounced shape resonances, especially in the p and d partial waves. We found that the resonant structures were sensitive to the initial rovibrational state of H2; in particular, we showed that the effect of the nuclear-spin symmetry was very important, since ortho- and para- H2 gave significantly different results. We now investigate the reaction D2 + H for vibrationally excited ortho- and para- D2, and compare and contrast these results with those for H2 + D. We remark that this benchmark system is a prototypical example of reactions with a strong barrier, which have very small cross sections in the cold and ultracold regimes. However, shape resonances can enhance the reaction cross sections by orders of magnitude for temperatures around and below T = 1 K. Moreover, resonant features would provide stringent tests for quantum chemistry calculations of potential energy surfaces. Partial support from the US Army Research Office (Grant No. W911NF-13-1-0213).

Shadow-driven 4D haptic visualization.

PubMed

Zhang, Hui; Hanson, Andrew

2007-01-01

Just as we can work with two-dimensional floor plans to communicate 3D architectural design, we can exploit reduced-dimension shadows to manipulate the higher-dimensional objects generating the shadows. In particular, by taking advantage of physically reactive 3D shadow-space controllers, we can transform the task of interacting with 4D objects to a new level of physical reality. We begin with a teaching tool that uses 2D knot diagrams to manipulate the geometry of 3D mathematical knots via their projections; our unique 2D haptic interface allows the user to become familiar with sketching, editing, exploration, and manipulation of 3D knots rendered as projected imageson a 2D shadow space. By combining graphics and collision-sensing haptics, we can enhance the 2D shadow-driven editing protocol to successfully leverage 2D pen-and-paper or blackboard skills. Building on the reduced-dimension 2D editing tool for manipulating 3D shapes, we develop the natural analogy to produce a reduced-dimension 3D tool for manipulating 4D shapes. By physically modeling the correct properties of 4D surfaces, their bending forces, and their collisions in the 3D haptic controller interface, we can support full-featured physical exploration of 4D mathematical objects in a manner that is otherwise far beyond the experience accessible to human beings. As far as we are aware, this paper reports the first interactive system with force-feedback that provides "4D haptic visualization" permitting the user to model and interact with 4D cloth-like objects.

New 3-D coordination polymers based on semi-rigid V-shape tetracarboxylates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Jing-Jing; Xu, Wei; Wang, Yan-Ning

Under the hydrothermal conditions, the reactions of transition-metal salts, tetracarboxylic acids and N,N′-donor ligands yielded three new coordination polymers as [Cu{sub 4}(fph){sub 2}(bpe){sub 3}(H{sub 2}O){sub 2}]·2H{sub 2}O (fph=4,4′-(hexafluoroisopropylidene)diphthalate, bpe=1,2-bis(pyridyl)ethylene) 1, [Co{sub 2}(fph)(bpa){sub 2}(H{sub 2}O){sub 2}]·3H{sub 2}O (bpa=1,2-bis(pyridyl)ethylane) 2, and [Ni(H{sub 2}O)(H{sub 2}oph)(bpa)] (oph=4,4′-oxydiphthalate) 3. X-ray single-crystal diffraction analysis revealed that the title three compounds all possess the three-dimensional (3-D) network structures. For compound 1, the fph molecules first link the Cu{sup 2+} ions into a two-dimensional (2-D) wave-like layer with a (4,4) topology. The bpe molecules act as the second linkers, extending the 2-D layers into a 3-D network. Formore » compound 2, the fph molecules still serve as the first connectors, linking the Co{sup 2+} ions into a one-dimensional (1-D) tube-like chain. Then the bpa molecules propagate the chains into a 3-D (4,4,4)-connected network. In the formation of the 3-D network of compound 3, the oph molecule does not play a role. The bpa molecules as well as the water molecules act as a mixed bridge. Only a kind of 4-connected metal node is observed in compound 3. The magnetic properties of compounds 1–3 were investigated and all exhibit the predominant antiferromegnetic magnetic behaviors. - Graphical abstract: Structures of three semi-rigid V-shape tetracarboxylate-based coordination polymers were reported, and their magnetic properties were investigated. - Highlights: • Structures of three tetracarboxylate-based coordination polymers were reported. • Role of organic bases in metal–tetracarboxylate compounds was discussed. • Characters of V-shape and semi-rigidity for tetracarboxylate play a key role in crystal growth. • Their magnetic properties were investigated.« less

Enhanced magnetoelectric effects in composite of piezoelectric ceramics, rare-earth iron alloys, and shape-optimized nanocrystalline alloys.

PubMed

Zhang, Jitao; Li, Ping; Wen, Yumei; He, Wei; Yang, Aichao; Lu, Caijiang

2014-03-01

An enhancement for magnetoelectric (ME) effects is studied in a three-phase ME architecture consisting of two magnetostrictive Terfenol-D (Tb(0.3)Dy(0.7)Fe(1.92)) plates, a piezoelectric PZT (Pb(Zr,Ti)O3) plate, and a pair of shape-optimized FeCuNbSiB nanocrystalline alloys. By modifying the conventional shape of the magnetic flux concentrator, the shape-optimized flux concentrator has an improved effective permeability (μ(eff)) due to the shape-induced demagnetizing effect at its end surface. The flux concentrator concentrates and amplifies the external magnetic flux into Terfenol-D plate by means of changing its internal flux concentrating manner. Consequently, more flux lines can be uniformly concentrated into Terfenol-D plates. The effective piezomagnetic coefficients (d(33m)) of Terfenol-D plate and the ME voltage coefficients (α(ME)) can be further improved under a lower magnetic bias field. The dynamic magneto-elastic properties and the effective magnetic induction of Terfenol-D are taken into account to derive the enhanced effective ME voltage coefficients (α(ME,eff)), the consistency of experimental results and theoretical analyses verifies this enhancement. The experimental results demonstrate that the maximum d(33m) in our proposed architecture achieves 22.48 nm/A under a bias of 114 Oe. The maximum α(ME) in the bias magnetic range 0-900 Oe reaches 84.73 mV/Oe under the low frequency of 1 kHz, and 2.996 V/Oe under the resonance frequency of 102.3 kHz, respectively. It exhibits a 1.43 times larger piezomagnetic coefficient and a 1.87 times higher ME voltage coefficient under a smaller magnetic bias of 82 Oe than those of a conventional Terfenol-D/PZT/Terfenol-D composite. These shape-induced magnetoelectric behaviors provide the possibility of using this ME architecture in ultra-sensitive magnetic sensors.

'Berries' on the Ground 2 (3-D)

NASA Technical Reports Server (NTRS)

2004-01-01

This is the 3-D anaglyph showing a microscopic image taken of soil featuring round, blueberry-shaped rock formations on the crater floor at Meridiani Planum, Mars. This image was taken on the 13th day of the Mars Exploration Rover Opportunity's journey, after the Moessbauer spectrometer, an instrument located on the rover's instrument deployment device, or 'arm,' was pressed down to measure the soil's iron mineralogy. Note the donut-shaped imprint of the instrument in the lower part of the image. The area in this image is approximately 3 centimeters (1.2 inches) across.

Dissociated active and passive tactile shape recognition: a case study of pure tactile apraxia.

PubMed

Valenza, N; Ptak, R; Zimine, I; Badan, M; Lazeyras, F; Schnider, A

2001-11-01

Disorders of tactile object recognition (TOR) may result from primary motor or sensory deficits or higher cognitive impairment of tactile shape representations or semantic memory. Studies with healthy participants suggest the existence of exploratory motor procedures directly linked to the extraction of specific properties of objects. A pure deficit of these procedures without concomitant gnostic disorders has never been described in a brain-damaged patient. Here, we present a patient with a right hemispheric infarction who, in spite of intact sensorimotor functions, had impaired TOR with the left hand. Recognition of 2D shapes and objects was severely deficient under the condition of spontaneous exploration. Tactile exploration of shapes was disorganized and exploratory procedures, such as the contour-following strategy, which is necessary to identify the precise shape of an object, were severely disturbed. However, recognition of 2D shapes under manually or verbally guided exploration and the recognition of shapes traced on the skin were intact, indicating a dissociation in shape recognition between active and passive touch. Functional MRI during sensory stimulation of the left hand showed preserved activation of the spared primary sensory cortex in the right hemisphere. We interpret the deficit of our patient as a pure tactile apraxia without tactile agnosia, i.e. a specific inability to use tactile feedback to generate the exploratory procedures necessary for tactile shape recognition.

Berries on the Ground 2 3-D

NASA Image and Video Library

2004-02-12

This 3-D anaglyph, from NASA Mars Exploration Rover Spirit, shows a microscopic image taken of soil featuring round, blueberry-shaped rock formations on the crater floor at Meridiani Planum, Mars. 3D glasses are necessary to view this image.

Long-Lived Triplet Excited States of Bent-Shaped Pentacene Dimers by Intramolecular Singlet Fission.

PubMed

Sakuma, Takao; Sakai, Hayato; Araki, Yasuyuki; Mori, Tadashi; Wada, Takehiko; Tkachenko, Nikolai V; Hasobe, Taku

2016-03-24

Intramolecular singlet fission (ISF) is a promising photophysical process to construct more efficient light energy conversion systems as one excited singlet state converts into two excited triplet states. Herein we synthesized and evaluated bent-shaped pentacene dimers as a prototype of ISF to reveal intrinsic characters of triplet states (e.g., lifetimes of triplet excited states). In this study, meta-phenylene-bridged TIPS-pentacene dimer (PcD-3Ph) and 2,2'-bipheynyl bridged TIPS-pentacene dimer (PcD-Biph) were newly synthesized as bent-shaped dimers. In the steady-state spectroscopy, absorption and emission bands of these dimers were fully characterized, suggesting the appropriate degree of electronic coupling between pentacene moieties in these dimers. In addition, the electrochemical measurements were also performed to check the electronic interaction between two pentacene moieties. Whereas the successive two oxidation peaks owing to the delocalization were observed in a directly linked-pentacene dimer (PcD) by a single bond, the cyclic voltammograms in PcD-Biph and PcD-3Ph implied the weaker interaction compared to that of p-phenylene-bridged TIPS-pentacene dimer (PcD-4Ph) and PcD. The femtosecond and nanosecond transient absorption spectra clearly revealed the slower ISF process in bent-shaped pentacene dimers (PcD-Biph and PcD-3Ph), more notably, the slower relaxation of the excited triplet states in PcD-Biph and PcD-3Ph. Namely, the quantum yields of triplet states (ΦT) by ISF approximately remain constant (ca. 180-200%) in all dimer systems, whereas the lifetimes of the triplet excited states became much longer (up to 360 ns) in PcD-Biph as compared to PcD-4Ph (15 ns). Additionally, the lifetimes of the corresponding triplet states in PcD-Biph and PcD-3Ph were sufficiently affected by solvent viscosity. In particular, the lifetimes of PcD-Biph triplet state in THF/paraffin (1.0 μs) increased up to approximately three times as compared to that in THF (360 ns), whereas those of PcD-4Ph were quite similar in both solvent.

Conformational Rearrangement Within the Soluble Domains of the CD4 Receptor is Ligand-Specific

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ashish,F.; Juncadella, I.; Garg, R.

2008-01-01

Ligand binding induces shape changes within the four modular ectodomains (D1-D4) of the CD4 receptor, an important receptor in immune signaling. Small angle x-ray scattering (SAXS) on both a two-domain and a four-domain construct of the soluble CD4 (sCD4) is consistent with known crystal structures demonstrating a bilobal and a semi-extended tetralobal Z conformation in solution, respectively. Detection of conformational changes within sCD4 as a result of ligand binding was followed by SAXS on sCD4 bound to two different glycoprotein ligands: the tick saliva immunosuppressor Salp15 and the HIV-1 envelope protein gp120. Ab initio modeling of these data showed thatmore » both Salp15 and gp120 bind to the D1 domain of sCD4 and yet induce drastically different structural rearrangements. Upon binding, Salp15 primarily distorts the characteristic lobal architecture of the sCD4 without significantly altering the semi-extended shape of the sCD4 receptor. In sharp contrast, the interaction of gp120 with sCD4 induces a shape change within sCD4 that can be described as a Z-to-U bi-fold closure of the four domains across its flexible D2-D3 linker. Placement of known crystal structures within the boundaries of the SAXS-derived models suggests that the ligand-induced shape changes could be a result of conformational changes within this D2-D3 linker. Functionally, the observed shape changes in CD4 receptor causes dissociation of lymphocyte kinase from the cytoplasmic domain of Salp15-bound CD4 and facilitates an interaction between the exposed V3 loops of CD4-bound gp120 molecule to the extracellular loops of its co-receptor, a step essential for HIV-1 viral entry.« less

Increasing dimension of structures by 4D printing shape memory polymers via fused deposition modeling

NASA Astrophysics Data System (ADS)

Hu, G. F.; Damanpack, A. R.; Bodaghi, M.; Liao, W. H.

2017-12-01

The main objective of this paper is to introduce a 4D printing method to program shape memory polymers (SMPs) during fabrication process. Fused deposition modeling (FDM) as a filament-based printing method is employed to program SMPs during depositing the material. This method is implemented to fabricate complicated polymeric structures by self-bending features without need of any post-programming. Experiments are conducted to demonstrate feasibility of one-dimensional (1D)-to 2D and 2D-to-3D self-bending. It is shown that 3D printed plate structures can transform into masonry-inspired 3D curved shell structures by simply heating. Good reliability of SMP programming during printing process is also demonstrated. A 3D macroscopic constitutive model is established to simulate thermo-mechanical features of the printed SMPs. Governing equations are also derived to simulate programming mechanism during printing process and shape change of self-bending structures. In this respect, a finite element formulation is developed considering von-Kármán geometric nonlinearity and solved by implementing iterative Newton-Raphson scheme. The accuracy of the computational approach is checked with experimental results. It is demonstrated that the theoretical model is able to replicate the main characteristics observed in the experiments. This research is likely to advance the state of the art FDM 4D printing, and provide pertinent results and computational tool that are instrumental in design of smart materials and structures with self-bending features.

Direct-write fabrication of 4D active shape-changing behavior based on a shape memory polymer and its nanocomposite (Conference Presentation)

NASA Astrophysics Data System (ADS)

Wei, Hongqiu; Zhang, Qiwei; Yao, Yongtao; Liu, Liwu; Liu, Yanju; Leng, Jinsong

2017-04-01

Shape memory polymers (SMPs), a typical class of smart materials, have been witnessed significant advances in the past decades. Based on the unique performance to recover the initial shape after going through a shape deformation, the applications of SMPs have aroused growing interests. However, most of the researches are hindered by traditional processing technologies which limit the design space of SMPs-based structures. Three-dimension (3D) printing as an emerging technology endows design freedom to manufacture materials with complex structures. In present article, we show that by employing direct-write printing method; one can realize the printing of SMPs to achieve 4D active shape-changing structures. We first fabricated a kind of 3D printable polylactide (PLA)-based SMPs and characterized the overall properties of such materials. Results demonstrated the prepared PLA-based SMPs presenting excellent shape memory effect. In what follows, the rheological properties of such PLA-based SMP ink during printing process were discussed in detail. Finally, we designed and printed several 3D configurations for investigation. By combining 3D printing with shape memory behavior, these printed structures achieve 4D active shape-changing performance under heat stimuli. This research presents a high flexible method to realize the fabrication of SMP-based 4D active shape-changing structures, which opens the way for further developments and improvements of high-tech fields like 4D printing, soft robotics, micro-systems and biomedical devices.

Extracting cardiac shapes and motion of the chick embryo heart outflow tract from four-dimensional optical coherence tomography images

NASA Astrophysics Data System (ADS)

Yin, Xin; Liu, Aiping; Thornburg, Kent L.; Wang, Ruikang K.; Rugonyi, Sandra

2012-09-01

Recent advances in optical coherence tomography (OCT), and the development of image reconstruction algorithms, enabled four-dimensional (4-D) (three-dimensional imaging over time) imaging of the embryonic heart. To further analyze and quantify the dynamics of cardiac beating, segmentation procedures that can extract the shape of the heart and its motion are needed. Most previous studies analyzed cardiac image sequences using manually extracted shapes and measurements. However, this is time consuming and subject to inter-operator variability. Automated or semi-automated analyses of 4-D cardiac OCT images, although very desirable, are also extremely challenging. This work proposes a robust algorithm to semi automatically detect and track cardiac tissue layers from 4-D OCT images of early (tubular) embryonic hearts. Our algorithm uses a two-dimensional (2-D) deformable double-line model (DLM) to detect target cardiac tissues. The detection algorithm uses a maximum-likelihood estimator and was successfully applied to 4-D in vivo OCT images of the heart outflow tract of day three chicken embryos. The extracted shapes captured the dynamics of the chick embryonic heart outflow tract wall, enabling further analysis of cardiac motion.

Adding a dimension to the infrared spectra of interfaces using heterodyne detected 2D sum-frequency generation (HD 2D SFG) spectroscopy

PubMed Central

Xiong, Wei; Laaser, Jennifer E.; Mehlenbacher, Randy D.; Zanni, Martin T.

2011-01-01

In the last ten years, two-dimensional infrared spectroscopy has become an important technique for studying molecular structures and dynamics. We report the implementation of heterodyne detected two-dimensional sum-frequency generation (HD 2D SFG) spectroscopy, which is the analog of 2D infrared (2D IR) spectroscopy, but is selective to noncentrosymmetric systems such as interfaces. We implement the technique using mid-IR pulse shaping, which enables rapid scanning, phase cycling, and automatic phasing. Absorptive spectra are obtained, that have the highest frequency resolution possible, from which we extract the rephasing and nonrephasing signals that are sometimes preferred. Using this technique, we measure the vibrational mode of CO adsorbed on a polycrystalline Pt surface. The 2D spectrum reveals a significant inhomogenous contribution to the spectral line shape, which is quantified by simulations. This observation indicates that the surface conformation and environment of CO molecules is more complicated than the simple “atop” configuration assumed in previous work. Our method can be straightforwardly incorporated into many existing SFG spectrometers. The technique enables one to quantify inhomogeneity, vibrational couplings, spectral diffusion, chemical exchange, and many other properties analogous to 2D IR spectroscopy, but specifically for interfaces. PMID:22143772

Adding a dimension to the infrared spectra of interfaces using heterodyne detected 2D sum-frequency generation (HD 2D SFG) spectroscopy.

PubMed

Xiong, Wei; Laaser, Jennifer E; Mehlenbacher, Randy D; Zanni, Martin T

2011-12-27

In the last ten years, two-dimensional infrared spectroscopy has become an important technique for studying molecular structures and dynamics. We report the implementation of heterodyne detected two-dimensional sum-frequency generation (HD 2D SFG) spectroscopy, which is the analog of 2D infrared (2D IR) spectroscopy, but is selective to noncentrosymmetric systems such as interfaces. We implement the technique using mid-IR pulse shaping, which enables rapid scanning, phase cycling, and automatic phasing. Absorptive spectra are obtained, that have the highest frequency resolution possible, from which we extract the rephasing and nonrephasing signals that are sometimes preferred. Using this technique, we measure the vibrational mode of CO adsorbed on a polycrystalline Pt surface. The 2D spectrum reveals a significant inhomogenous contribution to the spectral line shape, which is quantified by simulations. This observation indicates that the surface conformation and environment of CO molecules is more complicated than the simple "atop" configuration assumed in previous work. Our method can be straightforwardly incorporated into many existing SFG spectrometers. The technique enables one to quantify inhomogeneity, vibrational couplings, spectral diffusion, chemical exchange, and many other properties analogous to 2D IR spectroscopy, but specifically for interfaces.

Simple Parametric Model for Airfoil Shape Description

NASA Astrophysics Data System (ADS)

Ziemkiewicz, David

2017-12-01

We show a simple, analytic equation describing a class of two-dimensional shapes well suited for representation of aircraft airfoil profiles. Our goal was to create a description characterized by a small number of parameters with easily understandable meaning, providing a tool to alter the shape with optimization procedures as well as manual tweaks by the designer. The generated shapes are well suited for numerical analysis with 2D flow solving software such as XFOIL.

Shape component analysis: structure-preserving dimension reduction on biological shape spaces.

PubMed

Lee, Hao-Chih; Liao, Tao; Zhang, Yongjie Jessica; Yang, Ge

2016-03-01

Quantitative shape analysis is required by a wide range of biological studies across diverse scales, ranging from molecules to cells and organisms. In particular, high-throughput and systems-level studies of biological structures and functions have started to produce large volumes of complex high-dimensional shape data. Analysis and understanding of high-dimensional biological shape data require dimension-reduction techniques. We have developed a technique for non-linear dimension reduction of 2D and 3D biological shape representations on their Riemannian spaces. A key feature of this technique is that it preserves distances between different shapes in an embedded low-dimensional shape space. We demonstrate an application of this technique by combining it with non-linear mean-shift clustering on the Riemannian spaces for unsupervised clustering of shapes of cellular organelles and proteins. Source code and data for reproducing results of this article are freely available at https://github.com/ccdlcmu/shape_component_analysis_Matlab The implementation was made in MATLAB and supported on MS Windows, Linux and Mac OS. geyang@andrew.cmu.edu. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Initial velocity V-shapes of young asteroid families

NASA Astrophysics Data System (ADS)

Bolin, Bryce T.; Walsh, Kevin J.; Morbidelli, Alessandro; Delbó, Marco

2018-01-01

Ejection velocity fields of asteroid families are largely unconstrained due to the fact that members disperse relatively quickly on Myr time-scales by secular resonances and the Yarkovsky effect. The spreading of fragments in a by the Yarkovsky effect is indistinguishable from the spreading caused by the initial ejection of fragments. By examining families <20 Myr old, we can use the V-shape identification technique to separate family shapes that are due to the initial ejection velocity field and those that are due to the Yarkovsky effect. Asteroid families that are <20 Myr old provide an opportunity to study the velocity field of family fragments before they become too dispersed. Only the Karin family's initial velocity field has been determined and scales inversely with diameter, D-1. We have applied the V-shape identification technique to constrain young families' initial ejection velocity fields by measuring the curvature of their fragments' V-shape correlation in semimajor axis, a, versus D-1 space. Curvature from a straight line implies a deviation from a scaling of D-1. We measure the V-shape curvature of 11 young asteroid families including the 1993 FY12, Aeolia, Brangane, Brasilia, Clarissa, Iannini, Karin, Konig, Koronis(2), Theobalda and Veritas asteroid families. We find that the majority of asteroid families have initial ejection velocity fields consistent with ∼D-1 supporting laboratory impact experiments and computer simulations of disrupting asteroid parent bodies.

Short-Term Visual Deprivation, Tactile Acuity, and Haptic Solid Shape Discrimination

PubMed Central

Crabtree, Charles E.; Norman, J. Farley

2014-01-01

Previous psychophysical studies have reported conflicting results concerning the effects of short-term visual deprivation upon tactile acuity. Some studies have found that 45 to 90 minutes of total light deprivation produce significant improvements in participants' tactile acuity as measured with a grating orientation discrimination task. In contrast, a single 2011 study found no such improvement while attempting to replicate these earlier findings. A primary goal of the current experiment was to resolve this discrepancy in the literature by evaluating the effects of a 90-minute period of total light deprivation upon tactile grating orientation discrimination. We also evaluated the potential effect of short-term deprivation upon haptic 3-D shape discrimination using a set of naturally-shaped solid objects. According to previous research, short-term deprivation enhances performance in a tactile 2-D shape discrimination task – perhaps a similar improvement also occurs for haptic 3-D shape discrimination. The results of the current investigation demonstrate that not only does short-term visual deprivation not enhance tactile acuity, it additionally has no effect upon haptic 3-D shape discrimination. While visual deprivation had no effect in our study, there was a significant effect of experience and learning for the grating orientation task – the participants' tactile acuity improved over time, independent of whether they had, or had not, experienced visual deprivation. PMID:25397327

Evolution of cranial telescoping in echolocating whales (Cetacea: Odontoceti).

PubMed

Churchill, Morgan; Geisler, Jonathan H; Beatty, Brian L; Goswami, Anjali

2018-05-01

Odontocete (echolocating whale) skulls exhibit extreme posterior displacement and overlapping of facial bones, here referred to as retrograde cranial telescoping. To examine retrograde cranial telescoping across 40 million years of whale evolution, we collected 3D scans of whale skulls spanning odontocete evolution. We used a sliding semilandmark morphometric approach with Procrustes superimposition and PCA to capture and describe the morphological variation present in the facial region, followed by Ancestral Character State Reconstruction (ACSR) and evolutionary model fitting on significant components to determine how retrograde cranial telescoping evolved. The first PC score explains the majority of variation associated with telescoping and reflects the posterior migration of the external nares and premaxilla alongside expansion of the maxilla and frontal. The earliest diverging fossil odontocetes were found to exhibit a lesser degree of cranial telescoping than later diverging but contemporary whale taxa. Major shifts in PC scores and centroid size are identified at the base of Odontoceti, and early burst and punctuated equilibrium models best fit the evolution of retrograde telescoping. This indicates that the Oligocene was a period of unusually high diversity and evolution in whale skull morphology, with little subsequent evolution in telescoping. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Measuring the 2D baryon acoustic oscillation signal of galaxies in WiggleZ: cosmological constraints

PubMed Central

Hinton, Samuel R.; Kazin, Eyal; Davis, Tamara M.; Blake, Chris; Brough, Sarah; Colless, Matthew; Couch, Warrick J.; Drinkwater, Michael J.; Glazebrook, Karl; Jurek, Russell J.; Parkinson, David; Pimbblet, Kevin A.; Poole, Gregory B.; Pracy, Michael; Woods, David

2016-01-01

We present results from the 2D anisotropic baryon acoustic oscillation (BAO) signal present in the final data set from the WiggleZ Dark Energy Survey. We analyse the WiggleZ data in two ways: first using the full shape of the 2D correlation function and secondly focusing only on the position of the BAO peak in the reconstructed data set. When fitting for the full shape of the 2D correlation function we use a multipole expansion to compare with theory. When we use the reconstructed data we marginalize over the shape and just measure the position of the BAO peak, analysing the data in wedges separating the signal along the line of sight from that parallel to the line of sight. We verify our method with mock data and find the results to be free of bias or systematic offsets. We also redo the pre-reconstruction angle-averaged (1D) WiggleZ BAO analysis with an improved covariance and present an updated result. The final results are presented in the form of Ωc h2, H(z), and DA(z) for three redshift bins with effective redshifts z = 0.44, 0.60, and 0.73. Within these bins and methodologies, we recover constraints between 5 and 22 per cent error. Our cosmological constraints are consistent with flat ΛCDM cosmology and agree with results from the Baryon Oscillation Spectroscopic Survey. PMID:28066154

A Multi Directional Perfect Reconstruction Filter Bank Designed with 2-D Eigenfilter Approach: Application to Ultrasound Speckle Reduction.

PubMed

Nagare, Mukund B; Patil, Bhushan D; Holambe, Raghunath S

2017-02-01

B-Mode ultrasound images are degraded by inherent noise called Speckle, which creates a considerable impact on image quality. This noise reduces the accuracy of image analysis and interpretation. Therefore, reduction of speckle noise is an essential task which improves the accuracy of the clinical diagnostics. In this paper, a Multi-directional perfect-reconstruction (PR) filter bank is proposed based on 2-D eigenfilter approach. The proposed method used for the design of two-dimensional (2-D) two-channel linear-phase FIR perfect-reconstruction filter bank. In this method, the fan shaped, diamond shaped and checkerboard shaped filters are designed. The quadratic measure of the error function between the passband and stopband of the filter has been used an objective function. First, the low-pass analysis filter is designed and then the PR condition has been expressed as a set of linear constraints on the corresponding synthesis low-pass filter. Subsequently, the corresponding synthesis filter is designed using the eigenfilter design method with linear constraints. The newly designed 2-D filters are used in translation invariant pyramidal directional filter bank (TIPDFB) for reduction of speckle noise in ultrasound images. The proposed 2-D filters give better symmetry, regularity and frequency selectivity of the filters in comparison to existing design methods. The proposed method is validated on synthetic and real ultrasound data which ensures improvement in the quality of ultrasound images and efficiently suppresses the speckle noise compared to existing methods.

Measuring the 2D baryon acoustic oscillation signal of galaxies in WiggleZ: cosmological constraints

NASA Astrophysics Data System (ADS)

Hinton, Samuel R.; Kazin, Eyal; Davis, Tamara M.; Blake, Chris; Brough, Sarah; Colless, Matthew; Couch, Warrick J.; Drinkwater, Michael J.; Glazebrook, Karl; Jurek, Russell J.; Parkinson, David; Pimbblet, Kevin A.; Poole, Gregory B.; Pracy, Michael; Woods, David

2017-02-01

We present results from the 2D anisotropic baryon acoustic oscillation (BAO) signal present in the final data set from the WiggleZ Dark Energy Survey. We analyse the WiggleZ data in two ways: first using the full shape of the 2D correlation function and secondly focusing only on the position of the BAO peak in the reconstructed data set. When fitting for the full shape of the 2D correlation function we use a multipole expansion to compare with theory. When we use the reconstructed data we marginalize over the shape and just measure the position of the BAO peak, analysing the data in wedges separating the signal along the line of sight from that parallel to the line of sight. We verify our method with mock data and find the results to be free of bias or systematic offsets. We also redo the pre-reconstruction angle-averaged (1D) WiggleZ BAO analysis with an improved covariance and present an updated result. The final results are presented in the form of Ωc h2, H(z), and DA(z) for three redshift bins with effective redshifts z = 0.44, 0.60, and 0.73. Within these bins and methodologies, we recover constraints between 5 and 22 per cent error. Our cosmological constraints are consistent with flat ΛCDM cosmology and agree with results from the Baryon Oscillation Spectroscopic Survey.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tokola, Ryan A; Mikkilineni, Aravind K; Boehnen, Chris Bensing

Despite being increasingly easy to acquire, 3D data is rarely used for face-based biometrics applications beyond identification. Recent work in image-based demographic biometrics has enjoyed much success, but these approaches suffer from the well-known limitations of 2D representations, particularly variations in illumination, texture, and pose, as well as a fundamental inability to describe 3D shape. This paper shows that simple 3D shape features in a face-based coordinate system are capable of representing many biometric attributes without problem-specific models or specialized domain knowledge. The same feature vector achieves impressive results for problems as diverse as age estimation, gender classification, and racemore » classification.« less

Shape coexistence and evolution in 98Sr

NASA Astrophysics Data System (ADS)

Park, J.; Garnsworthy, A. B.; Krücken, R.; Andreoiu, C.; Ball, G. C.; Bender, P. C.; Chester, A.; Close, A.; Finlay, P.; Garrett, P. E.; Glister, J.; Hackman, G.; Hadinia, B.; Leach, K. G.; Rand, E. T.; Sjue, S.; Starosta, K.; Svensson, C. E.; Tardiff, E.

2016-01-01

Shape coexistence between the strongly deformed ground state and the weakly deformed 02+ state in 98Sr has been a major topic of interest due to the energy difference of 215 keV, which is the smallest in all even-even nuclei. The electric monopole transition strength ρ2(E 0 ) is an important quantity that can relate the deformation difference and the shape mixing between the two 0+ states, which are admixtures of the vibrational (S) and the rotational (D) states in a simple mixing model. In a β -decay spectroscopy experiment, the experimental ρ2(E 0 ) was measured. A value of 0.053(5) is consistent with the previous measurement and was combined with known electric quadrupole transition strengths B (E 2 ) in calculations of a two-state mixing model. Based on a systematic study on neighboring Kr, Zr, and Mo isotopes, the mixing of the 0+ and 2+ states in 98Sr was determined to be 8.6% and 1.3%, respectively, corresponding to deformation parameters βD=0.38 (1 ) and βS=-0.23 (2 ) . These parameters reproduce experimental transition strengths well except for the 41+→21+ transition, which suggests a smaller D-band deformation for J ≥4 .

Plant cell shape: modulators and measurements

PubMed Central

Ivakov, Alexander; Persson, Staffan

2013-01-01

Plant cell shape, seen as an integrative output, is of considerable interest in various fields, such as cell wall research, cytoskeleton dynamics and biomechanics. In this review we summarize the current state of knowledge on cell shape formation in plants focusing on shape of simple cylindrical cells, as well as in complex multipolar cells such as leaf pavement cells and trichomes. We summarize established concepts as well as recent additions to the understanding of how cells construct cell walls of a given shape and the underlying processes. These processes include cell wall synthesis, activity of the actin and microtubule cytoskeletons, in particular their regulation by microtubule associated proteins, actin-related proteins, GTP'ases and their effectors, as well as the recently-elucidated roles of plant hormone signaling and vesicular membrane trafficking. We discuss some of the challenges in cell shape research with a particular emphasis on quantitative imaging and statistical analysis of shape in 2D and 3D, as well as novel developments in this area. Finally, we review recent examples of the use of novel imaging techniques and how they have contributed to our understanding of cell shape formation. PMID:24312104

Separation of plastics by froth flotation. The role of size, shape and density of the particles.

PubMed

Pita, Fernando; Castilho, Ana

2017-02-01

Over the last few years, new methods for plastic separation in mining have been developed. Froth flotation is one of these techniques, which is based on hydrophobicity differences between particles. Unlike minerals, most of the plastics are naturally hydrophobic, thus requiring the addition of chemicals that promote the selective wettability of one of its components, for a flotation separation. The floatability of six granulated post-consumer plastic - Polystyrene (PS), Polymethyl methacrylate (PMMA), Polyethylene Terephthalate (PET-S, PET-D) and Polyvinyl Chloride (PVC-M, PVC-D) - in the presence of tannic acid (wetting agent), and the performance of the flotation separation of five bi-component plastic mixtures - PS/PMMA, PS/PET-S, PS/PET-D, PS/PVC-M and PS/PVC-D - were evaluated. Moreover, the effect of the contact angle, density, size and shape of the particles was also analysed. Results showed that all plastics were naturally hydrophobic, with PS exhibiting the highest floatability. The contact angle and the flotation recovery of six plastics decreased with increasing tannic acid concentration, occurring depression of plastics at very low concentrations. Floatability differed also with the size and shape of plastic particles. For regular-shaped plastics (PS, PMMA and PVC-D) floatability decreased with the increase of particle size, while for lamellar-shaped particles (PET-D) floatability was slightly greater for coarser particles. Thus, plastic particles with small size, lamellar shape and low density present a greater floatability. The quality of separation varied with the mixture type, depending not only on the plastics hydrophobicity, but also on the size, density and shape of the particles, i.e. the particle weight. Flotation separation of plastics can be enhanced by differences in hydrophobicity. In addition, flotation separation improves if the most hydrophobic plastic, that floats, has a lamellar shape and lower density and if the most hydrophilic plastic, that sinks, has a regular shape and higher density. The results obtained show that froth flotation is a potential method for plastics separation, in particular for plastics with particle size greater than 2.0mm. Copyright © 2016 Elsevier Ltd. All rights reserved.

Pulmonary tumor measurements from x-ray computed tomography in one, two, and three dimensions.

PubMed

Villemaire, Lauren; Owrangi, Amir M; Etemad-Rezai, Roya; Wilson, Laura; O'Riordan, Elaine; Keller, Harry; Driscoll, Brandon; Bauman, Glenn; Fenster, Aaron; Parraga, Grace

2011-11-01

We evaluated the accuracy and reproducibility of three-dimensional (3D) measurements of lung phantoms and patient tumors from x-ray computed tomography (CT) and compared these to one-dimensional (1D) and two-dimensional (2D) measurements. CT images of three spherical and three irregularly shaped tumor phantoms were evaluated by three observers who performed five repeated measurements. Additionally, three observers manually segmented 29 patient lung tumors five times each. Follow-up imaging was performed for 23 tumors and response criteria were compared. For a single subject, imaging was performed on nine occasions over 2 years to evaluate multidimensional tumor response. To evaluate measurement accuracy, we compared imaging measurements to ground truth using analysis of variance. For estimates of precision, intraobserver and interobserver coefficients of variation and intraclass correlations (ICC) were used. Linear regression and Pearson correlations were used to evaluate agreement and tumor response was descriptively compared. For spherical shaped phantoms, all measurements were highly accurate, but for irregularly shaped phantoms, only 3D measurements were in high agreement with ground truth measurements. All phantom and patient measurements showed high intra- and interobserver reproducibility (ICC >0.900). Over a 2-year period for a single patient, there was disagreement between tumor response classifications based on 3D measurements and those generated using 1D and 2D measurements. Tumor volume measurements were highly reproducible and accurate for irregular, spherical phantoms and patient tumors with nonuniform dimensions. Response classifications obtained from multidimensional measurements suggest that 3D measurements provide higher sensitivity to tumor response. Copyright © 2011 AUR. Published by Elsevier Inc. All rights reserved.

Structural Basis of the Heterodimer Formation between Cell Shape-Determining Proteins Csd1 and Csd2 from Helicobacter pylori.

PubMed

An, Doo Ri; Im, Ha Na; Jang, Jun Young; Kim, Hyoun Sook; Kim, Jieun; Yoon, Hye Jin; Hesek, Dusan; Lee, Mijoon; Mobashery, Shahriar; Kim, Soon-Jong; Suh, Se Won

2016-01-01

Colonization of the human gastric mucosa by Helicobacter pylori requires its high motility, which depends on the helical cell shape. In H. pylori, several genes (csd1, csd2, csd3/hdpA, ccmA, csd4, csd5, and csd6) play key roles in determining the cell shape by alteration of cross-linking or by trimming of peptidoglycan stem peptides. H. pylori Csd1, Csd2, and Csd3/HdpA are M23B metallopeptidase family members and may act as d,d-endopeptidases to cleave the d-Ala4-mDAP3 peptide bond of cross-linked dimer muropeptides. Csd3 functions also as the d,d-carboxypeptidase to cleave the d-Ala4-d-Ala5 bond of the muramyl pentapeptide. To provide a basis for understanding molecular functions of Csd1 and Csd2, we have carried out their structural characterizations. We have discovered that (i) Csd2 exists in monomer-dimer equilibrium and (ii) Csd1 and Csd2 form a heterodimer. We have determined crystal structures of the Csd2121-308 homodimer and the heterodimer between Csd1125-312 and Csd2121-308. Overall structures of Csd1125-312 and Csd2121-308 monomers are similar to each other, consisting of a helical domain and a LytM domain. The helical domains of both Csd1 and Csd2 play a key role in the formation of homodimers or heterodimers. The Csd1 LytM domain contains a catalytic site with a Zn2+ ion, which is coordinated by three conserved ligands and two water molecules, whereas the Csd2 LytM domain has incomplete metal ligands and no metal ion is bound. Structural knowledge of these proteins sheds light on the events that regulate the cell wall in H. pylori.

Structural Basis of the Heterodimer Formation between Cell Shape-Determining Proteins Csd1 and Csd2 from Helicobacter pylori

PubMed Central

An, Doo Ri; Im, Ha Na; Jang, Jun Young; Kim, Hyoun Sook; Kim, Jieun; Yoon, Hye Jin; Hesek, Dusan; Lee, Mijoon; Mobashery, Shahriar; Kim, Soon-Jong

2016-01-01

Colonization of the human gastric mucosa by Helicobacter pylori requires its high motility, which depends on the helical cell shape. In H. pylori, several genes (csd1, csd2, csd3/hdpA, ccmA, csd4, csd5, and csd6) play key roles in determining the cell shape by alteration of cross-linking or by trimming of peptidoglycan stem peptides. H. pylori Csd1, Csd2, and Csd3/HdpA are M23B metallopeptidase family members and may act as d,d-endopeptidases to cleave the d-Ala4-mDAP3 peptide bond of cross-linked dimer muropeptides. Csd3 functions also as the d,d-carboxypeptidase to cleave the d-Ala4-d-Ala5 bond of the muramyl pentapeptide. To provide a basis for understanding molecular functions of Csd1 and Csd2, we have carried out their structural characterizations. We have discovered that (i) Csd2 exists in monomer-dimer equilibrium and (ii) Csd1 and Csd2 form a heterodimer. We have determined crystal structures of the Csd2121–308 homodimer and the heterodimer between Csd1125–312 and Csd2121–308. Overall structures of Csd1125–312 and Csd2121–308 monomers are similar to each other, consisting of a helical domain and a LytM domain. The helical domains of both Csd1 and Csd2 play a key role in the formation of homodimers or heterodimers. The Csd1 LytM domain contains a catalytic site with a Zn2+ ion, which is coordinated by three conserved ligands and two water molecules, whereas the Csd2 LytM domain has incomplete metal ligands and no metal ion is bound. Structural knowledge of these proteins sheds light on the events that regulate the cell wall in H. pylori. PMID:27711177

Determination of Steering Wheel Angles during CAR Alignment by Image Analysis Methods

NASA Astrophysics Data System (ADS)

Mueller, M.; Voegtle, T.

2016-06-01

Optical systems for automatic visual inspections are of increasing importance in the field of automation in the industrial domain. A new application is the determination of steering wheel angles during wheel track setting of the final inspection of car manufacturing. The camera has to be positioned outside the car to avoid interruptions of the processes and therefore, oblique images of the steering wheel must be acquired. Three different approaches of computer vision are considered in this paper, i.e. a 2D shape-based matching (by means of a plane to plane rectification of the oblique images and detection of a shape model with a particular rotation), a 3D shape-based matching approach (by means of a series of different perspectives of the spatial shape of the steering wheel derived from a CAD design model) and a point-to-point matching (by means of the extraction of significant elements (e.g. multifunctional buttons) of a steering wheel and a pairwise connection of these points to straight lines). The HALCON system (HALCON, 2016) was used for all software developments and necessary adaptions. As reference a mechanical balance with an accuracy of 0.1° was used. The quality assessment was based on two different approaches, a laboratory test and a test during production process. In the laboratory a standard deviation of ±0.035° (2D shape-based matching), ±0.12° (3D approach) and ±0.029° (point-to-point matching) could be obtained. The field test of 291 measurements (27 cars with varying poses and angles of the steering wheel) results in a detection rate of 100% and ±0.48° (2D matching) and ±0.24° (point-to-point matching). Both methods also fulfil the request of real time processing (three measurements per second).

Comparative analysis of 3D data accuracy of single tooth and full dental arch captured by different intraoral and laboratory digital impression systems.

PubMed

Ryakhovskiy, A N; Kostyukova, V V

2016-01-01

The aim of this study was to compare the accuracy of digital impressions taken by different intraoral and laboratory scanners. For this purpose a synthetic jaw model with prepared tooth was scanned using intraoral scanning systems: 3D Progress (MHT S.P.A., IT - MHT Optic Research AG, CH); True Definition (3M ESPE, USA); Trios (3Shape A/S, DNK); CEREC AC Bluecam, CEREC Omnicam (Sirona Dental System GmbH, DE); Planscan (Planmeca, FIN); and laboratory scanning systems: s600 ARTI (Zirkonzahn GmbH, IT); Imetric Iscan D104, CH); D900 (3Shape A/S, DNK); Zfx Evolution (Zfx GmbH, DE) (each n=10). Reference-scanning was done by ATOS Core (GOM mbH, DE). The resulting digital impressions were superimposed with the master-scan. The measured deviations by points (trueness) for intraoral scanners were: True Definition - 15.0±2.85 μm (single tooth) and 45.0±19.11 µm (full arch); Trios - 17.1±1.44 and 58.8±27.36 µm; CEREC AC Bluecam - 22.3±5.58 and 20.3±4.13 µm; CEREC Omnicam - 25.0±1.06 and 78.5±27.03 µm; 3D Progress - 26.4±5.75 and 213.5±47.44 µm; Planscan - 54.6±11.58 and 205.2±21.73 µm. For laboratory scanners: Imetric Iscan D104 - 10.2±0.87 μm (stamp) and 65.3±5.36 µm (full arch); Zfx Evolution - 12.8±0.83 and 66.4±2.80 µm; Zirkonzahn s600 ARTI - 15.1±1.36 and 65.9±1.33 µm; 3Shape D900 - 19.9±0.53 and 63.6±0.83 µm. Precision was: True Definition - 19.9±2.77 μm (single tooth) and 40.1±11.04 µm (full arch); Trios - 25.8±2.49 and 69.9±18.95 µm; CEREC AC Bluecam - 36.4±2.78 and 46.6±3.44 µm; CEREC Omnicam - 37.6±3.29 and 76.2±13.36 µm; 3D Progress - 76.9±11.04 and 102.2±8.06 µm; Planscan - 74.3±6.58 and 93.9±15.32 µm. For laboratory scanners: Imetric Iscan D104 - 11.7±4.39 μm (stamp) and 31.2±5.58 µm (full arch); Zfx Evolution - 8.4±0.49 and 24.8±3.98 µm; Zirkonzahn s600 ARTI - 13.4±6.74 and 20.7±4.34 µm; 3Shape D900 - 10.4±0.93 and 17.8±0.62 µm. Whole deviation of the dental arch was: 3D Progress - 98.0±5.70 µm; True Definition - 47.1±9.61 µm; Trios - 59.6±18.77 µm; Omnicam - 77.8±8.79 µm; Planscan - 107.9±1.58 µm; Bluecam - 46.8±1.22 µm; Imetric - 36.4±1.62 µm; Zfx Evolution - 29.5±0.58 µm; S600 ARTI - 35.0±1.04 µm; 3Shape D900 - 32.7±0.29 µm. The results indicate that digital impressions provide enough accuracy for clinical application.

Orthogonal switching of AMS axes during type-2 fold interference: Insights from integrated X-ray computed tomography, AMS and 3D petrography

NASA Astrophysics Data System (ADS)

Sayab, Mohammad; Miettinen, Arttu; Aerden, Domingo; Karell, Fredrik

2017-10-01

We applied X-ray computed microtomography (μ-CT) in combination with anisotropy of magnetic susceptibility (AMS) analysis to study metamorphic rock fabrics in an oriented drill core sample of pyrite-pyrrhotite-quartz-mica schist. The sample is extracted from the Paleoproterozoic Martimo metasedimentary belt of northern Finland. The μ-CT resolves the spatial distribution, shape and orientation of 25,920 pyrrhotite and 153 pyrite grains localized in mm-thick metapelitic laminae. Together with microstructural analysis, the μ-CT allows us to interpret the prolate symmetry of the AMS ellipsoid and its relationship to the deformation history. AMS of the sample is controlled by pyrrhotite porphyroblasts that grew syntectonically during D1 in subhorizontal microlithons. The short and intermediate axes (K3 and K2) of the AMS ellipsoid interchanged positions during a subsequent deformation (D2) that intensely crenulated S1 and deformed pyrrhotite, while the long axes (K1) maintained a constant position parallel to the maximum stretching direction. However, it is likely that all the three AMS axes switched, similar to the three principal axes of the shape ellipsoid of pyrite porphyroblasts from D1 to D2. The superposition of D1 and D2 produced a type-2 fold interference pattern.

Visual Semantic Based 3D Video Retrieval System Using HDFS.

PubMed

Kumar, C Ranjith; Suguna, S

2016-08-01

This paper brings out a neoteric frame of reference for visual semantic based 3d video search and retrieval applications. Newfangled 3D retrieval application spotlight on shape analysis like object matching, classification and retrieval not only sticking up entirely with video retrieval. In this ambit, we delve into 3D-CBVR (Content Based Video Retrieval) concept for the first time. For this purpose, we intent to hitch on BOVW and Mapreduce in 3D framework. Instead of conventional shape based local descriptors, we tried to coalesce shape, color and texture for feature extraction. For this purpose, we have used combination of geometric & topological features for shape and 3D co-occurrence matrix for color and texture. After thriving extraction of local descriptors, TB-PCT (Threshold Based- Predictive Clustering Tree) algorithm is used to generate visual codebook and histogram is produced. Further, matching is performed using soft weighting scheme with L 2 distance function. As a final step, retrieved results are ranked according to the Index value and acknowledged to the user as a feedback .In order to handle prodigious amount of data and Efficacious retrieval, we have incorporated HDFS in our Intellection. Using 3D video dataset, we future the performance of our proposed system which can pan out that the proposed work gives meticulous result and also reduce the time intricacy.

A method to calculate fission-fragment yields Y(Z,N) versus proton and neutron number in the Brownian shape-motion model

DOE PAGES

Moller, Peter; Ichikawa, Takatoshi

2015-12-23

In this study, we propose a method to calculate the two-dimensional (2D) fission-fragment yield Y(Z,N) versus both proton and neutron number, with inclusion of odd-even staggering effects in both variables. The approach is to use the Brownian shape-motion on a macroscopic-microscopic potential-energy surface which, for a particular compound system is calculated versus four shape variables: elongation (quadrupole moment Q 2), neck d, left nascent fragment spheroidal deformation ϵ f1, right nascent fragment deformation ϵ f2 and two asymmetry variables, namely proton and neutron numbers in each of the two fragments. The extension of previous models 1) introduces a method tomore » calculate this generalized potential-energy function and 2) allows the correlated transfer of nucleon pairs in one step, in addition to sequential transfer. In the previous version the potential energy was calculated as a function of Z and N of the compound system and its shape, including the asymmetry of the shape. We outline here how to generalize the model from the “compound-system” model to a model where the emerging fragment proton and neutron numbers also enter, over and above the compound system composition.« less

A new approach for shaping of dual-reflector antennas

NASA Technical Reports Server (NTRS)

Lee, Teh-Hong; Burnside, W. D.; Rudduck, Roger C.

1987-01-01

The shaping of 2-D dual-reflector antenna systems to generate a prescribed distribution with uniform phase at the aperture of the second reflector is examined. This method is based on the geometrical nature of Cassegrain and Gregorian dual-reflector antennas. The method of syntheses satisfies the principles of geometrical optics which are the foundations of dual-reflector designs. Instead of setting up differential equations or heuristically designing the subreflector, a set of algebraic equations is formulated and solved numerically to obtain the desired surfaces. The caustics of the reflected rays from the subreflector can be obtained and examined. Several examples of 2-D dual-reflector shaping are shown to validate the study. Geometrical optics and physical optics are used to calculate the scattered fields from the reflectors.

The general 2-D moments via integral transform method for acoustic radiation and scattering

NASA Astrophysics Data System (ADS)

Smith, Jerry R.; Mirotznik, Mark S.

2004-05-01

The moments via integral transform method (MITM) is a technique to analytically reduce the 2-D method of moments (MoM) impedance double integrals into single integrals. By using a special integral representation of the Green's function, the impedance integral can be analytically simplified to a single integral in terms of transformed shape and weight functions. The reduced expression requires fewer computations and reduces the fill times of the MoM impedance matrix. Furthermore, the resulting integral is analytic for nearly arbitrary shape and weight function sets. The MITM technique is developed for mixed boundary conditions and predictions with basic shape and weight function sets are presented. Comparisons of accuracy and speed between MITM and brute force are presented. [Work sponsored by ONR and NSWCCD ILIR Board.

Design and Implementation of Low Profile Antenna for Dual-Band Applications Using Rotated E-Shaped Conductor-Backed Plane

PubMed Central

Jalali, Mahdi; Sedghi, Tohid; Shafei, Shahin

2014-01-01

A novel configuration of a printed monopole antenna with a very compact size for satisfying WLAN operations at the 5.2/5.8 GHz and also for X-band operations at the 10 GHz has been proposed. The antenna includes a simple square-shaped patch as the radiator, the rotated U-shaped conductor back plane element with embedded strip on it, and the partial rectangular ground surface. By using the rotated U-shaped conductor-backed plane with proper values, good impedance matching and improvement in bandwidth can be achieved, at the lower and upper bands. The impedance bandwidth for S 11 < −10 dB is about 1.15 GHz for 5 GHz band and 5.3 GHz for X-band. The measured peak gains are about 1.9 dBi at WLAN-band and 4.2 dBi at X-band. The experimental results represent that the realized antenna with good omnidirectional radiation characteristics, enough impedance bandwidth, and reasonable gains can be appropriate for various applications of the future developed technologies and handheld devices. PMID:24711732

Pop-up assembly of 3D structures actuated by heat shrinkable polymers

NASA Astrophysics Data System (ADS)

Cui, Jianxun; Adams, J. G. M.; Zhu, Yong

2017-12-01

Folding 2D sheets into desired 3D structures is a promising fabrication technique that can find a wide range of applications. Compressive buckling provides an attractive strategy to actuate the folding and can be applied to a broad range of materials. Here a new and simple method is reported to achieve controlled compressive buckling, which is actuated by a heat shrinkable polymer sheet. The buckling deformation is localized at the pre-defined creases in the 2D sheet, resulting in sharp folding. Two approaches are developed to actuate the transformation, which follow similar geometric rules. In the first approach, the 2D precursor is pushed from outside, which leads to a 3D structure surrounded by the shrunk polymer sheet. Assembled 3D structures include prisms/pyramids with different base shapes, house roof, partial soccer ball, Miura-ori structure and insect wing. In the second approach, the 2D precursor is pulled from inside, which leads to a 3D structure enclosing the shrunk polymer sheet. Prisms/pyramids with different base shapes are assembled. The assembled structures are further tessellated to fabricate cellular structures that can be used as thermal insulator and crash energy absorber. They are also stacked vertically to fabricate complex multilayer structures.

Creation of three-dimensional craniofacial standards from CBCT images

NASA Astrophysics Data System (ADS)

Subramanyan, Krishna; Palomo, Martin; Hans, Mark

2006-03-01

Low-dose three-dimensional Cone Beam Computed Tomography (CBCT) is becoming increasingly popular in the clinical practice of dental medicine. Two-dimensional Bolton Standards of dentofacial development are routinely used to identify deviations from normal craniofacial anatomy. With the advent of CBCT three dimensional imaging, we propose a set of methods to extend these 2D Bolton Standards to anatomically correct surface based 3D standards to allow analysis of morphometric changes seen in craniofacial complex. To create 3D surface standards, we have implemented series of steps. 1) Converting bi-plane 2D tracings into set of splines 2) Converting the 2D splines curves from bi-plane projection into 3D space curves 3) Creating labeled template of facial and skeletal shapes and 4) Creating 3D average surface Bolton standards. We have used datasets from patients scanned with Hitachi MercuRay CBCT scanner providing high resolution and isotropic CT volume images, digitized Bolton Standards from age 3 to 18 years of lateral and frontal male, female and average tracings and converted them into facial and skeletal 3D space curves. This new 3D standard will help in assessing shape variations due to aging in young population and provide reference to correct facial anomalies in dental medicine.

Fully automatic segmentation of arbitrarily shaped fiducial markers in cone-beam CT projections

NASA Astrophysics Data System (ADS)

Bertholet, J.; Wan, H.; Toftegaard, J.; Schmidt, M. L.; Chotard, F.; Parikh, P. J.; Poulsen, P. R.

2017-02-01

Radio-opaque fiducial markers of different shapes are often implanted in or near abdominal or thoracic tumors to act as surrogates for the tumor position during radiotherapy. They can be used for real-time treatment adaptation, but this requires a robust, automatic segmentation method able to handle arbitrarily shaped markers in a rotational imaging geometry such as cone-beam computed tomography (CBCT) projection images and intra-treatment images. In this study, we propose a fully automatic dynamic programming (DP) assisted template-based (TB) segmentation method. Based on an initial DP segmentation, the DPTB algorithm generates and uses a 3D marker model to create 2D templates at any projection angle. The 2D templates are used to segment the marker position as the position with highest normalized cross-correlation in a search area centered at the DP segmented position. The accuracy of the DP algorithm and the new DPTB algorithm was quantified as the 2D segmentation error (pixels) compared to a manual ground truth segmentation for 97 markers in the projection images of CBCT scans of 40 patients. Also the fraction of wrong segmentations, defined as 2D errors larger than 5 pixels, was calculated. The mean 2D segmentation error of DP was reduced from 4.1 pixels to 3.0 pixels by DPTB, while the fraction of wrong segmentations was reduced from 17.4% to 6.8%. DPTB allowed rejection of uncertain segmentations as deemed by a low normalized cross-correlation coefficient and contrast-to-noise ratio. For a rejection rate of 9.97%, the sensitivity in detecting wrong segmentations was 67% and the specificity was 94%. The accepted segmentations had a mean segmentation error of 1.8 pixels and 2.5% wrong segmentations.

Use of Image Based Modelling for Documentation of Intricately Shaped Objects

NASA Astrophysics Data System (ADS)

Marčiš, M.; Barták, P.; Valaška, D.; Fraštia, M.; Trhan, O.

2016-06-01

In the documentation of cultural heritage, we can encounter three dimensional shapes and structures which are complicated to measure. Such objects are for example spiral staircases, timber roof trusses, historical furniture or folk costume where it is nearly impossible to effectively use the traditional surveying or the terrestrial laser scanning due to the shape of the object, its dimensions and the crowded environment. The actual methods of digital photogrammetry can be very helpful in such cases with the emphasis on the automated processing of the extensive image data. The created high resolution 3D models and 2D orthophotos are very important for the documentation of architectural elements and they can serve as an ideal base for the vectorization and 2D drawing documentation. This contribution wants to describe the various usage of image based modelling in specific interior spaces and specific objects. The advantages and disadvantages of the photogrammetric measurement of such objects in comparison to other surveying methods are reviewed.

Indomethacin causes prostaglandin D(2)-like and eotaxin-like selective responses in eosinophils and basophils.

PubMed

Stubbs, Victoria E L; Schratl, Petra; Hartnell, Adele; Williams, Timothy J; Peskar, Bernhard A; Heinemann, Akos; Sabroe, Ian

2002-07-19

We investigated the actions of a panel of nonsteroidal anti-inflammatory drugs on eosinophils, basophils, neutrophils, and monocytes. Indomethacin alone was a potent and selective inducer of eosinophil and basophil shape change. In eosinophils, indomethacin induced chemotaxis, CD11b up-regulation, respiratory burst, and L-selectin shedding but did not cause up-regulation of CD63 expression. Pretreatment of eosinophils with indomethacin also enhanced subsequent eosinophil shape change induced by eotaxin, although treatment with higher concentrations of indomethacin resulted in a decrease in the expression of the major eosinophil chemokine receptor, CCR3. Indomethacin activities and cell selectivity closely resembled those of prostaglandin D(2) (PGD(2)). Eosinophil shape change in response to eotaxin was inhibited by pertussis toxin, but indomethacin- and PGD(2)-induced shape change responses were not. Treatment of eosinophils with specific inhibitors of phospholipase C (U-73122), phosphatidylinositol 3-kinase (LY-294002), and p38 mitogen-activated protein kinase (SB-202190) revealed roles for these pathways in indomethacin signaling. Indomethacin and its analogues may therefore provide a structural basis from which selective PGD(2) receptor small molecule antagonists may be designed and which may have utility in the treatment of allergic inflammatory disease.

3D Printing of Thermo-Responsive Methylcellulose Hydrogels for Cell-Sheet Engineering

PubMed Central

Cochis, Andrea; Sorrentino, Rita; Grassi, Federico; Leigheb, Massimiliano; Farè, Silvia

2018-01-01

A possible strategy in regenerative medicine is cell-sheet engineering (CSE), i.e., developing smart cell culture surfaces from which to obtain intact cell sheets (CS). The main goal of this study was to develop 3D printing via extrusion-based bioprinting of methylcellulose (MC)-based hydrogels. Hydrogels were prepared by mixing MC powder in saline solutions (Na2SO4 and PBS). MC-based hydrogels were analyzed to investigate the rheological behavior and thus optimize the printing process parameters. Cells were tested in vitro on ring-shaped printed hydrogels; bulk MC hydrogels were used for comparison. In vitro tests used murine embryonic fibroblasts (NIH/3T3) and endothelial murine cells (MS1), and the resulting cell sheets were characterized analyzing cell viability and immunofluorescence. In terms of CS preparation, 3D printing proved to be an optimal approach to obtain ring-shaped CS. Cell orientation was observed for the ring-shaped CS and was confirmed by the degree of circularity of their nuclei: cell nuclei in ring-shaped CS were more elongated than those in sheets detached from bulk hydrogels. The 3D printing process appears adequate for the preparation of cell sheets of different shapes for the regeneration of complex tissues. PMID:29642573

Profile Optimization Method for Robust Airfoil Shape Optimization in Viscous Flow

NASA Technical Reports Server (NTRS)

Li, Wu

2003-01-01

Simulation results obtained by using FUN2D for robust airfoil shape optimization in transonic viscous flow are included to show the potential of the profile optimization method for generating fairly smooth optimal airfoils with no off-design performance degradation.

Deformable segmentation via sparse representation and dictionary learning.

PubMed

Zhang, Shaoting; Zhan, Yiqiang; Metaxas, Dimitris N

2012-10-01

"Shape" and "appearance", the two pillars of a deformable model, complement each other in object segmentation. In many medical imaging applications, while the low-level appearance information is weak or mis-leading, shape priors play a more important role to guide a correct segmentation, thanks to the strong shape characteristics of biological structures. Recently a novel shape prior modeling method has been proposed based on sparse learning theory. Instead of learning a generative shape model, shape priors are incorporated on-the-fly through the sparse shape composition (SSC). SSC is robust to non-Gaussian errors and still preserves individual shape characteristics even when such characteristics is not statistically significant. Although it seems straightforward to incorporate SSC into a deformable segmentation framework as shape priors, the large-scale sparse optimization of SSC has low runtime efficiency, which cannot satisfy clinical requirements. In this paper, we design two strategies to decrease the computational complexity of SSC, making a robust, accurate and efficient deformable segmentation system. (1) When the shape repository contains a large number of instances, which is often the case in 2D problems, K-SVD is used to learn a more compact but still informative shape dictionary. (2) If the derived shape instance has a large number of vertices, which often appears in 3D problems, an affinity propagation method is used to partition the surface into small sub-regions, on which the sparse shape composition is performed locally. Both strategies dramatically decrease the scale of the sparse optimization problem and hence speed up the algorithm. Our method is applied on a diverse set of biomedical image analysis problems. Compared to the original SSC, these two newly-proposed modules not only significant reduce the computational complexity, but also improve the overall accuracy. Copyright © 2012 Elsevier B.V. All rights reserved.

STM/STS Observation on Layered Nitride Superconductor α-(DDA)xTiNCl

NASA Astrophysics Data System (ADS)

Sugimoto, Akira; Ukita, Ryuichi; Ekino, Toshikazu; Zheng, Zhanfeng; Yamanaka, Shoji

2012-12-01

Scanning tunneling microscopy/spectroscopy (STM/STS) measurements on α-(DDA)xTiNCl (DDA=H2N-(CH2)10-NH2, Tc=16 K) have been carried out. The STM topography exhibits simple rectangular shaped atomic lattice with the periods of |a|=0.38 nm and |b| =0.33 nm. The averaged dI / dV spectrum shows the gap value of Δ ~ 9 meV, giving an unusual large gap ratio 2Δ/kBTc ≃ 13. The STS results show the bar-shaped domain structures along the b-axis direction in the bias range of V = +5 ~ +15 mV, demonstrating the possible existence of intercalated molecules.

Unobtrusive Multi-Static Serial LiDAR Imager (UMSLI) First Generation Shape-Matching Based Classifier for 2D Contours

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Zheng; Ouyang, Bing; Principe, Jose

A multi-static serial LiDAR system prototype was developed under DE-EE0006787 to detect, classify, and record interactions of marine life with marine hydrokinetic generation equipment. This software implements a shape-matching based classifier algorithm for the underwater automated detection of marine life for that system. In addition to applying shape descriptors, the algorithm also adopts information theoretical learning based affine shape registration, improving point correspondences found by shape descriptors as well as the final similarity measure.

On the orbits that generate the X-shape in the Milky Way bulge

NASA Astrophysics Data System (ADS)

Abbott, Caleb G.; Valluri, Monica; Shen, Juntai; Debattista, Victor P.

2017-09-01

The Milky Way (MW) bulge shows a boxy/peanut or X-shaped bulge (hereafter BP/X) when viewed in infrared or microwave bands. We examine orbits in an N-body model of a barred disc galaxy that is scaled to match the kinematics of the MW bulge. We generate maps of projected stellar surface density, unsharp masked images, 3D excess-mass distributions (showing mass outside ellipsoids), line-of-sight number count distributions, and 2D line-of-sight kinematics for the simulation as well as co-added orbit families, in order to identify the orbits primarily responsible for the BP/X shape. We estimate that between 19 and 23 per cent of the mass of the bar in this model is associated with the BP/X shape and that the majority of bar orbits contribute to this shape that is clearly seen in projected surface density maps and 3D excess mass for non-resonant box orbits, 'banana' orbits, 'fish/pretzel' orbits and 'brezel' orbits. Although only the latter two families (comprising 7.5 per cent of the total mass) show a distinct X-shape in unsharp masked images, we find that nearly all bar orbit families contribute some mass to the 3D BP/X-shape. All co-added orbit families show a bifurcation in stellar number count distribution with distance that resembles the bifurcation observed in red clump stars in the MW. However, only the box orbit family shows an increasing separation of peaks with increasing galactic latitude |b|, similar to that observed. Our analysis suggests that no single orbit family fully explains all the observed features associated with the MW's BP/X-shaped bulge, but collectively the non-resonant boxes and various resonant boxlet orbits contribute at different distances from the centre to produce this feature. We propose that since box orbits (which are the dominant population in bars) have three incommensurable orbital fundamental frequencies, their 3D shapes are highly flexible and, like Lissajous figures, this family of orbits is most easily able to adapt to evolution in the shape of the underlying potential.

Error in geometric morphometric data collection: Combining data from multiple sources.

PubMed

Robinson, Chris; Terhune, Claire E

2017-09-01

This study compares two- and three-dimensional morphometric data to determine the extent to which intra- and interobserver and intermethod error influence the outcomes of statistical analyses. Data were collected five times for each method and observer on 14 anthropoid crania using calipers, a MicroScribe, and 3D models created from NextEngine and microCT scans. ANOVA models were used to examine variance in the linear data at the level of genus, species, specimen, observer, method, and trial. Three-dimensional data were analyzed using geometric morphometric methods; principal components analysis was employed to examine how trials of all specimens were distributed in morphospace and Procrustes distances among trials were calculated and used to generate UPGMA trees to explore whether all trials of the same individual grouped together regardless of observer or method. Most variance in the linear data was at the genus level, with greater variance at the observer than method levels. In the 3D data, interobserver and intermethod error were similar to intraspecific distances among Callicebus cupreus individuals, with interobserver error being higher than intermethod error. Generally, taxa separate well in morphospace, with different trials of the same specimen typically grouping together. However, trials of individuals in the same species overlapped substantially with one another. Researchers should be cautious when compiling data from multiple methods and/or observers, especially if analyses are focused on intraspecific variation or closely related species, as in these cases, patterns among individuals may be obscured by interobserver and intermethod error. Conducting interobserver and intermethod reliability assessments prior to the collection of data is recommended. © 2017 Wiley Periodicals, Inc.

Dentine morphology of Atapuerca-Sima de los Huesos lower molars: Evolutionary implications through three-dimensional geometric morphometric analysis.

PubMed

Hanegraef, Hester; Martinón-Torres, María; Martínez de Pinillos, Marina; Martín-Francés, Laura; Vialet, Amélie; Arsuaga, Juan Luis; Bermúdez de Castro, José María

2018-06-01

This study aims to explore the affinities of the Sima de los Huesos (SH) population in relation to Homo neanderthalensis, Arago, and early and contemporary Homo sapiens. By characterizing SH intra-population variation, we test current models to explain the Neanderthal origins. Three-dimensional reconstructions of dentine surfaces of lower first and second molars were produced by micro-computed tomography. Landmarks and sliding semilandmarks were subjected to generalized Procrustes analysis and principal components analysis. SH is often similar in shape to Neanderthals, and both groups are generally discernible from Homo sapiens. For example, the crown height of SH and Neanderthals is lower than for modern humans. Differences in the presence of a mid-trigonid crest are also observed, with contemporary Homo sapiens usually lacking this feature. Although SH and Neanderthals show strong affinities, they can be discriminated based on certain traits. SH individuals are characterized by a lower intra-population variability, and show a derived dental reduction in lower second molars compared to Neanderthals. SH also differs in morphological features from specimens that are often classified as Homo heidelbergensis, such as a lower crown height and less pronounced mid-trigonid crest in the Arago fossils. Our results are compatible with the idea that multiple evolutionary lineages or populations coexisted in Europe during the Middle Pleistocene, with the SH paradigm phylogenetically closer to Homo neanderthalensis. Further research could support the possibility of SH as a separate taxon. Alternatively, SH could be a subspecies of Neanderthals, with the variability of this clade being remarkably higher than previously thought. © 2018 Wiley Periodicals, Inc.

Precipitate shape fitting and reconstruction by means of 3D Zernike functions

NASA Astrophysics Data System (ADS)

Callahan, P. G.; De Graef, M.

2012-01-01

3D Zernike functions are defined and used for the reconstruction of precipitate shapes. These functions are orthogonal over the unit ball and allow for an arbitrary shape, scaled to fit inside an embedding sphere, to be decomposed into 3D harmonics. Explicit expressions are given for the general Zernike moments, correcting typographical errors in the literature. Explicit expressions of the Zernike moments for the ellipsoid and the cube are given. The 3D Zernike functions and moments are applied to the reconstruction of γ' precipitate shapes in two Ni-based superalloys, one with nearly cuboidal precipitate shapes, and one with more complex dendritic shapes.

gWEGA: GPU-accelerated WEGA for molecular superposition and shape comparison.

PubMed

Yan, Xin; Li, Jiabo; Gu, Qiong; Xu, Jun

2014-06-05

Virtual screening of a large chemical library for drug lead identification requires searching/superimposing a large number of three-dimensional (3D) chemical structures. This article reports a graphic processing unit (GPU)-accelerated weighted Gaussian algorithm (gWEGA) that expedites shape or shape-feature similarity score-based virtual screening. With 86 GPU nodes (each node has one GPU card), gWEGA can screen 110 million conformations derived from an entire ZINC drug-like database with diverse antidiabetic agents as query structures within 2 s (i.e., screening more than 55 million conformations per second). The rapid screening speed was accomplished through the massive parallelization on multiple GPU nodes and rapid prescreening of 3D structures (based on their shape descriptors and pharmacophore feature compositions). Copyright © 2014 Wiley Periodicals, Inc.

Second to fourth digit ratio and face shape

PubMed Central

Fink, Bernhard; Grammer, Karl; Mitteroecker, Philipp; Gunz, Philipp; Schaefer, Katrin; Bookstein, Fred L; Manning, John T

2005-01-01

The average human male face differs from the average female face in size and shape of the jaws, cheek-bones, lips, eyes and nose. It is possible that this dimorphism is determined by sex steroids such as testosterone (T) and oestrogen (E), and several studies on the perception of such characteristics have been based on this assumption, but those studies focussed mainly on the relationship of male faces with circulating hormone levels; the corresponding biology of the female face remains mainly speculative. This paper is concerned with the relative importance of prenatal T and E levels (assessed via the 2D : 4D finger length ratio, a proxy for the ratio of T/E) and sex in the determination of facial form as characterized by 64 landmark points on facial photographs of 106 Austrians of college age. We found that (i) prenatal sex steroid ratios (in terms of 2D : 4D) and actual chromosomal sex dimorphism operate differently on faces, (ii) 2D : 4D affects male and female face shape by similar patterns, but (iii) is three times more intense in men than in women. There was no evidence that these effects were confounded by allometry or facial asymmetry. Our results suggest that studies on the perception of facial characteristics need to consider differential effects of prenatal hormone exposure and actual chromosomal gender in order to understand how characteristics have come to be rated ‘masculine’ or ‘feminine’ and the consequences of these perceptions in terms of mate preferences. PMID:16191608

Graph Theoretical Representation of Atomic Asymmetry and Molecular Chirality of Benzenoids in Two-Dimensional Space

PubMed Central

Zhao, Tanfeng; Zhang, Qingyou; Long, Hailin; Xu, Lu

2014-01-01

In order to explore atomic asymmetry and molecular chirality in 2D space, benzenoids composed of 3 to 11 hexagons in 2D space were enumerated in our laboratory. These benzenoids are regarded as planar connected polyhexes and have no internal holes; that is, their internal regions are filled with hexagons. The produced dataset was composed of 357,968 benzenoids, including more than 14 million atoms. Rather than simply labeling the huge number of atoms as being either symmetric or asymmetric, this investigation aims at exploring a quantitative graph theoretical descriptor of atomic asymmetry. Based on the particular characteristics in the 2D plane, we suggested the weighted atomic sum as the descriptor of atomic asymmetry. This descriptor is measured by circulating around the molecule going in opposite directions. The investigation demonstrates that the weighted atomic sums are superior to the previously reported quantitative descriptor, atomic sums. The investigation of quantitative descriptors also reveals that the most asymmetric atom is in a structure with a spiral ring with the convex shape going in clockwise direction and concave shape going in anticlockwise direction from the atom. Based on weighted atomic sums, a weighted F index is introduced to quantitatively represent molecular chirality in the plane, rather than merely regarding benzenoids as being either chiral or achiral. By validating with enumerated benzenoids, the results indicate that the weighted F indexes were in accordance with their chiral classification (achiral or chiral) over the whole benzenoids dataset. Furthermore, weighted F indexes were superior to previously available descriptors. Benzenoids possess a variety of shapes and can be extended to practically represent any shape in 2D space—our proposed descriptor has thus the potential to be a general method to represent 2D molecular chirality based on the difference between clockwise and anticlockwise sums around a molecule. PMID:25032832

Prospective evaluation of shape similarity based pose prediction method in D3R Grand Challenge 2015

NASA Astrophysics Data System (ADS)

Kumar, Ashutosh; Zhang, Kam Y. J.

2016-09-01

Evaluation of ligand three-dimensional (3D) shape similarity is one of the commonly used approaches to identify ligands similar to one or more known active compounds from a library of small molecules. Apart from using ligand shape similarity as a virtual screening tool, its role in pose prediction and pose scoring has also been reported. We have recently developed a method that utilizes ligand 3D shape similarity with known crystallographic ligands to predict binding poses of query ligands. Here, we report the prospective evaluation of our pose prediction method through the participation in drug design data resource (D3R) Grand Challenge 2015. Our pose prediction method was used to predict binding poses of heat shock protein 90 (HSP90) and mitogen activated protein kinase kinase kinase kinase (MAP4K4) ligands and it was able to predict the pose within 2 Å root mean square deviation (RMSD) either as the top pose or among the best of five poses in a majority of cases. Specifically for HSP90 protein, a median RMSD of 0.73 and 0.68 Å was obtained for the top and the best of five predictions respectively. For MAP4K4 target, although the median RMSD for our top prediction was only 2.87 Å but the median RMSD of 1.67 Å for the best of five predictions was well within the limit for successful prediction. Furthermore, the performance of our pose prediction method for HSP90 and MAP4K4 ligands was always among the top five groups. Particularly, for MAP4K4 protein our pose prediction method was ranked number one both in terms of mean and median RMSD when the best of five predictions were considered. Overall, our D3R Grand Challenge 2015 results demonstrated that ligand 3D shape similarity with the crystal ligand is sufficient to predict binding poses of new ligands with acceptable accuracy.

Application of Shape Similarity in Pose Selection and Virtual Screening in CSARdock2014 Exercise.

PubMed

Kumar, Ashutosh; Zhang, Kam Y J

2016-06-27

To evaluate the applicability of shape similarity in docking-based pose selection and virtual screening, we participated in the CSARdock2014 benchmark exercise for identifying the correct docking pose of inhibitors targeting factor XA, spleen tyrosine kinase, and tRNA methyltransferase. This exercise provides a valuable opportunity for researchers to test their docking programs, methods, and protocols in a blind testing environment. In the CSARdock2014 benchmark exercise, we have implemented an approach that uses ligand 3D shape similarity to facilitate docking-based pose selection and virtual screening. We showed here that ligand 3D shape similarity between bound poses could be used to identify the native-like pose from an ensemble of docking-generated poses. Our method correctly identified the native pose as the top-ranking pose for 73% of test cases in a blind testing environment. Moreover, the pose selection results also revealed an excellent correlation between ligand 3D shape similarity scores and RMSD to X-ray crystal structure ligand. In the virtual screening exercise, the average RMSD for our pose prediction was found to be 1.02 Å, and it was one of the top performances achieved in CSARdock2014 benchmark exercise. Furthermore, the inclusion of shape similarity improved virtual screening performance of docking-based scoring and ranking. The coefficient of determination (r(2)) between experimental activities and docking scores for 276 spleen tyrosine kinase inhibitors was found to be 0.365 but reached 0.614 when the ligand 3D shape similarity was included.

Reorganization of equivalence classes: effects of preliminary training and meaningful stimuli.

PubMed

Arntzen, Erik; Nartey, Richard K; Fields, Lanny

2018-05-01

In Condition 1, adults learned the baseline relations for the three equivalence classes A1-B1-C1-D1-E1, A2-B2-C2-D2-E2, and A3-B3-C3-D3-E3. Classes contained abstract shapes in the ABS and four preliminary training groups. Each class in the PIC group contained one picture and four abstract shapes. Before class formation for four other groups, preliminary training involved establishing identity (CC) or arbitrary (CX) relations either with or without a delay. Without preliminary training, classes formed with low and high likelihoods in the ABS and PIC groups, respectively. Preliminary training with no delay produced modest increases in class formation, while preliminary training with delay produced large increases in class formation. Condition 2 replicated Condition 1 but with training of reassigned BC and CD relations that linked C from one class to B and D from another class: B1-C2, B2-C3, B3-C1, C2-D1, C3-D2, and C1-D3. Subsequent tests assessed the emergence of the reorganized classes A1-B1-C2-D1-E1, A2-B2-C3-D2-E2, and A3-B3-C1-D3-E3. All preliminary training procedures increased likelihood of forming the reorganized classes to the level seen in the PIC group. Greater gains were produced by preliminary training with no delays than with delays. Test performances also showed how preliminary training influenced baseline acquisition speed and participant-defined relations. © 2018 Society for the Experimental Analysis of Behavior.

A Multi-D-Shaped Optical Fiber for Refractive Index Sensing

PubMed Central

Chen, Chien-Hsing; Tsao, Tzu-Chein; Tang, Jaw-Luen; Wu, Wei-Te

2010-01-01

A novel class of multi-D-shaped optical fiber suited for refractive index measurements is presented. The multi-D-shaped optical fiber was constructed by forming several D-sections in a multimode optical fiber at localized regions with femtosecond laser pulses. The total number of D-shaped zones fabricated could range from three to seven. Each D-shaped zone covered a sensor volume of 100 μm depth, 250 μm width, and 1 mm length. The mean roughness of the core surface obtained by the AFM images was 231.7 nm, which is relatively smooth. Results of the tensile test indicated that the fibers have sufficient mechanical strength to resist damage from further processing. The multi-D-shaped optical fiber as a high sensitive refractive-index sensor to detect changes in the surrounding refractive index was studied. The results for different concentrations of sucrose solution show that a resolution of 1.27 × 10−3–3.13 × 10−4 RIU is achieved for refractive indices in the range of 1.333 to 1.403, suggesting that the multi-D-shaped fibers are attractive for chemical, biological, and biochemical sensing with aqueous solutions. PMID:22399908

Interactive shape metamorphosis

NASA Technical Reports Server (NTRS)

Chen, David T.; State, Andrei; Banks, David

1994-01-01

A technique for controlled metamorphosis between surfaces in 3-space is described. Well-understood techniques to produce shape metamorphosis between models in a 2D parametric space is applied. The user selects morphable features interactively, and the morphing process executes in real time on a high-performance graphics multicomputer.

Intraoperative three-dimensional transesophageal echocardiography for assessing the defect geometries of mitral prosthetic paravalvular leak during transcatheter closure.

PubMed

Wei, Jeng; Yin, Wei-Hsian; Lee, Yung-Tsai; Hsiung, Ming C; Tsai, Shen-Kou; Chuang, Yi Cheng; Ou, Ching-Huei; Chou, Yi-Pen

2015-03-01

Paravalvular leaks (PVLs) are a common complication of prosthetic valve replacement. Use of the transcatheter intervention technique is a suitable alternative in high-risk patients who may not tolerate repeat surgery. Common reasons for failure of this demanding intervention include poor imaging quality and unsuitable anatomy. The purpose of this study was to assess the usefulness and the incremental value of real-time three-dimensional (RT 3D) transesophageal echocardiography (TEE) over two-dimensional (2D) TEE findings in the evaluation of the geometry and track of mitral PVLs during transcatheter closure. Five patients with six mitral PVLs at high risk for repeat surgery underwent transcatheter leak closure. Intraoperative RT 3DTEE was used to assess the location, shape, number, and size of the defects. Transapical approaches were used in all cases with fluoroscopic and RT 3D TEE guidance of the wire and catheter, device positioning, and assessment of residual leak after the procedure. In all of the cases, defects with irregular crescent shapes and distorted tracks were clearly delineated by RT 3D TEE. This was compared to those results obtained through 2D TEE, which was unable to characterize the defects. Three cases showed small leaks, which were completely occluded with a patent ductus arteriosus (PDA) device in two cases, and a muscular ventricular septal defect (mVSD) occluder combined with coil devices in one case. One case involved a large leak and early device embolization of the muscular VSD occluder, which was removed surgically, and demonstrated a crescent-shaped defect. One patient had two releaks 2 months subsequent to the procedure due to two new extended leaks at the tails of the crescent-shaped defect. RT 3D TEE can clearly delineate the geometries of defects in their entirety, including shape, size, and location of the defect and track canal. It would also appear that RT 3D TEE is superior to 2D TEE in the process of guiding the wire through the difficult canal anatomy, facilitating the overall procedure. The small mitral PVLs can be completely occluded, but subsequent complications occurred with large defect closures because of embolization or releak. Therefore, transcatheter closure of PVLs seems to be an attractive alternative for these patients, but newer occluder designs that better conform to leak geometry will be required to improve outcomes. Copyright © 2014. Published by Elsevier Taiwan.

Goal-Directed Grasping: The Dimensional Properties of an Object Influence the Nature of the Visual Information Mediating Aperture Shaping

ERIC Educational Resources Information Center

Holmes, Scott A.; Heath, Matthew

2013-01-01

An issue of continued debate in the visuomotor control literature surrounds whether a 2D object serves as a representative proxy for a 3D object in understanding the nature of the visual information supporting grasping control. In an effort to reconcile this issue, we examined the extent to which aperture profiles for grasping 2D and 3D objects…

Infrared spectra of C2H4 dimer and trimer

NASA Astrophysics Data System (ADS)

Barclay, A. J.; Esteki, K.; McKellar, A. R. W.; Moazzen-Ahmadi, N.

2018-05-01

Spectra of ethylene dimers and trimers are studied in the ν11 and (for the dimer) ν9 fundamental band regions of C2H4 (≈2990 and 3100 cm-1) using a tunable optical parametric oscillator source to probe a pulsed supersonic slit jet expansion. The deuterated trimer has been observed previously, but this represents the first rotationally resolved spectrum of (C2H4)3. The results support the previously determined cross-shaped (D2d) dimer and barrel-shaped (C3h or C3) trimer structures. However, the dimer spectrum in the ν9 fundamental region of C2H4 is apparently very perturbed and a previous rotational analysis is not well verified.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yingjie, E-mail: yzx@ansto.gov.au; Bhadbhade, Mohan; Karatchevtseva, Inna

Three new coordination polymers of uranium(VI) with pyromellitic acid (H{sub 4}btca) have been synthesized and structurally characterized. (ED)[(UO{sub 2})(btca)]·(DMSO)·3H{sub 2}O (1) (ED=ethylenediammonium; DMSO=dimethylsulfoxide) has a lamellar structure with intercalation of ED and DMSO. (NH{sub 4}){sub 2}[(UO{sub 2}){sub 6}O{sub 2}(OH){sub 6}(btca)]·~6H{sub 2}O (2) has a 3D framework built from 7-fold coordinated uranyl trinuclear units and btca ligands with 1D diamond-shaped channels (~8.5 Å×~8.6 Å). [(UO{sub 2}){sub 2}(H{sub 2}O)(btca)]·4H{sub 2}O (3) has a 3D network constructed by two types of 7-fold coordinated uranium polyhedron. The unique μ{sub 5}-coordination mode of btca in 3 enables the formation of 1D olive-shaped large channels (~4.5more » Å×~19 Å). Vibrational modes, thermal stabilities and fluorescence properties have been investigated. - Graphical abstract: Table of content: three new uranium(VI) coordination polymers with pyromellitic acid (H{sub 4}btca) have been synthesized via room temperature and hydrothermal synthesis methods, and structurally characterized. Two to three dimensional (3D) frameworks are revealed. All 3D frameworks have unique 1D large channels. Their vibrational modes, thermal stabilities and photoluminescence properties have been investigated. - Highlights: • Three new coordination polymers of U(VI) with pyromellitic acid (H{sub 4}btca). • Structures from a 2D layer to 3D frameworks with unique 1D channels. • Unusual µ{sub 5}-(η{sub 1}:η{sub 2}:η{sub 1}:η{sub 2:}η{sub 1}) coordination mode of btca ligand. • Vibrational modes, thermal stabilities and luminescent properties reported.« less

1D and 2D diffusion pore imaging on a preclinical MR system using adaptive rephasing: Feasibility and pulse sequence comparison

NASA Astrophysics Data System (ADS)

Bertleff, Marco; Domsch, Sebastian; Laun, Frederik B.; Kuder, Tristan A.; Schad, Lothar R.

2017-05-01

Diffusion pore imaging (DPI) has recently been proposed as a means to acquire images of the average pore shape in an image voxel or region of interest. The highly asymmetric gradient scheme of its sequence makes it substantially demanding in terms of the hardware of the NMR system. The aim of this work is to show the feasibility of DPI on a preclinical 9.4 T animal scanner. Using water-filled capillaries with an inner radius of 10 μm, four different variants of the DPI sequence were compared in 1D and 2D measurements. The pulse sequences applied cover the basic implementation using one long and one temporally narrow gradient pulse, a CPMG-like variant with multiple refocusing RF pulses as well as two variants splitting up the long gradient and distributing it on either side of the refocusing pulse. Substantial differences between the methods were found in terms of signal-to-noise ratio, contrast, blurring, deviations from the expected results and sensitivity to gradient imperfections. Each of the tested sequences was found to produce characteristic gradient mismatches dependent on the absolute value, direction and sign of the applied q-value. Read gradients were applied to compensate these mismatches translating them into time shifts, which enabled 1D DPI yielding capillary radius estimations within the tolerances specified by the manufacturer. For a successful DPI application in 2D, a novel gradient amplitude adaption scheme was implemented to correct for the occurring time shifts. Using this adaption, higher conformity to the expected pore shape, reduced blurring and enhanced contrast were achieved. Images of the phantom's pore shape could be acquired with a nominal resolution of 2.2 μm.

Effect of in vitro degradation of poly(D,L-lactide)/beta-tricalcium composite on its shape-memory properties.

PubMed

Zheng, Xiaotong; Zhou, Shaobing; Yu, Xiongjun; Li, Xiaohong; Feng, Bo; Qu, Shuxin; Weng, Jie

2008-07-01

The in vitro degradation characteristic and shape-memory properties of poly(D,L-lactide) (PDLLA)/beta-tricalcium phosphate (beta-TCP) composites were investigated because of their wide application in biomedical fields. In this article, PDLLA and crystalline beta-TCP were compounded and interesting shape-memory behaviors of the composite were first investigated. Then, in vitro degradation of the PDLLA/beta-TCP composites with weight ratios of 1:1, 2:1, and 3:1 was performed in phosphate buffer saline solution (PBS) (154 mM, pH 7.4) at 37 degrees C. The effect of in vitro degradation time for PDLLA/beta-TCP composites on shape-memory properties was studied by scanning electron microscopy, differential scanning calorimetry, gel permeation chromatography, X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR). The changes of structural morphology, glass transition temperature (T(g)), molecular weight, and weight loss of composites matrix and pH change of degradation medium indicated that shape-memory effects at different degradation time were nonlinearly influenced because of the breaking down of polymer chain and the formation of degradation products. Furthermore, the results from XRD and FTIR implied that the degradation products, for example, hydroxyapatite (HA), calcium hydrogen phosphate (CaHPO(4)), and calcium pyrophosphate (Ca(2)P(2)O(7)) phases also had some effects on shape-memory properties during the degradation. 2007 Wiley Periodicals, Inc.

Acoustic measurements of a full-scale rotor with four tip shapes. Volume 2: Appendices C, D, E and F

NASA Technical Reports Server (NTRS)

Mosher, M.

1984-01-01

A full scale helicopter with four different blade tip geometries is tested in a 40- by 80-foot wind tunnel. Performance, loads, and noise are measured. The four tip shapes tested were rectangular, tapered, swept, and swept/tapered. The noise data include measurements of the sound pressure levels in decibels dB, decibels adjusted dBA, and tone-corrected PNdB, for all of the conditions tested. Also included are the detailed measurements, 1/3 octave spectra and time histories for some selected data, and plots of dBA as function of test condition. Some performance measurements are included to aid interpretation of the noise data.

Aerodynamic Heating Computations for Projectiles. Volume 2. Swept Wing Calculations Using the Planar Version of the ABRES Shape Change Code (PLNRASCC)

DTIC Science & Technology

1984-06-01

Mt n o ro " g < - OD-O)C 0N v : _grI40N40 O I0 eeg gr, Wn *, c.M b-C N Z ý VN dN N C4 C4 C4 e"Ř!02AWVý 00 0 P- 1( or . . . . . . . . . i...the ABRES Shape Change Code (ASCC)," Acurex Report TM -80-31/AS, July 1980. 3. M. J. Abbett, "Finite Difference Solution of the Subsonic/Supersonic...Development Command US Army AMCCOM Technical Support Activity ATTN: DRSMC- TDC (D) ATTN: DELSD-L DRSMC-TSS (D) Fort Monmouth, NJ 07703 DRSMC-LCA-F (D) Mr. 0

Figure-ground effects on shape memory for objects versus holes.

PubMed

Palmer, Stephen; Davis, Janet; Nelson, Rolf; Rock, Irvin

2008-01-01

The circumstances under which the shapes of figure-versus-ground regions are perceived and remembered were investigated in three experiments that replicate, extend, and clarify Rubin's [1921 Visuell wahrgenommene Figuren (Copenhagen: Gyldendals)] classic study on this topic. In experiment 1, observers reported which of two regions they perceived as figure within ambiguous, bipartite, 2-D displays. In a later shape-recognition test, the shapes of regions previously seen as figures were remembered well, but the shapes of regions previously seen as grounds were remembered no better than novel distractor regions. In experiment 2 we examined the same question about memory for the shape of figure-versus-ground regions in nested displays in which the central region could be perceived either as a closer figure surrounded by a farther ground (ie as a solid object) or as a farther ground surrounded by a closer figure (ie as an empty hole). Unlike experiment 1, the shapes of regions initially perceived as grounds (holes) were remembered as well as those of regions initially perceived as figures (solid objects), and much better than those of novel distractor regions. In experiment 3 we further demonstrated that this outcome did not depend on the figure-ground instructions employed in experiment 2, because the same result was obtained with unambiguous 3-D cardboard displays of objects versus holes with no figure ground instructions at all. The present findings support an account of hole perception in which the shape of an intrinsic hole is encoded as a shaped, immaterial (or virtual) surface where the absence of matter is coded by a functional 'missing' symbol (analogous to a minus sign in mathematics) to represent its non-material status.

Optofluidic fabrication for 3D-shaped particles

NASA Astrophysics Data System (ADS)

Paulsen, Kevin S.; di Carlo, Dino; Chung, Aram J.

2015-04-01

Complex three-dimensional (3D)-shaped particles could play unique roles in biotechnology, structural mechanics and self-assembly. Current methods of fabricating 3D-shaped particles such as 3D printing, injection moulding or photolithography are limited because of low-resolution, low-throughput or complicated/expensive procedures. Here, we present a novel method called optofluidic fabrication for the generation of complex 3D-shaped polymer particles based on two coupled processes: inertial flow shaping and ultraviolet (UV) light polymerization. Pillars within fluidic platforms are used to deterministically deform photosensitive precursor fluid streams. The channels are then illuminated with patterned UV light to polymerize the photosensitive fluid, creating particles with multi-scale 3D geometries. The fundamental advantages of optofluidic fabrication include high-resolution, multi-scalability, dynamic tunability, simple operation and great potential for bulk fabrication with full automation. Through different combinations of pillar configurations, flow rates and UV light patterns, an infinite set of 3D-shaped particles is available, and a variety are demonstrated.

Learning the 3-D structure of objects from 2-D views depends on shape, not format

PubMed Central

Tian, Moqian; Yamins, Daniel; Grill-Spector, Kalanit

2016-01-01

Humans can learn to recognize new objects just from observing example views. However, it is unknown what structural information enables this learning. To address this question, we manipulated the amount of structural information given to subjects during unsupervised learning by varying the format of the trained views. We then tested how format affected participants' ability to discriminate similar objects across views that were rotated 90° apart. We found that, after training, participants' performance increased and generalized to new views in the same format. Surprisingly, the improvement was similar across line drawings, shape from shading, and shape from shading + stereo even though the latter two formats provide richer depth information compared to line drawings. In contrast, participants' improvement was significantly lower when training used silhouettes, suggesting that silhouettes do not have enough information to generate a robust 3-D structure. To test whether the learned object representations were format-specific or format-invariant, we examined if learning novel objects from example views transfers across formats. We found that learning objects from example line drawings transferred to shape from shading and vice versa. These results have important implications for theories of object recognition because they suggest that (a) learning the 3-D structure of objects does not require rich structural cues during training as long as shape information of internal and external features is provided and (b) learning generates shape-based object representations independent of the training format. PMID:27153196

Shape-designed frustration by local polymorphism in a near-equilibrium colloidal glass.

PubMed

Zhao, Kun; Mason, Thomas G

2015-09-29

We show that hard, convex, lithographic, prismatic kite platelets, each having three 72° vertices and one 144° vertex, preferentially form a disordered and arrested 2D glass when concentrated quasi-statically in a monolayer while experiencing thermal Brownian fluctuations. By contrast with 2D systems of other hard convex shapes, such as squares, rhombs, and pentagons, which readily form crystals at high densities, 72° kites retain a liquid-like disordered structure that becomes frozen-in as their long-time translational and rotational diffusion become highly bounded, yielding a 2D colloidal glass. This robust glass-forming propensity arises from competition between highly diverse few-particle local polymorphic configurations (LPCs) that have incommensurate features and symmetries. Thus, entropy maximization is consistent with the preservation of highly diverse LPCs en route to the arrested glass.

A spherical harmonics intensity model for 3D segmentation and 3D shape analysis of heterochromatin foci.

PubMed

Eck, Simon; Wörz, Stefan; Müller-Ott, Katharina; Hahn, Matthias; Biesdorf, Andreas; Schotta, Gunnar; Rippe, Karsten; Rohr, Karl

2016-08-01

The genome is partitioned into regions of euchromatin and heterochromatin. The organization of heterochromatin is important for the regulation of cellular processes such as chromosome segregation and gene silencing, and their misregulation is linked to cancer and other diseases. We present a model-based approach for automatic 3D segmentation and 3D shape analysis of heterochromatin foci from 3D confocal light microscopy images. Our approach employs a novel 3D intensity model based on spherical harmonics, which analytically describes the shape and intensities of the foci. The model parameters are determined by fitting the model to the image intensities using least-squares minimization. To characterize the 3D shape of the foci, we exploit the computed spherical harmonics coefficients and determine a shape descriptor. We applied our approach to 3D synthetic image data as well as real 3D static and real 3D time-lapse microscopy images, and compared the performance with that of previous approaches. It turned out that our approach yields accurate 3D segmentation results and performs better than previous approaches. We also show that our approach can be used for quantifying 3D shape differences of heterochromatin foci. Copyright © 2016 Elsevier B.V. All rights reserved.

D1 dopamine receptor is involved in shell formation in larvae of Pacific oyster Crassostrea gigas.

PubMed

Liu, Zhaoqun; Wang, Lingling; Yan, Yunchen; Zheng, Yan; Ge, Wenjing; Li, Meijia; Wang, Weilin; Song, Xiaorui; Song, Linsheng

2018-07-01

Dopamine (DA), a significant member of catecholamines, is reported to induce biomineralization of calcium carbonate vaterite microspheres via dopamine receptor (DR) in bivalves, implying the modulation of dopaminergic system on shell formation during larval development. In this research, a homologue of D1 type DR (CgD1DR-1) was identified from oyster Crassostrea gigas, whose full length cDNA was 1197 bp. It was widely expressed in various tissues of C. gigas, with the significantly higher levels in hepatopancreas, mantle, muscle and gill. During developmental stages, the mRNA transcripts of CgD1DR-1 in D-shape larvae were obviously higher (p < 0.05) than those in trochophore and umbo larvae, and CO 2 exposure could inhibit the synthesis of DA and mRNA expression of CgD1DR-1. After cell transfection and DA treatment, intracellular cAMP in cells with the expression of CgD1DR-1 increased significantly (p < 0.05). Furthermore, the incubation with SCH 23390 for the blockage of CgD1DR-1 significantly restrained the expressions of six shell formation-related genes including CgTyrosinase-1, CgTyrosinase-3, CgChitinaseLP, CgAMC, CgBMP and CgBMPR in trochophore and D-shape larvae. These results jointly suggested that DA together with its receptor CgD1DR-1 might be involved in shell formation during oyster larval development from trochophore to D-shape larvae, and CO 2 -induced ocean acidification (OA) might influence marine bivalves by inhibiting the DA-D1DR pathway to prohibit their shell formation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Simulation Study on Jet Formability and Damage Characteristics of a Low-Density Material Liner

PubMed Central

Tang, Wenhui; Ran, Xianwen

2018-01-01

The shaped charge tandem warhead is an effective weapon against the ERA (explosive reactive armor). Whether the pre-warhead can reliably initiate the ERA directly determines the entire performance of the tandem warhead. The existing shaped charge pre-warhead mostly adopts a metal shaped jet, which effectively initiates the ERA, but interferes the main shaped jet. This article, on the other hand, explores the possibility of producing a pre-warhead using a low-density material as the liner. The nonlinear dynamic analysis software Autodyn-2D is used to simulate and compare three kinds of low-density shaped jets, including floatglass, Lucite, and Plexiglas, to the copper shaped jet in the effectiveness of impacting ERA. Based on the integrative criteria (including u-d initiation criterion, explosive reactive degree, explosive pressure, and particle velocity of the panels), it can be determined whether the low-density shaped jet can reliably initiate the sandwich charge. The results show that the three kinds of low-density shaped jets can not only initiate the reaction armor, but are also superior to the existing copper shaped jet in ductility, jet tip velocity, jet tip diameter, and the mass; namely, it is feasible to use the low-density material shaped jet to destroy the ERA. PMID:29300351

Target Classification of Canonical Scatterers Using Classical Estimation and Dictionary Based Techniques

DTIC Science & Technology

2012-03-22

shapes tested , when the objective parameter set was confined to a dictionary’s de - fined parameter space. These physical characteristics included...8 2.3 Hypothesis Testing and Detection Theory . . . . . . . . . . . . . . . 8 2.4 3-D SAR Scattering Models...basis pursuit de -noising (BPDN) algorithm is chosen to perform extraction due to inherent efficiency and error tolerance. Multiple shape dictionaries

TU-CD-207-10: Dedicated Cone-Beam Breast CT: Design of a 3-D Beam-Shaping Filter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vedantham, S; Shi, L; Karellas, A

2015-06-15

Purpose: To design a 3 -D beam-shaping filter for cone-beam breast CT for equalizing x-ray photon fluence incident on the detector along both fan and cone angle directions. Methods: The 3-D beam-shaping filter was designed as the sum of two filters: a bow-tie filter assuming cylindrical breast and a 3D difference filter equivalent to the difference in projected thickness between the cylinder and the real breast. Both filters were designed with breast-equivalent material and converted to Al for the targeted x-ray spectrum. The bow-tie was designed for the largest diameter cylindrical breast by determining the fan-angle dependent path-length and themore » filter thickness needed to equalize the fluence. A total of 23,760 projections (180 projections of 132 binary breast CT volumes) were averaged, scaled for the largest breast, and subtracted from the projection of the largest diameter cylindrical breast to provide the 3D difference filter. The 3 -D beam shaping filter was obtained by summing the two filters. Numerical simulations with semi-ellipsoidal breasts of 10–18 cm diameter (chest-wall to nipple length=0.75 x diameter) were conducted to evaluate beam equalization. Results: The proposed 3-D beam-shaping filter showed a 140% -300% improvement in equalizing the photon fluence along the chest-wall to nipple (cone-angle) direction compared to a bow-tie filter. The improvement over bow-tie filter was larger for breasts with longer chest-wall to nipple length. Along the radial (fan-angle) direction, the performance of the 3-D beam shaping filter was marginally better than the bow-tie filter, with 4%-10% improvement in equalizing the photon fluence. For a ray traversing the chest-wall diameter of the breast, the filter transmission ratio was >0.95. Conclusion: The 3-D beam shaping filter provided substantial advantage over bow-tie filter in equalizing the photon fluence along the cone-angle direction. In conjunction with a 2-axis positioner, the filter can accommodate breasts of varying dimensions and chest-wall inclusion. Supported in part by NIH R01 CA128906 and R21 CA134128. The contents are solely the responsibility of the authors and do not reflect the official views of the NIH or NCI.« less

In Vitro Validation of Real-Time Three-Dimensional Color Doppler Echocardiography for Direct Measurement of Proximal Isovelocity Surface Area in Mitral Regurgitation

PubMed Central

Little, Stephen H.; Igo, Stephen R.; Pirat, Bahar; McCulloch, Marti; Hartley, Craig J.; Nosé, Yukihiko; Zoghbi, William A.

2012-01-01

The 2-dimensional (2D) color Doppler (2D-CD) proximal isovelocity surface area (PISA) method assumes a hemispheric flow convergence zone to estimate transvalvular flow. Recently developed 3-dimensional (3D)-CD can directly visualize PISA shape and surface area without geometric assumptions. To validate a novel method to directly measure PISA using real-time 3D-CD echocardiography, a circulatory loop with an ultrasound imaging chamber was created to model mitral regurgitation (MR). Thirty-two different regurgitant flow conditions were tested using symmetric and asymmetric flow orifices. Three-dimensional–PISA was reconstructed from a hand-held real-time 3D-CD data set. Regurgitant volume was derived using both 2D-CD and 3D-CD PISA methods, and each was compared against a flowmeter standard. The circulatory loop achieved regurgitant volume within the clinical range of MR (11 to 84 ml). Three-dimensional–PISA geometry reflected the 2D geometry of the regurgitant orifice. Correlation between the 2D-PISA method regurgitant volume and actual regurgitant volume was significant (r2 = 0.47, p <0.001). Mean 2D-PISA regurgitant volume underestimate was 19.1 ± 25 ml (2 SDs). For the 3D-PISA method, correlation with actual regurgitant volume was significant (r2 = 0.92, p <0.001), with a mean regurgitant volume underestimate of 2.7 ± 10 ml (2 SDs). The 3D-PISA method showed less regurgitant volume underestimation for all orifice shapes and regurgitant volumes tested. In conclusion, in an in vitro model of MR, 3D-CD was used to directly measure PISA without geometric assumption. Compared with conventional 2D-PISA, regurgitant volume was more accurate when derived from 3D-PISA across symmetric and asymmetric orifices within a broad range of hemodynamic flow conditions. PMID:17493476

Model-based measurement of food portion size for image-based dietary assessment using 3D/2D registration

PubMed Central

Chen, Hsin-Chen; Jia, Wenyan; Yue, Yaofeng; Li, Zhaoxin; Sun, Yung-Nien; Fernstrom, John D.; Sun, Mingui

2013-01-01

Dietary assessment is important in health maintenance and intervention in many chronic conditions, such as obesity, diabetes, and cardiovascular disease. However, there is currently a lack of convenient methods for measuring the volume of food (portion size) in real-life settings. We present a computational method to estimate food volume from a single photographical image of food contained in a typical dining plate. First, we calculate the food location with respect to a 3D camera coordinate system using the plate as a scale reference. Then, the food is segmented automatically from the background in the image. Adaptive thresholding and snake modeling are implemented based on several image features, such as color contrast, regional color homogeneity and curve bending degree. Next, a 3D model representing the general shape of the food (e.g., a cylinder, a sphere, etc.) is selected from a pre-constructed shape model library. The position, orientation and scale of the selected shape model are determined by registering the projected 3D model and the food contour in the image, where the properties of the reference are used as constraints. Experimental results using various realistically shaped foods with known volumes demonstrated satisfactory performance of our image based food volume measurement method even if the 3D geometric surface of the food is not completely represented in the input image. PMID:24223474

Model-based measurement of food portion size for image-based dietary assessment using 3D/2D registration

NASA Astrophysics Data System (ADS)

Chen, Hsin-Chen; Jia, Wenyan; Yue, Yaofeng; Li, Zhaoxin; Sun, Yung-Nien; Fernstrom, John D.; Sun, Mingui

2013-10-01

Dietary assessment is important in health maintenance and intervention in many chronic conditions, such as obesity, diabetes and cardiovascular disease. However, there is currently a lack of convenient methods for measuring the volume of food (portion size) in real-life settings. We present a computational method to estimate food volume from a single photographic image of food contained on a typical dining plate. First, we calculate the food location with respect to a 3D camera coordinate system using the plate as a scale reference. Then, the food is segmented automatically from the background in the image. Adaptive thresholding and snake modeling are implemented based on several image features, such as color contrast, regional color homogeneity and curve bending degree. Next, a 3D model representing the general shape of the food (e.g., a cylinder, a sphere, etc) is selected from a pre-constructed shape model library. The position, orientation and scale of the selected shape model are determined by registering the projected 3D model and the food contour in the image, where the properties of the reference are used as constraints. Experimental results using various realistically shaped foods with known volumes demonstrated satisfactory performance of our image-based food volume measurement method even if the 3D geometric surface of the food is not completely represented in the input image.

Atomistic study of the graphene nanobubbles

NASA Astrophysics Data System (ADS)

Iakovlev, Evgeny; Zhilyaev, Petr; Akhatov, Iskander

2017-11-01

A two-dimensional (2D) heterostructures can be created using 2D crystals stacking method. Substance can be trapped between the layers which leads to formation of the surface nanobubbles. We study nanobubbles trapped between graphene layers with argon atoms inside using molecular dynamics approach. For bubbles with radius in range 7-34 nm the solid close-packed state of argon is found, although according to bulk argon phase diagram the fluid phase must be observed. The universal shape scaling (constant ratio of height to radius), which is found experimentally and proved by the theory of elasticity of membranes, is also observed in our atomistic simulations. An unusual pancake shape (extremely small height to radius ratio) is found for smallest nanobubble with radius 7 nm. The nanobubbles with similar shape were experimentally observed at the interface between water and hydrophobic surface.

Fast three-dimensional inner volume excitations using parallel transmission and optimized k-space trajectories.

PubMed

Davids, Mathias; Schad, Lothar R; Wald, Lawrence L; Guérin, Bastien

2016-10-01

To design short parallel transmission (pTx) pulses for excitation of arbitrary three-dimensional (3D) magnetization patterns. We propose a joint optimization of the pTx radiofrequency (RF) and gradient waveforms for excitation of arbitrary 3D magnetization patterns. Our optimization of the gradient waveforms is based on the parameterization of k-space trajectories (3D shells, stack-of-spirals, and cross) using a small number of shape parameters that are well-suited for optimization. The resulting trajectories are smooth and sample k-space efficiently with few turns while using the gradient system at maximum performance. Within each iteration of the k-space trajectory optimization, we solve a small tip angle least-squares RF pulse design problem. Our RF pulse optimization framework was evaluated both in Bloch simulations and experiments on a 7T scanner with eight transmit channels. Using an optimized 3D cross (shells) trajectory, we were able to excite a cube shape (brain shape) with 3.4% (6.2%) normalized root-mean-square error in less than 5 ms using eight pTx channels and a clinical gradient system (Gmax  = 40 mT/m, Smax  = 150 T/m/s). This compared with 4.7% (41.2%) error for the unoptimized 3D cross (shells) trajectory. Incorporation of B0 robustness in the pulse design significantly altered the k-space trajectory solutions. Our joint gradient and RF optimization approach yields excellent excitation of 3D cube and brain shapes in less than 5 ms, which can be used for reduced field of view imaging and fat suppression in spectroscopy by excitation of the brain only. Magn Reson Med 76:1170-1182, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

[APPLICATION OF THREE DIMENSIONAL PRINTING ON MANUFACTURING BIONIC SCAFFOLDS OF SPINAL CORD IN RATS].

PubMed

Chen, Yisheng; Wang, Jingjing; Chen, Xuyi; Chen, Chong; Tu, Yue; Zhang, Sai; Li, Xiaohong

2015-03-01

To fabricate the bionic scaffolds of rat spinal cord by combining three dimensional (3D) printer and 3D software, so as to lay the foundation of theory and technology for the manufacture of scaffolds by using biomaterials. Three female Sprague Dawley rats were scanned by 7.0T MRI to obtain the shape and position data of the cross section and gray matter of T8 to T10 spinal cord. Combined with data of position and shape of nerve conduction beam, the relevant data were obtained via Getdata software. Then the 3D graphics were made and converted to stereolithography (STL) format by using SolidWorks software. Photosensitive resin was used as the materials of spinal cord scaffolds. The bionic scaffolds were fabricated by 3D printer. MRI showed that the section shape of T8 to T10 segments of the spinal cord were approximately oval with a relatively long sagittal diameter of (2.20 ± 0.52) mm and short transverse diameter of (2.05 ± 0.24) mm, and the data of nerve conduction bundle were featured in the STL format. The spinal cord bionic scaffolds of the target segments made by 3D printer were similar to the spinal cord of rat in the morphology and size, and the position of pores simulated normal nerve conduction of rat spinal cord. Spinal cord scaffolds produced by 3D printer which have similar shape and size of normal rat spinal cord are more bionic, and the procedure is simple. This technology combined with biomaterials is also promising in spinal cord repairing after spinal cord injury.

Computer vision-based evaluation of pre- and postrigor changes in size and shape of Atlantic cod (Gadus morhua) and Atlantic salmon (Salmo salar) fillets during rigor mortis and ice storage: effects of perimortem handling stress.

PubMed

Misimi, E; Erikson, U; Digre, H; Skavhaug, A; Mathiassen, J R

2008-03-01

The present study describes the possibilities for using computer vision-based methods for the detection and monitoring of transient 2D and 3D changes in the geometry of a given product. The rigor contractions of unstressed and stressed fillets of Atlantic salmon (Salmo salar) and Atlantic cod (Gadus morhua) were used as a model system. Gradual changes in fillet shape and size (area, length, width, and roundness) were recorded for 7 and 3 d, respectively. Also, changes in fillet area and height (cross-section profiles) were tracked using a laser beam and a 3D digital camera. Another goal was to compare rigor developments of the 2 species of farmed fish, and whether perimortem stress affected the appearance of the fillets. Some significant changes in fillet size and shape were found (length, width, area, roundness, height) between unstressed and stressed fish during the course of rigor mortis as well as after ice storage (postrigor). However, the observed irreversible stress-related changes were small and would hardly mean anything for postrigor fish processors or consumers. The cod were less stressed (as defined by muscle biochemistry) than the salmon after the 2 species had been subjected to similar stress bouts. Consequently, the difference between the rigor courses of unstressed and stressed fish was more extreme in the case of salmon. However, the maximal whole fish rigor strength was judged to be about the same for both species. Moreover, the reductions in fillet area and length, as well as the increases in width, were basically of similar magnitude for both species. In fact, the increases in fillet roundness and cross-section height were larger for the cod. We conclude that the computer vision method can be used effectively for automated monitoring of changes in 2D and 3D shape and size of fish fillets during rigor mortis and ice storage. In addition, it can be used for grading of fillets according to uniformity in size and shape, as well as measurement of fillet yield measured in thickness. The methods are accurate, rapid, nondestructive, and contact-free and can therefore be regarded as suitable for industrial purposes.

A shape-based statistical method to retrieve 2D TRUS-MR slice correspondence for prostate biopsy

NASA Astrophysics Data System (ADS)

Mitra, Jhimli; Srikantha, Abhilash; Sidibé, Désiré; Martí, Robert; Oliver, Arnau; Lladó, Xavier; Ghose, Soumya; Vilanova, Joan C.; Comet, Josep; Meriaudeau, Fabrice

2012-02-01

This paper presents a method based on shape-context and statistical measures to match interventional 2D Trans Rectal Ultrasound (TRUS) slice during prostate biopsy to a 2D Magnetic Resonance (MR) slice of a pre-acquired prostate volume. Accurate biopsy tissue sampling requires translation of the MR slice information on the TRUS guided biopsy slice. However, this translation or fusion requires the knowledge of the spatial position of the TRUS slice and this is only possible with the use of an electro-magnetic (EM) tracker attached to the TRUS probe. Since, the use of EM tracker is not common in clinical practice and 3D TRUS is not used during biopsy, we propose to perform an analysis based on shape and information theory to reach close enough to the actual MR slice as validated by experts. The Bhattacharyya distance is used to find point correspondences between shape-context representations of the prostate contours. Thereafter, Chi-square distance is used to find out those MR slices where the prostates closely match with that of the TRUS slice. Normalized Mutual Information (NMI) values of the TRUS slice with each of the axial MR slices are computed after rigid alignment and consecutively a strategic elimination based on a set of rules between the Chi-square distances and the NMI leads to the required MR slice. We validated our method for TRUS axial slices of 15 patients, of which 11 results matched at least one experts validation and the remaining 4 are at most one slice away from the expert validations.

Understanding the Structure of Large, Diverse Collections of Shapes

DTIC Science & Technology

2013-06-01

lowest weight edges as candidates, and for each candidate, we compute its edge rank, which is a metric proposed by Heath et al. [51] that estimates the... Neil D. McKay. A method for registration of 3-d shapes. IEEE PAMI, 14(2):239–256, February 1992. [10] V. Blanz, K. Scherbaum, and H.-P. Seidel. Fitting...2011. [50] C. Gu and X. Ren. Discriminative mixture-of-templates for viewpoint classification. In ECCV, 2010. [51] K. Heath , N. Gelfand, M

3D shape decomposition and comparison for gallbladder modeling

NASA Astrophysics Data System (ADS)

Huang, Weimin; Zhou, Jiayin; Liu, Jiang; Zhang, Jing; Yang, Tao; Su, Yi; Law, Gim Han; Chui, Chee Kong; Chang, Stephen

2011-03-01

This paper presents an approach to gallbladder shape comparison by using 3D shape modeling and decomposition. The gallbladder models can be used for shape anomaly analysis and model comparison and selection in image guided robotic surgical training, especially for laparoscopic cholecystectomy simulation. The 3D shape of a gallbladder is first represented as a surface model, reconstructed from the contours segmented in CT data by a scheme of propagation based voxel learning and classification. To better extract the shape feature, the surface mesh is further down-sampled by a decimation filter and smoothed by a Taubin algorithm, followed by applying an advancing front algorithm to further enhance the regularity of the mesh. Multi-scale curvatures are then computed on the regularized mesh for the robust saliency landmark localization on the surface. The shape decomposition is proposed based on the saliency landmarks and the concavity, measured by the distance from the surface point to the convex hull. With a given tolerance the 3D shape can be decomposed and represented as 3D ellipsoids, which reveal the shape topology and anomaly of a gallbladder. The features based on the decomposed shape model are proposed for gallbladder shape comparison, which can be used for new model selection. We have collected 19 sets of abdominal CT scan data with gallbladders, some shown in normal shape and some in abnormal shapes. The experiments have shown that the decomposed shapes reveal important topology features.

Visualization of the variability of 3D statistical shape models by animation.

PubMed

Lamecker, Hans; Seebass, Martin; Lange, Thomas; Hege, Hans-Christian; Deuflhard, Peter

2004-01-01

Models of the 3D shape of anatomical objects and the knowledge about their statistical variability are of great benefit in many computer assisted medical applications like images analysis, therapy or surgery planning. Statistical model of shapes have successfully been applied to automate the task of image segmentation. The generation of 3D statistical shape models requires the identification of corresponding points on two shapes. This remains a difficult problem, especially for shapes of complicated topology. In order to interpret and validate variations encoded in a statistical shape model, visual inspection is of great importance. This work describes the generation and interpretation of statistical shape models of the liver and the pelvic bone.

Taiwanese adult foot shape classification using 3D scanning data.

PubMed

Lee, Yu-Chi; Wang, Mao-Jiun

2015-01-01

This study classifies the foot shapes of Taiwanese using 3D foot scanning data from 2000 males and 1000 females. Nine foot dimensions relative to foot length and absolute measures in the common foot length categories were applied to compare the gender differences. Using foot breadth in % foot length (% FL), ball of foot length in % FL and arch height in % FL as feature parameters, three foot shape types for males and females can be classified. Significant gender differences were found in seven of the nine foot dimensions. Females had greater ball of foot length than males (0.2% FL). When comparing feet of the same foot length, males had greater breadth, girth and height dimensions than females, except for toe height. In addition, ethnic differences in foot shape were also observed. The findings can provide very useful information for building gender-specific shoe lasts and designing footwear insoles. 3D foot scanning data of 2000 males and 1000 females were classified into three different footshapes for males and females, respectively. Gender and ethnic differences on foot shape were also compared. The finding scan provide very useful information for gender-specific shoe last design and footwear production.

A double perturbation method of postbuckling analysis in 2D curved beams for assembly of 3D ribbon-shaped structures

NASA Astrophysics Data System (ADS)

Fan, Zhichao; Hwang, Keh-Chih; Rogers, John A.; Huang, Yonggang; Zhang, Yihui

2018-02-01

Mechanically-guided 3D assembly based on controlled, compressive buckling represents a promising, emerging approach for forming complex 3D mesostructures in advanced materials. Due to the versatile applicability to a broad set of material types (including device-grade single-crystal silicon) over length scales from nanometers to centimeters, a wide range of novel applications have been demonstrated in soft electronic systems, interactive bio-interfaces as well as tunable electromagnetic devices. Previously reported 3D designs relied mainly on finite element analyses (FEA) as a guide, but the massive numerical simulations and computational efforts necessary to obtain the assembly parameters for a targeted 3D geometry prevent rapid exploration of engineering options. A systematic understanding of the relationship between a 3D shape and the associated parameters for assembly requires the development of a general theory for the postbuckling process. In this paper, a double perturbation method is established for the postbuckling analyses of planar curved beams, of direct relevance to the assembly of ribbon-shaped 3D mesostructures. By introducing two perturbation parameters related to the initial configuration and the deformation, the highly nonlinear governing equations can be transformed into a series of solvable, linear equations that give analytic solutions to the displacements and curvatures during postbuckling. Systematic analyses of postbuckling in three representative ribbon shapes (sinusoidal, polynomial and arc configurations) illustrate the validity of theoretical method, through comparisons to the results of experiment and FEA. These results shed light on the relationship between the important deformation quantities (e.g., mode ratio and maximum strain) and the assembly parameters (e.g., initial configuration and the applied strain). This double perturbation method provides an attractive route to the inverse design of ribbon-shaped 3D geometries, as demonstrated in a class of helical mesostructures.

Laser cutting of irregular shape object based on stereo vision laser galvanometric scanning system

NASA Astrophysics Data System (ADS)

Qi, Li; Zhang, Yixin; Wang, Shun; Tang, Zhiqiang; Yang, Huan; Zhang, Xuping

2015-05-01

Irregular shape objects with different 3-dimensional (3D) appearances are difficult to be shaped into customized uniform pattern by current laser machining approaches. A laser galvanometric scanning system (LGS) could be a potential candidate since it can easily achieve path-adjustable laser shaping. However, without knowing the actual 3D topography of the object, the processing result may still suffer from 3D shape distortion. It is desirable to have a versatile auxiliary tool that is capable of generating 3D-adjusted laser processing path by measuring the 3D geometry of those irregular shape objects. This paper proposed the stereo vision laser galvanometric scanning system (SLGS), which takes the advantages of both the stereo vision solution and conventional LGS system. The 3D geometry of the object obtained by the stereo cameras is used to guide the scanning galvanometers for 3D-shape-adjusted laser processing. In order to achieve precise visual-servoed laser fabrication, these two independent components are integrated through a system calibration method using plastic thin film target. The flexibility of SLGS has been experimentally demonstrated by cutting duck feathers for badminton shuttle manufacture.

Correlating hydrodynamic radii with that of two-dimensional nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yue, Yuan; Kan, Yuwei; Clearfield, Abraham

2015-12-21

Dynamic light scattering (DLS) is one of the most adapted methods to measure the size of nanoparticles, as referred to the hydrodynamic radii (R{sub h}). However, the R{sub h} represents only that of three-dimensional spherical nanoparticles. In the present research, the size of two-dimensional (2D) nanoparticles of yttrium oxide (Y{sub 2}O{sub 3}) and zirconium phosphate (ZrP) was evaluated through comparing their hydrodynamic diameters via DLS with lateral sizes obtained using scanning and transmission electron microscopy. We demonstrate that the hydrodynamic radii are correlated with the lateral sizes of both square and circle shaped 2D nanoparticles. Two proportional coefficients, i.e., correctingmore » factors, are proposed for the Brownian motion status of 2D nanoparticles. The correction is possible by simplifying the calculation of integrals in the case of small thickness approximation. The correcting factor has great significance for investigating the translational diffusion behavior of 2D nanoparticles in a liquid and in effective and low-cost measurement in terms of size and morphology of shape-specific nanoparticles.« less

Integral refractive index imaging of flowing cell nuclei using quantitative phase microscopy combined with fluorescence microscopy.

PubMed

Dardikman, Gili; Nygate, Yoav N; Barnea, Itay; Turko, Nir A; Singh, Gyanendra; Javidi, Barham; Shaked, Natan T

2018-03-01

We suggest a new multimodal imaging technique for quantitatively measuring the integral (thickness-average) refractive index of the nuclei of live biological cells in suspension. For this aim, we combined quantitative phase microscopy with simultaneous 2-D fluorescence microscopy. We used 2-D fluorescence microscopy to localize the nucleus inside the quantitative phase map of the cell, as well as for measuring the nucleus radii. As verified offline by both 3-D confocal fluorescence microscopy and 2-D fluorescence microscopy while rotating the cells during flow, the nucleus of cells in suspension that are not during division can be assumed to be an ellipsoid. The entire shape of a cell in suspension can be assumed to be a sphere. Then, the cell and nucleus 3-D shapes can be evaluated based on their in-plain radii available from the 2-D phase and fluorescent measurements, respectively. Finally, the nucleus integral refractive index profile is calculated. We demonstrate the new technique on cancer cells, obtaining nucleus refractive index values that are lower than those of the cytoplasm, coinciding with recent findings. We believe that the proposed technique has the potential to be used for flow cytometry, where full 3-D refractive index tomography is too slow to be implemented during flow.

Resistively detected NMR line shapes in a quasi-one-dimensional electron system

NASA Astrophysics Data System (ADS)

Fauzi, M. H.; Singha, A.; Sahdan, M. F.; Takahashi, M.; Sato, K.; Nagase, K.; Muralidharan, B.; Hirayama, Y.

2017-06-01

We observe variation in the resistively detected nuclear magnetic resonance (RDNMR) line shapes in quantum Hall breakdown. The breakdown occurs locally in a gate-defined quantum point contact (QPC) region. Of particular interest is the observation of a dispersive line shape occurring when the bulk two-dimensional electron gas (2DEG) set to νb=2 and the QPC filling factor to the vicinity of νQPC=1 , strikingly resemble the dispersive line shape observed on a 2D quantum Hall state. This previously unobserved line shape in a QPC points to a simultaneous occurrence of two hyperfine-mediated spin flip-flop processes within the QPC. Those events give rise to two different sets of nuclei polarized in the opposite direction and positioned at a separate region with different degrees of electronic spin polarization.

A two-level generative model for cloth representation and shape from shading.

PubMed

Han, Feng; Zhu, Song-Chun

2007-07-01

In this paper, we present a two-level generative model for representing the images and surface depth maps of drapery and clothes. The upper level consists of a number of folds which will generate the high contrast (ridge) areas with a dictionary of shading primitives (for 2D images) and fold primitives (for 3D depth maps). These primitives are represented in parametric forms and are learned in a supervised learning phase using 3D surfaces of clothes acquired through photometric stereo. The lower level consists of the remaining flat areas which fill between the folds with a smoothness prior (Markov random field). We show that the classical ill-posed problem-shape from shading (SFS) can be much improved by this two-level model for its reduced dimensionality and incorporation of middle-level visual knowledge, i.e., the dictionary of primitives. Given an input image, we first infer the folds and compute a sketch graph using a sketch pursuit algorithm as in the primal sketch [10], [11]. The 3D folds are estimated by parameter fitting using the fold dictionary and they form the "skeleton" of the drapery/cloth surfaces. Then, the lower level is computed by conventional SFS method using the fold areas as boundary conditions. The two levels interact at the final stage by optimizing a joint Bayesian posterior probability on the depth map. We show a number of experiments which demonstrate more robust results in comparison with state-of-the-art work. In a broader scope, our representation can be viewed as a two-level inhomogeneous MRF model which is applicable to general shape-from-X problems. Our study is an attempt to revisit Marr's idea [23] of computing the 2(1/2)D sketch from primal sketch. In a companion paper [2], we study shape from stereo based on a similar two-level generative sketch representation.

Mom's shadow: structure-from-motion in newly hatched chicks as revealed by an imprinting procedure.

PubMed

Mascalzoni, Elena; Regolin, Lucia; Vallortigara, Giorgio

2009-03-01

The ability to recognize three-dimensional objects from two-dimensional (2-D) displays was investigated in domestic chicks, focusing on the role of the object's motion. In Experiment 1 newly hatched chicks, imprinted on a three-dimensional (3-D) object, were allowed to choose between the shadows of the familiar object and of an object never seen before. In Experiments 2 and 3 random-dot displays were used to produce the perception of a solid shape only when set in motion. Overall, the results showed that domestic chicks were able to recognize familiar shapes from 2-D motion stimuli. It is likely that similar general mechanisms underlying the perception of structure-from-motion and the extraction of 3-D information are shared by humans and animals. The present data shows that they occur similarly in birds as known for mammals, two separate vertebrate classes; this possibly indicates a common phylogenetic origin of these processes.

Constraining Cometary Crystal Shapes from IR Spectral Features

NASA Astrophysics Data System (ADS)

Wooden, D. H.; Lindsay, S.; Harker, D. E.; Kelley, M. S.; Woodward, C. E.; Murphy, J. R.

2013-12-01

A major challenge in deriving the silicate mineralogy of comets is ascertaining how the anisotropic nature of forsterite crystals affects the spectral features' wavelength, relative intensity, and asymmetry. Forsterite features are identified in cometary comae near 10, 11.05-11.2, 16, 19, 23.5, 27.5 and 33 μm [1-10], so accurate models for forsterite's absorption efficiency (Qabs) are a primary requirement to compute IR spectral energy distributions (SEDs, λFλ vs. λ) and constrain the silicate mineralogy of comets. Forsterite is an anisotropic crystal, with three crystallographic axes with distinct indices of refraction for the a-, b-, and c-axis. The shape of a forsterite crystal significantly affects its spectral features [13-16]. We need models that account for crystal shape. The IR absorption efficiencies of forsterite are computed using the discrete dipole approximation (DDA) code DDSCAT [11,12]. Starting from a fiducial crystal shape of a cube, we systematically elongate/reduce one of the crystallographic axes. Also, we elongate/reduce one axis while the lengths of the other two axes are slightly asymmetric (0.8:1.2). The most significant grain shape characteristic that affects the crystalline spectral features is the relative lengths of the crystallographic axes. The second significant grain shape characteristic is breaking the symmetry of all three axes [17]. Synthetic spectral energy distributions using seven crystal shape classes [17] are fit to the observed SED of comet C/1995 O1 (Hale-Bopp). The Hale-Bopp crystalline residual better matches equant, b-platelets, c-platelets, and b-columns spectral shape classes, while a-platelets, a-columns and c-columns worsen the spectral fits. Forsterite condensation and partial evaporation experiments demonstrate that environmental temperature and grain shape are connected [18-20]. Thus, grain shape is a potential probe for protoplanetary disk temperatures where the cometary crystalline forsterite formed. The forsterite crystal shapes (equant, b-platelets, c-platelets, b-colums - excluding a- and c-columns) derived from our modeling [17] of comet Hale-Bopp, compared to laboratory synthesis experiments [18], suggests that these crystals are high temperature condensates. By observing and modeling the crystalline features in comet ISON, we may constrain forsterite crystal shape(s) and link to their formation temperature(s) and environment(s). References: [1] Campins, H., Ryan, E.V. 1989. ApJ, 341, 1059 [2] Crovisier, J., et al. 1997. Science, 275, 1904 [3] Wooden, D.H., et al. 1999. ApJ, 517, 1034 [4] Wooden, D.H., et al. 2004. ApJL, 612, L77 [5] Harker, D.E., et al. 2002. ApJ, 580, 579 [6] --. 2004, ApJ, 615, 1081 [7] Lisse, C.M., et al. 2006. Icarus 195, 941-944. [8] Lisse, C.M., et.al. 2007. Icarus 191, 223-240. [9] Kelley, M.S., et al. 2010, LPSC, 41, #2375 [10] Harker, D.E., et al. 2011, AJ, 141, 26 [11] Draine, B.T., & Flatau, P.J. 1994, J. Opt. Soc. Am. A, 11, 1491 [12] Draine, B.T., & Flatau, P.J. 2008, J. Opt. Soc. Am. A, 25, 2693 [13] Fabian, D., et al., 2001, A&A, 378, 228 [14] Tamanai, A., et al. 2006. ApJ, 648, L147 [15] Tamanai, A., et al. 2009. ASP Conf. Ser., 414, 438 [16] Koike, C., et al. 2010. ApJ, 709, 983 [17] Lindsay, S.S., et al. 2013, ApJ, 766, 54 [18] Tsuchiyama, A. 1998. Mineralogical J., 20, 59 [19] Kobatake, H., et al., 2008. Icarus, 198, 208 [20] Takigawa, A., et al.. 2009. ApJL, 707, L97

Fast 3D shape screening of large chemical databases through alignment-recycling

PubMed Central

Fontaine, Fabien; Bolton, Evan; Borodina, Yulia; Bryant, Stephen H

2007-01-01

Background Large chemical databases require fast, efficient, and simple ways of looking for similar structures. Although such tasks are now fairly well resolved for graph-based similarity queries, they remain an issue for 3D approaches, particularly for those based on 3D shape overlays. Inspired by a recent technique developed to compare molecular shapes, we designed a hybrid methodology, alignment-recycling, that enables efficient retrieval and alignment of structures with similar 3D shapes. Results Using a dataset of more than one million PubChem compounds of limited size (< 28 heavy atoms) and flexibility (< 6 rotatable bonds), we obtained a set of a few thousand diverse structures covering entirely the 3D shape space of the conformers of the dataset. Transformation matrices gathered from the overlays between these diverse structures and the 3D conformer dataset allowed us to drastically (100-fold) reduce the CPU time required for shape overlay. The alignment-recycling heuristic produces results consistent with de novo alignment calculation, with better than 80% hit list overlap on average. Conclusion Overlay-based 3D methods are computationally demanding when searching large databases. Alignment-recycling reduces the CPU time to perform shape similarity searches by breaking the alignment problem into three steps: selection of diverse shapes to describe the database shape-space; overlay of the database conformers to the diverse shapes; and non-optimized overlay of query and database conformers using common reference shapes. The precomputation, required by the first two steps, is a significant cost of the method; however, once performed, querying is two orders of magnitude faster. Extensions and variations of this methodology, for example, to handle more flexible and larger small-molecules are discussed. PMID:17880744

Construction of Extended 3D Field of Views of the Internal Bladder Wall Surface: A Proof of Concept

NASA Astrophysics Data System (ADS)

Ben-Hamadou, Achraf; Daul, Christian; Soussen, Charles

2016-09-01

3D extended field of views (FOVs) of the internal bladder wall facilitate lesion diagnosis, patient follow-up and treatment traceability. In this paper, we propose a 3D image mosaicing algorithm guided by 2D cystoscopic video-image registration for obtaining textured FOV mosaics. In this feasibility study, the registration makes use of data from a 3D cystoscope prototype providing, in addition to each small FOV image, some 3D points located on the surface. This proof of concept shows that textured surfaces can be constructed with minimally modified cystoscopes. The potential of the method is demonstrated on numerical and real phantoms reproducing various surface shapes. Pig and human bladder textures are superimposed on phantoms with known shape and dimensions. These data allow for quantitative assessment of the 3D mosaicing algorithm based on the registration of images simulating bladder textures.

Morphological interaction between the nasal septum and nasofacial skeleton during human ontogeny.

PubMed

Goergen, Matthew J; Holton, Nathan E; Grünheid, Thorsten

2017-05-01

The nasal septal cartilage is thought to be a key growth center that contributes to nasofacial skeletal development. Despite the developmental influence of the nasal septum however, humans often exhibit a high frequency of septal deviation suggesting discordance in the growth between the septum and surrounding nasofacial skeleton. While there are numerous etiological factors that contribute to septal deviation, the surrounding nasofacial skeleton may also act to constrain the septum, resulting in altered patterns of growth. That is, while the nasal septum has a direct morphogenetic influence on aspects of the nasofacial skeleton, other nasofacial skeletal components may restrict septal growth resulting in deviation. Detailing the developmental relationship between these structures is important not only for understanding the causal determinants of nasal septal deviation, but also for developing a broader understanding of the complex interaction between the facial skeleton and chondrocranium. We selected 66 non-syndromic subjects from the University of Minnesota Orthodontic Clinic who ranged from 7 to 18 years in age and had an existing pretreatment cone-beam computed tomography (CBCT) scan. Using CBCT data, we examined the developmental relationship between nasal septal deviation and the surrounding nasofacial skeleton. We measured septal deviation as a percentage of septal volume relative to a modeled non-deviated septum. We then collected a series of coordinate landmark data in the region immediately surrounding the nasal septum in the midsagittal plane representing the nasofacial skeleton. First, we examined ontogenetic changes in the magnitude of nasal septal deviation relative to chronological age and nasofacial size. Next, using Procrustes-based geometric morphometric techniques, we assessed the morphological relationship between nasal septal deviation and nasofacial skeletal shape. Our results indicate that variation in the magnitude of nasal septal deviation was established in our earliest age group and maintained throughout ontogeny. Moreover, nasal septal deviation was correlated with non-allometric variation in nasofacial shape restricted to the region of the anterior sphenoid body. Ultimately, our results suggest that early developmental variation in midline basicranial components may act to alter or constrain patterns of nasal septal growth. © 2017 Anatomical Society.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Attota, Ravikiran, E-mail: Ravikiran.attota@nist.gov; Dixson, Ronald G.

We experimentally demonstrate that the three-dimensional (3-D) shape variations of nanometer-scale objects can be resolved and measured with sub-nanometer scale sensitivity using conventional optical microscopes by analyzing 4-D optical data using the through-focus scanning optical microscopy (TSOM) method. These initial results show that TSOM-determined cross-sectional (3-D) shape differences of 30 nm–40 nm wide lines agree well with critical-dimension atomic force microscope measurements. The TSOM method showed a linewidth uncertainty of 1.22 nm (k = 2). Complex optical simulations are not needed for analysis using the TSOM method, making the process simple, economical, fast, and ideally suited for high volume nanomanufacturing process monitoring.

Unoccupied electronic structure of Ni 2MnGa ferromagnetic shape memory alloy

DOE PAGES

Maniraj, M.; D׳Souza, S. W.; Rai, Abhishek; ...

2015-08-20

Momentum resolved inverse photoemission spectroscopy measurements show that the dispersion of the unoccupied bands of Ni 2MnGa is significant in the austenite phase. Furthermore, in the martensite phase, it is markedly reduced, which is possibly related to the structural transition to an incommensurate modulated state in the martensite phase. Finally, based on the first principle calculations of the electronic structure of Ni–Mn–Ga, we show that the modification of the spectral shape with surface composition is related to change in the hybridization between the Mn 3d and Ni 3d-like states that dominate the unoccupied conduction band.

Unoccupied electronic structure of Ni2MnGa ferromagnetic shape memory alloy

NASA Astrophysics Data System (ADS)

Maniraj, M.; D`Souza, S. W.; Rai, Abhishek; Schlagel, D. L.; Lograsso, T. A.; Chakrabarti, Aparna; Barman, S. R.

2015-11-01

Momentum resolved inverse photoemission spectroscopy measurements show that the dispersion of the unoccupied bands of Ni2MnGa is significant in the austenite phase. In the martensite phase, it is markedly reduced, which is possibly related to the structural transition to an incommensurate modulated state in the martensite phase. Based on the first principle calculations of the electronic structure of Ni-Mn-Ga, we show that the modification of the spectral shape with surface composition is related to change in the hybridization between the Mn 3d and Ni 3d-like states that dominate the unoccupied conduction band.

Processing convexity and concavity along a 2-D contour: figure-ground, structural shape, and attention.

PubMed

Bertamini, Marco; Wagemans, Johan

2013-04-01

Interest in convexity has a long history in vision science. For smooth contours in an image, it is possible to code regions of positive (convex) and negative (concave) curvature, and this provides useful information about solid shape. We review a large body of evidence on the role of this information in perception of shape and in attention. This includes evidence from behavioral, neurophysiological, imaging, and developmental studies. A review is necessary to analyze the evidence on how convexity affects (1) separation between figure and ground, (2) part structure, and (3) attention allocation. Despite some broad agreement on the importance of convexity in these areas, there is a lack of consensus on the interpretation of specific claims--for example, on the contribution of convexity to metric depth and on the automatic directing of attention to convexities or to concavities. The focus is on convexity and concavity along a 2-D contour, not convexity and concavity in 3-D, but the important link between the two is discussed. We conclude that there is good evidence for the role of convexity information in figure-ground organization and in parsing, but other, more specific claims are not (yet) well supported.

Aging and the visual, haptic, and cross-modal perception of natural object shape.

PubMed

Norman, J Farley; Crabtree, Charles E; Norman, Hideko F; Moncrief, Brandon K; Herrmann, Molly; Kapley, Noah

2006-01-01

One hundred observers participated in two experiments designed to investigate aging and the perception of natural object shape. In the experiments, younger and older observers performed either a same/different shape discrimination task (experiment 1) or a cross-modal matching task (experiment 2). Quantitative effects of age were found in both experiments. The effect of age in experiment 1 was limited to cross-modal shape discrimination: there was no effect of age upon unimodal (ie within a single perceptual modality) shape discrimination. The effect of age in experiment 2 was eliminated when the older observers were either given an unlimited amount of time to perform the task or when the number of response alternatives was decreased. Overall, the results of the experiments reveal that older observers can effectively perceive 3-D shape from both vision and haptics.

D-shaped tilted fiber Bragg grating using magnetic fluid for magnetic field sensor

NASA Astrophysics Data System (ADS)

Ying, Yu; Zhang, Rui; Si, Guang-Yuan; Wang, Xin; Qi, Yuan-Wei

2017-12-01

In our work, a numerical investigation of a magnetic field sensor based on a D-shaped tilted fiber Bragg grating and magnetic fluid is performed. The sensing probe is constructed by placing the magnetic fluid film on the flat surface of the D-shaped tilted fiber Bragg grating. We investigate the resonance wavelengths of the proposed structure with different tilted angles of grating ranging from 0° to 20°, and analyze the magnetic field sensing characteristics. The simulation results show that the optical fiber sensor exhibits optimal transmission characteristics with a tilted angle of 8°. The wavelength sensitivity of the magnetic field sensor is as high as -0.18nm/Oe in the range of 30Oe-270Oe, and it demonstrates a linearity up to R2= -0.9998. Such sensor has potential applications in determining magnetic sensing field.

Single-shot three-dimensional reconstruction based on structured light line pattern

NASA Astrophysics Data System (ADS)

Wang, ZhenZhou; Yang, YongMing

2018-07-01

Reconstruction of the object by single-shot is of great importance in many applications, in which the object is moving or its shape is non-rigid and changes irregularly. In this paper, we propose a single-shot structured light 3D imaging technique that calculates the phase map from the distorted line pattern. This technique makes use of the image processing techniques to segment and cluster the projected structured light line pattern from one single captured image. The coordinates of the clustered lines are extracted to form a low-resolution phase matrix which is then transformed to full-resolution phase map by spline interpolation. The 3D shape of the object is computed from the full-resolution phase map and the 2D camera coordinates. Experimental results show that the proposed method was able to reconstruct the three-dimensional shape of the object robustly from one single image.

TRO-2D - A code for rational transonic aerodynamic optimization

NASA Technical Reports Server (NTRS)

Davis, W. H., Jr.

1985-01-01

Features and sample applications of the transonic rational optimization (TRO-2D) code are outlined. TRO-2D includes the airfoil analysis code FLO-36, the CONMIN optimization code and a rational approach to defining aero-function shapes for geometry modification. The program is part of an effort to develop an aerodynamically smart optimizer that will simplify and shorten the design process. The user has a selection of drag minimization and associated minimum lift, moment, and the pressure distribution, a choice among 14 resident aero-function shapes, and options on aerodynamic and geometric constraints. Design variables such as the angle of attack, leading edge radius and camber, shock strength and movement, supersonic pressure plateau control, etc., are discussed. The results of calculations of a reduced leading edge camber transonic airfoil and an airfoil with a natural laminar flow are provided, showing that only four design variables need be specified to obtain satisfactory results.

Protein-protein docking using region-based 3D Zernike descriptors

PubMed Central

2009-01-01

Background Protein-protein interactions are a pivotal component of many biological processes and mediate a variety of functions. Knowing the tertiary structure of a protein complex is therefore essential for understanding the interaction mechanism. However, experimental techniques to solve the structure of the complex are often found to be difficult. To this end, computational protein-protein docking approaches can provide a useful alternative to address this issue. Prediction of docking conformations relies on methods that effectively capture shape features of the participating proteins while giving due consideration to conformational changes that may occur. Results We present a novel protein docking algorithm based on the use of 3D Zernike descriptors as regional features of molecular shape. The key motivation of using these descriptors is their invariance to transformation, in addition to a compact representation of local surface shape characteristics. Docking decoys are generated using geometric hashing, which are then ranked by a scoring function that incorporates a buried surface area and a novel geometric complementarity term based on normals associated with the 3D Zernike shape description. Our docking algorithm was tested on both bound and unbound cases in the ZDOCK benchmark 2.0 dataset. In 74% of the bound docking predictions, our method was able to find a near-native solution (interface C-αRMSD ≤ 2.5 Å) within the top 1000 ranks. For unbound docking, among the 60 complexes for which our algorithm returned at least one hit, 60% of the cases were ranked within the top 2000. Comparison with existing shape-based docking algorithms shows that our method has a better performance than the others in unbound docking while remaining competitive for bound docking cases. Conclusion We show for the first time that the 3D Zernike descriptors are adept in capturing shape complementarity at the protein-protein interface and useful for protein docking prediction. Rigorous benchmark studies show that our docking approach has a superior performance compared to existing methods. PMID:20003235

Protein-protein docking using region-based 3D Zernike descriptors.

PubMed

Venkatraman, Vishwesh; Yang, Yifeng D; Sael, Lee; Kihara, Daisuke

2009-12-09

Protein-protein interactions are a pivotal component of many biological processes and mediate a variety of functions. Knowing the tertiary structure of a protein complex is therefore essential for understanding the interaction mechanism. However, experimental techniques to solve the structure of the complex are often found to be difficult. To this end, computational protein-protein docking approaches can provide a useful alternative to address this issue. Prediction of docking conformations relies on methods that effectively capture shape features of the participating proteins while giving due consideration to conformational changes that may occur. We present a novel protein docking algorithm based on the use of 3D Zernike descriptors as regional features of molecular shape. The key motivation of using these descriptors is their invariance to transformation, in addition to a compact representation of local surface shape characteristics. Docking decoys are generated using geometric hashing, which are then ranked by a scoring function that incorporates a buried surface area and a novel geometric complementarity term based on normals associated with the 3D Zernike shape description. Our docking algorithm was tested on both bound and unbound cases in the ZDOCK benchmark 2.0 dataset. In 74% of the bound docking predictions, our method was able to find a near-native solution (interface C-alphaRMSD < or = 2.5 A) within the top 1000 ranks. For unbound docking, among the 60 complexes for which our algorithm returned at least one hit, 60% of the cases were ranked within the top 2000. Comparison with existing shape-based docking algorithms shows that our method has a better performance than the others in unbound docking while remaining competitive for bound docking cases. We show for the first time that the 3D Zernike descriptors are adept in capturing shape complementarity at the protein-protein interface and useful for protein docking prediction. Rigorous benchmark studies show that our docking approach has a superior performance compared to existing methods.

Control of minimum member size in parameter-free structural shape optimization by a medial axis approximation

NASA Astrophysics Data System (ADS)

Schmitt, Oliver; Steinmann, Paul

2018-06-01

We introduce a manufacturing constraint for controlling the minimum member size in structural shape optimization problems, which is for example of interest for components fabricated in a molding process. In a parameter-free approach, whereby the coordinates of the FE boundary nodes are used as design variables, the challenging task is to find a generally valid definition for the thickness of non-parametric geometries in terms of their boundary nodes. Therefore we use the medial axis, which is the union of all points with at least two closest points on the boundary of the domain. Since the effort for the exact computation of the medial axis of geometries given by their FE discretization highly increases with the number of surface elements we use the distance function instead to approximate the medial axis by a cloud of points. The approximation is demonstrated on three 2D examples. Moreover, the formulation of a minimum thickness constraint is applied to a sensitivity-based shape optimization problem of one 2D and one 3D model.

Control of minimum member size in parameter-free structural shape optimization by a medial axis approximation

NASA Astrophysics Data System (ADS)

Schmitt, Oliver; Steinmann, Paul

2017-09-01

We introduce a manufacturing constraint for controlling the minimum member size in structural shape optimization problems, which is for example of interest for components fabricated in a molding process. In a parameter-free approach, whereby the coordinates of the FE boundary nodes are used as design variables, the challenging task is to find a generally valid definition for the thickness of non-parametric geometries in terms of their boundary nodes. Therefore we use the medial axis, which is the union of all points with at least two closest points on the boundary of the domain. Since the effort for the exact computation of the medial axis of geometries given by their FE discretization highly increases with the number of surface elements we use the distance function instead to approximate the medial axis by a cloud of points. The approximation is demonstrated on three 2D examples. Moreover, the formulation of a minimum thickness constraint is applied to a sensitivity-based shape optimization problem of one 2D and one 3D model.

Shape-Reprogrammable Polymers: Encoding, Erasing, and Re-Encoding (Postprint)

DTIC Science & Technology

2014-11-01

printing , is a layer-by-layer technology for producing 3D objects directly from a digital model. While 3D printing allows the fabrication of increasingly...one linear shape-translation processes often increase rapidly with shape complexity. Additive manufacturing, also called three-dimensional ( 3D

Development and Application of 3D Printed Mesoreactors in Chemical Engineering Education

ERIC Educational Resources Information Center

Tabassum, Tahseen; Iloska, Marija; Scuereb, Daniel; Taira, Noriko; Jin, Chongguang; Zaitsev, Vladimir; Afshar, Fara; Kim, Taejin

2018-01-01

3D printing technology has an enormous potential to apply to chemical engineering education. In this paper, we describe several designs of 3D printed mesoreactors (Y-shape, T-shape, and Long channel shape) using the following steps: reactor sketching, CAD modeling, and reactor printing. With a focus on continuous plug flow mesoreactors (PFRs, i.d.…

Simultaneous shape and deformation measurements in a blood vessel model by two wavelength interferometry

NASA Astrophysics Data System (ADS)

Andrés, Nieves; Pinto, Cristina; Lobera, Julia; Palero, Virginia; Arroyo, M. Pilar

2017-06-01

Holographic techniques have been used to measure the shape and the radial deformation of a blood vessel model and a real sheep aorta. Measurements are obtained from several holograms recorded for different object states. For each object state, two holograms with two different wavelengths are multiplexed in the same digital recording. Thus both holograms are simultaneously recorded but the information from each of them is separately obtained. The shape analysis gives a wrapped phase map whose fringes are related to a synthetic wavelength. After a filtering and unwrapping process, the 3D shape can be obtained. The shape data for each line are fitted to a circumference in order to determine the local vessel radius and center. The deformation analysis also results in a wrapped phase map, but the fringes are related to the laser wavelength used in the corresponding hologram. After the filtering and unwrapping process, a 2D map of the deformation in an out-of-plane direction is reconstructed. The radial deformation is then calculated by using the shape information.

Towards true 3D textural analysis; using your crystal mush wisely.

NASA Astrophysics Data System (ADS)

Jerram, D. A.; Morgan, D. J.; Pankhurst, M. J.

2014-12-01

The crystal cargo that is found in volcanic and plutonic rocks contains a wealth of information about magmatic mush processes, crystallisation history, crystal entrainment and recycling. Phenocryst populations predominantly record episodes of growth/nucleation and bulk geochemical changes within an evolving crystal-melt body. Ante- and xeno-crysts provide useful clues to the nature of mush interaction with wall rock and with principal magma(s). Furthermore, crystal evolutions (core to rim) record pathways through pressure, temperature and compositional space. These can often illustrate complex recycling within systems, describing the plumbing architecture. Understanding this architecture underpins our knowledge of how igneous systems can interact with the crust, grow, freeze, re-mobilise and prime for eruption. Initially, 2D studies produced corrected 3D crystal size distributions to help provide information about nucleation and residence times. It immediately became clear that crystal shape is an important factor in determining the confidence placed upon 3D reconstructions of 2D data. Additionally studies utilised serial sections of medium- to coarse-grain-size populations which allowed 3D reconstruction using modelling software to be improved, since size and shape etc. can be directly constrained. Finally the advent of textural studies using X-ray tomography has revolutionised the way in which we can inspect the crystal cargo in mushy systems, allowing us to image in great detail crystal packing arrangements, 3D CSDs, shapes and orientations etc. The latest most innovative studies use X-ray micro-computed tomography to rapidly characterise chemical populations within the crystal cargo, adding a further dimension to this approach, and implies the ability to untangle magmatic chemical components to better understand their individual and combined evolution. In this contribution key examples of the different types of textural analysis techniques in 2D and 3D, including texture movie animations, are used from both plutonic and volcanic systems to highlight the roll of this approach towards a goal of true 3D textural analysis.

Analysis and 3D reconstruction of heterogeneity in malignant brain tumors: an interdisciplinary case study using a novel computational visualization approach.

PubMed

Mojsilovic, Aleksandra; Rogowitz, Bernice; Gomes, Jose; Deisboeck, Thomas S

2002-06-01

To explore how a multidisciplinary approach, combining modern visualization and image processing techniques with innovative experimental studies, can augment the understanding of tumor development. We analyzed histologic sections of a microscopic brain tumor and reconstructed these slices into a 3D representation. We processed these slices to: (1) identify tumor boundaries, (2) isolate proliferating tumor cells, and (3) segment the tumor into regions based on the density of proliferating cells. We then reconstructed the 3D shape of the tumor using a constrained deformable surface approach. This novel method allows the analyst to (1) see specific properties of histologic slices in the 3D environment with animation, (2) switch 2D "views" dynamically, and (3) see relationships between the 3D structure and structure on a plane. Using this method to analyze a specific "case," we were also able to shed light on the limitations of a widely held assumption about the shape of expanding microscopic solid tumors as well as find more indications that such tumors behave as adaptive biosystems. Implications of these case study results, as well as future applications of the method for tumor biology research, are discussed.

Correction tool for Active Shape Model based lumbar muscle segmentation.

PubMed

Valenzuela, Waldo; Ferguson, Stephen J; Ignasiak, Dominika; Diserens, Gaelle; Vermathen, Peter; Boesch, Chris; Reyes, Mauricio

2015-08-01

In the clinical environment, accuracy and speed of the image segmentation process plays a key role in the analysis of pathological regions. Despite advances in anatomic image segmentation, time-effective correction tools are commonly needed to improve segmentation results. Therefore, these tools must provide faster corrections with a low number of interactions, and a user-independent solution. In this work we present a new interactive correction method for correcting the image segmentation. Given an initial segmentation and the original image, our tool provides a 2D/3D environment, that enables 3D shape correction through simple 2D interactions. Our scheme is based on direct manipulation of free form deformation adapted to a 2D environment. This approach enables an intuitive and natural correction of 3D segmentation results. The developed method has been implemented into a software tool and has been evaluated for the task of lumbar muscle segmentation from Magnetic Resonance Images. Experimental results show that full segmentation correction could be performed within an average correction time of 6±4 minutes and an average of 68±37 number of interactions, while maintaining the quality of the final segmentation result within an average Dice coefficient of 0.92±0.03.

Ray-tracing of shape metrology data of grazing incidence x-ray astronomy mirrors

NASA Astrophysics Data System (ADS)

Zocchi, Fabio E.; Vernani, Dervis

2008-07-01

A number of future X-ray astronomy missions (e.g. Simbol-X, eROSITA) plan to utilize high throughput grazing incidence optics with very lightweight mirrors. The severe mass specifications require a further optimization of the existing technology with the consequent need of proper optical numerical modeling capabilities for both the masters and the mirrors. A ray tracing code has been developed for the simulation of the optical performance of type I Wolter masters and mirrors starting from 2D and 3D metrology data. In particular, in the case of 2D measurements, a 3D data set is reconstructed on the basis of dimensional references and used for the optical analysis by ray tracing. In this approach, the actual 3D shape is used for the optical analysis, thus avoiding the need of combining the separate contributions of different 2D measurements that require the knowledge of their interactions which is not normally available. The paper describes the proposed approach and presents examples of application on a prototype engineering master in the frame of ongoing activities carried out for present and future X-ray missions.

Protein Bricks: 2D and 3D Bio-Nanostructures with Shape and Function on Demand.

PubMed

Jiang, Jianjuan; Zhang, Shaoqing; Qian, Zhigang; Qin, Nan; Song, Wenwen; Sun, Long; Zhou, Zhitao; Shi, Zhifeng; Chen, Liang; Li, Xinxin; Mao, Ying; Kaplan, David L; Gilbert Corder, Stephanie N; Chen, Xinzhong; Liu, Mengkun; Omenetto, Fiorenzo G; Xia, Xiaoxia; Tao, Tiger H

2018-05-01

Precise patterning of polymer-based biomaterials for functional bio-nanostructures has extensive applications including biosensing, tissue engineering, and regenerative medicine. Remarkable progress is made in both top-down (based on lithographic methods) and bottom-up (via self-assembly) approaches with natural and synthetic biopolymers. However, most methods only yield 2D and pseudo-3D structures with restricted geometries and functionalities. Here, it is reported that precise nanostructuring on genetically engineered spider silk by accurately directing ion and electron beam interactions with the protein's matrix at the nanoscale to create well-defined 2D bionanopatterns and further assemble 3D bionanoarchitectures with shape and function on demand, termed "Protein Bricks." The added control over protein sequence and molecular weight of recombinant spider silk via genetic engineering provides unprecedented lithographic resolution (approaching the molecular limit), sharpness, and biological functions compared to natural proteins. This approach provides a facile method for patterning and immobilizing functional molecules within nanoscopic, hierarchical protein structures, which sheds light on a wide range of biomedical applications such as structure-enhanced fluorescence and biomimetic microenvironments for controlling cell fate. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemical Synthesis of Sea-Urchin Shaped 3D-MnO2 Nano Structures and Their Application in Supercapacitors.

PubMed

Singu, Bal Sydulu; Hong, Sang Eun; Yoon, Kuk Ro

2016-06-01

Sea-urchin shaped α-MnO2 hierarchical nano structures have been synthesized by facile thermal method without using any hard or soft template under the mild conditions. The structural and morphology of the 3D-MnO2 was characterized by X-ray diffraction (XRD) and field emission scanning electron microscopy (FE-SEM). From the XRD analysis indicates that MnO2 present in the α form. Morphology analysis shows that α-MnO2 sea-urchins are made by stacked nanorods, the diameter and length of the stacked nanorods present in the range of 50-120 nm and 200-400 nm respectively. The electrochemical behaviour of α-MnO2 has been investigated by cyclic voltammetry (CV) and charge-discharge (CD). The specific capacitance, energy density and power density are 212.0 F g(-1), 21.2 Wh kg(-1) and 1200 W kg(-1) respectively at the current density of 2 A g(-1). The retention of the specific capacitance after completion of 1000 charge-discharge cycles is around 97%. The results reveal that the prepared Sea-urchin shaped α-MnO2 has high specific capacitance and exhibit excellent cycle life.

A mobile ferromagnetic shape detection sensor using a Hall sensor array and magnetic imaging.

PubMed

Misron, Norhisam; Shin, Ng Wei; Shafie, Suhaidi; Marhaban, Mohd Hamiruce; Mailah, Nashiren Farzilah

2011-01-01

This paper presents a mobile Hall sensor array system for the shape detection of ferromagnetic materials that are embedded in walls or floors. The operation of the mobile Hall sensor array system is based on the principle of magnetic flux leakage to describe the shape of the ferromagnetic material. Two permanent magnets are used to generate the magnetic flux flow. The distribution of magnetic flux is perturbed as the ferromagnetic material is brought near the permanent magnets and the changes in magnetic flux distribution are detected by the 1-D array of the Hall sensor array setup. The process for magnetic imaging of the magnetic flux distribution is done by a signal processing unit before it displays the real time images using a netbook. A signal processing application software is developed for the 1-D Hall sensor array signal acquisition and processing to construct a 2-D array matrix. The processed 1-D Hall sensor array signals are later used to construct the magnetic image of ferromagnetic material based on the voltage signal and the magnetic flux distribution. The experimental results illustrate how the shape of specimens such as square, round and triangle shapes is determined through magnetic images based on the voltage signal and magnetic flux distribution of the specimen. In addition, the magnetic images of actual ferromagnetic objects are also illustrated to prove the functionality of mobile Hall sensor array system for actual shape detection. The results prove that the mobile Hall sensor array system is able to perform magnetic imaging in identifying various ferromagnetic materials.

A Mobile Ferromagnetic Shape Detection Sensor Using a Hall Sensor Array and Magnetic Imaging

PubMed Central

Misron, Norhisam; Shin, Ng Wei; Shafie, Suhaidi; Marhaban, Mohd Hamiruce; Mailah, Nashiren Farzilah

2011-01-01

This paper presents a Mobile Hall Sensor Array system for the shape detection of ferromagnetic materials that are embedded in walls or floors. The operation of the Mobile Hall Sensor Array system is based on the principle of magnetic flux leakage to describe the shape of the ferromagnetic material. Two permanent magnets are used to generate the magnetic flux flow. The distribution of magnetic flux is perturbed as the ferromagnetic material is brought near the permanent magnets and the changes in magnetic flux distribution are detected by the 1-D array of the Hall sensor array setup. The process for magnetic imaging of the magnetic flux distribution is done by a signal processing unit before it displays the real time images using a netbook. A signal processing application software is developed for the 1-D Hall sensor array signal acquisition and processing to construct a 2-D array matrix. The processed 1-D Hall sensor array signals are later used to construct the magnetic image of ferromagnetic material based on the voltage signal and the magnetic flux distribution. The experimental results illustrate how the shape of specimens such as square, round and triangle shapes is determined through magnetic images based on the voltage signal and magnetic flux distribution of the specimen. In addition, the magnetic images of actual ferromagnetic objects are also illustrated to prove the functionality of Mobile Hall Sensor Array system for actual shape detection. The results prove that the Mobile Hall Sensor Array system is able to perform magnetic imaging in identifying various ferromagnetic materials. PMID:22346653

Combined shape and topology optimization for minimization of maximal von Mises stress

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lian, Haojie; Christiansen, Asger N.; Tortorelli, Daniel A.

Here, this work shows that a combined shape and topology optimization method can produce optimal 2D designs with minimal stress subject to a volume constraint. The method represents the surface explicitly and discretizes the domain into a simplicial complex which adapts both structural shape and topology. By performing repeated topology and shape optimizations and adaptive mesh updates, we can minimize the maximum von Mises stress using the p-norm stress measure with p-values as high as 30, provided that the stress is calculated with sufficient accuracy.

Combined shape and topology optimization for minimization of maximal von Mises stress

DOE PAGES

Lian, Haojie; Christiansen, Asger N.; Tortorelli, Daniel A.; ...

2017-01-27

Here, this work shows that a combined shape and topology optimization method can produce optimal 2D designs with minimal stress subject to a volume constraint. The method represents the surface explicitly and discretizes the domain into a simplicial complex which adapts both structural shape and topology. By performing repeated topology and shape optimizations and adaptive mesh updates, we can minimize the maximum von Mises stress using the p-norm stress measure with p-values as high as 30, provided that the stress is calculated with sufficient accuracy.

5-(Perylen-3-yl)Ethynyl-arabino-Uridine (aUY11), an Arabino-Based Rigid Amphipathic Fusion Inhibitor, Targets Virion Envelope Lipids To Inhibit Fusion of Influenza Virus, Hepatitis C Virus, and Other Enveloped Viruses

PubMed Central

Colpitts, Che C.; Ustinov, Alexey V.; Epand, Raquel F.; Epand, Richard M.; Korshun, Vladimir A.

2013-01-01

Entry of enveloped viruses requires fusion of viral and cellular membranes. Fusion requires the formation of an intermediate stalk structure, in which only the outer leaflets are fused. The stalk structure, in turn, requires the lipid bilayer of the envelope to bend into negative curvature. This process is inhibited by enrichment in the outer leaflet of lipids with larger polar headgroups, which favor positive curvature. Accordingly, phospholipids with such shape inhibit viral fusion. We previously identified a compound, 5-(perylen-3-yl)ethynyl-2′-deoxy-uridine (dUY11), with overall shape and amphipathicity similar to those of these phospholipids. dUY11 inhibited the formation of the negative curvature necessary for stalk formation and the fusion of a model enveloped virus, vesicular stomatitis virus (VSV). We proposed that dUY11 acted by biophysical mechanisms as a result of its shape and amphipathicity. To test this model, we have now characterized the mechanisms against influenza virus and HCV of 5-(perylen-3-yl)ethynyl-arabino-uridine (aUY11), which has shape and amphipathicity similar to those of dUY11 but contains an arabino-nucleoside. aUY11 interacted with envelope lipids to inhibit the infectivity of influenza virus, hepatitis C virus (HCV), herpes simplex virus 1 and 2 (HSV-1/2), and other enveloped viruses. It specifically inhibited the fusion of influenza virus, HCV, VSV, and even protein-free liposomes to cells. Furthermore, aUY11 inhibited the formation of negative curvature in model lipid bilayers. In summary, the arabino-derived aUY11 and the deoxy-derived dUY11 act by the same antiviral mechanisms against several enveloped but otherwise unrelated viruses. Therefore, chemically unrelated compounds of appropriate shape and amphipathicity target virion envelope lipids to inhibit formation of the negative curvature required for fusion, inhibiting infectivity by biophysical, not biochemical, mechanisms. PMID:23283943

Fabrication of sophisticated two-dimensional organic nanoarchitectures thought hydrogen bond mediated molecular self assembly

NASA Astrophysics Data System (ADS)

Silly, Fabien

2012-02-01

Complex supramolecular two-dimensional (2D) networks are attracting considerable interest as highly ordered functional materials for applications in nanotechnology. The challenge consists in tailoring the ordering of one or more molecular species into specific architectures over an extended length scale with molecular precision. Highly organized supramolecular arrays can be obtained through self-assembly of complementary molecules which can interlock via intermolecular interactions. Molecules forming hydrogen bonds (H-bonds) are especially interesting building blocks for creating sophisticated organic architectures due to high selectivity and directionality of these bindings. We used scanning tunnelling microscopy to investigate at the atomic scale the formation of H-bonded 2D organic nanoarchitectures on surfaces. We mixed perylene derivatives having rectangular shape with melamine and DNA base having triangular and non symmetric shape respectively. We observe that molecule substituents play a key role in formation of the multicomponent H-bonded architectures. We show that the 2D self-assembly of these molecules can be tailored by adjusting the temperature and molecular ratio. We used these stimuli to successfully create numerous close-packed and porous 2D multicomponent structures.

Building CX peanut-shaped disk galaxy profiles. The relative importance of the 3D families of periodic orbits bifurcating at the vertical 2:1 resonance

NASA Astrophysics Data System (ADS)

Patsis, P. A.; Harsoula, M.

2018-05-01

Context. We present and discuss the orbital content of a rather unusual rotating barred galaxy model, in which the three-dimensional (3D) family, bifurcating from x1 at the 2:1 vertical resonance with the known "frown-smile" side-on morphology, is unstable. Aims: Our goal is to study the differences that occur in the phase space structure at the vertical 2:1 resonance region in this case, with respect to the known, well studied, standard case, in which the families with the frown-smile profiles are stable and support an X-shaped morphology. Methods: The potential used in the study originates in a frozen snapshot of an N-body simulation in which a fast bar has evolved. We follow the evolution of the vertical stability of the central family of periodic orbits as a function of the energy (Jacobi constant) and we investigate the phase space content by means of spaces of section. Results: The two bifurcating families at the vertical 2:1 resonance region of the new model change their stability with respect to that of most studied analytic potentials. The structure in the side-on view that is directly supported by the trapping of quasi-periodic orbits around 3D stable periodic orbits has now an infinity symbol (i.e. ∞-type) profile. However, the available sticky orbits can reinforce other types of side-on morphologies as well. Conclusions: In the new model, the dynamical mechanism of trapping quasi-periodic orbits around the 3D stable periodic orbits that build the peanut, supports the ∞-type profile. The same mechanism in the standard case supports the X shape with the frown-smile orbits. Nevertheless, in both cases (i.e. in the new and in the standard model) a combination of 3D quasi-periodic orbits around the stable x1 family with sticky orbits can support a profile reminiscent of the shape of the orbits of the 3D unstable family existing in each model.

3D-Printed Visceral Aneurysm Models Based on CT Data for Simulations of Endovascular Embolization: Evaluation of Size and Shape Accuracy.

PubMed

Shibata, Eisuke; Takao, Hidemasa; Amemiya, Shiori; Ohtomo, Kuni

2017-08-01

The objective of this study is to verify the accuracy of 3D-printed hollow models of visceral aneurysms created from CT angiography (CTA) data, by evaluating the sizes and shapes of aneurysms and related arteries. From March 2006 to August 2015, 19 true visceral aneurysms were embolized via interventional radiologic treatment provided by the radiology department at our institution; aneurysms with bleeding (n = 3) or without thin-slice (< 1 mm) preembolization CT data (n = 1) were excluded. A total of 15 consecutive true visceral aneurysms from 11 patients (eight women and three men; mean age, 61 years; range, 53-72 years) whose aneurysms were embolized via endovascular procedures were included in this study. Three-dimensional-printed hollow models of aneurysms and related arteries were fabricated from CTA data. The accuracies of the sizes and shapes of the 3D-printed hollow models were evaluated using the nonparametric Wilcoxon signed rank test and the Dice coefficient index. Aneurysm sizes ranged from 138 to 18,691 mm 3 (diameter, 6.1-35.7 mm), and no statistically significant difference was noted between patient data and 3D-printed models (p = 0.56). Shape analysis of whole aneurysms and related arteries indicated a high level of accuracy (Dice coefficient index value, 84.2-95.8%; mean [± SD], 91.1 ± 4.1%). The sizes and shapes of 3D-printed hollow visceral aneurysm models created from CTA data were accurate. These models can be used for simulations of endovascular treatment and precise anatomic information.

Time-Resolved Imaging of the Phase Transition in the Melt-Grown Spherulites of Isotactic Polybutene-1 as Detected by the Two-Dimensional Polarized IR Imaging Technique.

PubMed

Hu, Jian; Tashiro, Kohji

2016-05-26

In order to visualize the 2D spatial distribution of the structural change in the phase transition from crystal form II to I of isotactic polybutene-1 spherulite grown from the melt, the time-dependent measurement of the 2D polarized FTIR spectra has been performed. At a melt-isothermal crystallization temperature of 103 °C, the square-shape spherulite appeared from the melt and grew with time. When the isothermal crystallization occurred at 98 °C, the round-shaped spherulite was observed. In both cases, after the temperature jump to an ambient temperature, the 2D images changed clearly in the process of the phase transition from form II to form I, but the spherulite morphology itself was not changed detectably. The polarized IR imaging has revealed the preferential orientation of the crystallites in the spherulite. In the case of the spherulite grown at 103 °C, the ab plane is oriented in parallel to the spherulite plane and the molecular chains stand along the normal to the surface. On the other hand, in the spherulite grown at 98 °C, the chains were found to lie on the spherulite plane preferentially. Such a difference in the crystal orientation in the spherulite is related intimately with the outer shape of the spherulite and also with the growth mechanism of the spherulite. In this way, the polarized 2D IR imaging was found to be quite useful for the in situ detection of the time-dependently changing 2D spatial distribution of the crystallites in the spherulite.

Radiation-free quantification of head malformations in craniosynostosis patients from 3D photography

NASA Astrophysics Data System (ADS)

Tu, Liyun; Porras, Antonio R.; Oh, Albert; Lepore, Natasha; Mastromanolis, Manuel; Tsering, Deki; Paniagua, Beatriz; Enquobahrie, Andinet; Keating, Robert; Rogers, Gary F.; Linguraru, Marius George

2018-02-01

The evaluation of cranial malformations plays an essential role both in the early diagnosis and in the decision to perform surgical treatment for craniosynostosis. In clinical practice, both cranial shape and suture fusion are evaluated using CT images, which involve the use of harmful radiation on children. Three-dimensional (3D) photography offers noninvasive, radiation-free, and anesthetic-free evaluation of craniofacial morphology. The aim of this study is to develop an automated framework to objectively quantify cranial malformations in patients with craniosynostosis from 3D photography. We propose a new method that automatically extracts the cranial shape by identifying a set of landmarks from a 3D photograph. Specifically, it registers the 3D photograph of a patient to a reference template in which the position of the landmarks is known. Then, the method finds the closest cranial shape to that of the patient from a normative statistical shape multi-atlas built from 3D photographs of healthy cases, and uses it to quantify objectively cranial malformations. We calculated the cranial malformations on 17 craniosynostosis patients and we compared them with the malformations of the normative population used to build the multi-atlas. The average malformations of the craniosynostosis cases were 2.68 +/- 0.75 mm, which is significantly higher (p<0.001) than the average malformations of 1.70 +/- 0.41 mm obtained from the normative cases. Our approach can support the quantitative assessment of surgical procedures for cranial vault reconstruction without exposing pediatric patients to harmful radiation.

Numerical study on 3D composite morphing actuators

NASA Astrophysics Data System (ADS)

Oishi, Kazuma; Saito, Makoto; Anandan, Nishita; Kadooka, Kevin; Taya, Minoru

2015-04-01

There are a number of actuators using the deformation of electroactive polymer (EAP), where fewer papers seem to have focused on the performance of 3D morphing actuators based on the analytical approach, due mainly to their complexity. The present paper introduces a numerical analysis approach on the large scale deformation and motion of a 3D half dome shaped actuator composed of thin soft membrane (passive material) and EAP strip actuators (EAP active coupon with electrodes on both surfaces), where the locations of the active EAP strips is a key parameter. Simulia/Abaqus Static and Implicit analysis code, whose main feature is the high precision contact analysis capability among structures, are used focusing on the whole process of the membrane to touch and wrap around the object. The unidirectional properties of the EAP coupon actuator are used as input data set for the material properties for the simulation and the verification of our numerical model, where the verification is made as compared to the existing 2D solution. The numerical results can demonstrate the whole deformation process of the membrane to wrap around not only smooth shaped objects like a sphere or an egg, but also irregularly shaped objects. A parametric study reveals the proper placement of the EAP coupon actuators, with the modification of the dome shape to induce the relevant large scale deformation. The numerical simulation for the 3D soft actuators shown in this paper could be applied to a wider range of soft 3D morphing actuators.

High accuracy laboratory spectroscopy to support active greenhouse gas sensing

NASA Astrophysics Data System (ADS)

Long, D. A.; Bielska, K.; Cygan, A.; Havey, D. K.; Okumura, M.; Miller, C. E.; Lisak, D.; Hodges, J. T.

2011-12-01

Recent carbon dioxide (CO2) remote sensing missions have set precision targets as demanding as 0.25% (1 ppm) in order to elucidate carbon sources and sinks [1]. These ambitious measurement targets will require the most precise body of spectroscopic reference data ever assembled. Active sensing missions will be especially susceptible to subtle line shape effects as the narrow bandwidth of these measurements will greatly limit the number of spectral transitions which are employed in retrievals. In order to assist these remote sensing missions we have employed frequency-stabilized cavity ring-down spectroscopy (FS-CRDS) [2], a high-resolution, ultrasensitive laboratory technique, to measure precise line shape parameters for transitions of O2, CO2, and other atmospherically-relevant species within the near-infrared. These measurements have led to new HITRAN-style line lists for both 16O2 [3] and rare isotopologue [4] transitions in the A-band. In addition, we have performed detailed line shape studies of CO2 transitions near 1.6 μm under a variety of broadening conditions [5]. We will address recent measurements in these bands as well as highlight recent instrumental improvements to the FS-CRDS spectrometer. These improvements include the use of the Pound-Drever-Hall locking scheme, a high bandwidth servo which enables measurements to be made at rates greater than 10 kHz [6]. In addition, an optical frequency comb will be utilized as a frequency reference, which should allow for transition frequencies to be measured with uncertainties below 10 kHz (3×10-7 cm-1). [1] C. E. Miller, D. Crisp, P. L. DeCola, S. C. Olsen, et al., J. Geophys. Res.-Atmos. 112, D10314 (2007). [2] J. T. Hodges, H. P. Layer, W. W. Miller, G. E. Scace, Rev. Sci. Instrum. 75, 849-863 (2004). [3] D. A. Long, D. K. Havey, M. Okumura, C. E. Miller, et al., J. Quant. Spectrosc. Radiat. Transfer 111, 2021-2036 (2010). [4] D. A. Long, D. K. Havey, S. S. Yu, M. Okumura, et al., J. Quant. Spectrosc. Radiat. Transfer, In press (2011). [5] D. A. Long, K. Bielska, D. Lisak, D. K. Havey, et al., J. Chem. Phys., In press (2011). [6] A. Cygan, D. Lisak, P. Maslowski, K. Bielska, et al., Rev. Sci. Instrum. 82 (2011).

How Universal Is the Big Five? Testing the Five-Factor Model of Personality Variation Among Forager–Farmers in the Bolivian Amazon

PubMed Central

Gurven, Michael; von Rueden, Christopher; Massenkoff, Maxim; Kaplan, Hillard; Vie, Marino Lero

2014-01-01

The five-factor model (FFM) of personality variation has been replicated across a range of human societies, suggesting the FFM is a human universal. However, most studies of the FFM have been restricted to literate, urban populations, which are uncharacteristic of the majority of human evolutionary history. We present the first test of the FFM in a largely illiterate, indigenous society. Tsimane forager–horticulturalist men and women of Bolivia (n = 632) completed a translation of the 44-item Big Five Inventory (Benet-Martínez & John, 1998), a widely used metric of the FFM. We failed to find robust support for the FFM, based on tests of (a) internal consistency of items expected to segregate into the Big Five factors, (b) response stability of the Big Five, (c) external validity of the Big Five with respect to observed behavior, (d) factor structure according to exploratory and confirmatory factor analysis, and (e) similarity with a U.S. target structure based on Procrustes rotation analysis. Replication of the FFM was not improved in a separate sample of Tsimane adults (n = 430), who evaluated their spouses on the Big Five Inventory. Removal of reverse-scored items that may have elicited response biases produced factors suggestive of Extraversion, Agreeableness, and Conscientiousness, but fit to the FFM remained poor. Response styles may covary with exposure to education, but we found no better fit to the FFM among Tsimane who speak Spanish or have attended school. We argue that Tsimane personality variation displays 2 principal factors that may reflect socioecological characteristics common to small-scale societies. We offer evolutionary perspectives on why the structure of personality variation may not be invariant across human societies. PMID:23245291

How universal is the Big Five? Testing the five-factor model of personality variation among forager-farmers in the Bolivian Amazon.

PubMed

Gurven, Michael; von Rueden, Christopher; Massenkoff, Maxim; Kaplan, Hillard; Lero Vie, Marino

2013-02-01

The five-factor model (FFM) of personality variation has been replicated across a range of human societies, suggesting the FFM is a human universal. However, most studies of the FFM have been restricted to literate, urban populations, which are uncharacteristic of the majority of human evolutionary history. We present the first test of the FFM in a largely illiterate, indigenous society. Tsimane forager-horticulturalist men and women of Bolivia (n = 632) completed a translation of the 44-item Big Five Inventory (Benet-Martínez & John, 1998), a widely used metric of the FFM. We failed to find robust support for the FFM, based on tests of (a) internal consistency of items expected to segregate into the Big Five factors, (b) response stability of the Big Five, (c) external validity of the Big Five with respect to observed behavior, (d) factor structure according to exploratory and confirmatory factor analysis, and (e) similarity with a U.S. target structure based on Procrustes rotation analysis. Replication of the FFM was not improved in a separate sample of Tsimane adults (n = 430), who evaluated their spouses on the Big Five Inventory. Removal of reverse-scored items that may have elicited response biases produced factors suggestive of Extraversion, Agreeableness, and Conscientiousness, but fit to the FFM remained poor. Response styles may covary with exposure to education, but we found no better fit to the FFM among Tsimane who speak Spanish or have attended school. We argue that Tsimane personality variation displays 2 principal factors that may reflect socioecological characteristics common to small-scale societies. We offer evolutionary perspectives on why the structure of personality variation may not be invariant across human societies. (c) 2013 APA, all rights reserved.

Spatial variation of dental caries in late holocene samples of Southern South America: A geostatistical study.

PubMed

Menéndez, Lumila Paula

2016-11-01

The spatial variation of dental caries in late Holocene southern South American populations will be analyzed using geostatistical methods. The existence of a continuous geographical pattern of dental caries variation will be tested. The author recorded dental caries in 400 individuals, collated this information with published caries data from 666 additional individuals, and calculated a Caries Index. The caries spatial distribution was evaluated by means of 2D maps and scatterplots. Geostatistical analyses were performed by calculating Moran's I, correlograms and a Procrustes analysis. There is a relatively strong latitudinal continuous gradient of dental caries variation, especially in the extremes of the distribution. Moreover, the association between dental caries and geography was relatively high (m 12  = 0.6). Although northern and southern samples had the highest and lowest frequencies of dental caries, respectively, the central ones had the largest variation and had lower rates of caries than expected. The large variation in frequencies of dental caries in populations located in the center of the distribution could be explained by their subsistence strategies, characterized either by the consumption of wild cariogenic plants or cultigens (obtained locally or by exchange), a reliance on fishing, or the incorporation of plants rich in starch rather than carbohydrates. It is suggested that dental caries must be considered a multifactorial disease which results from the interaction of cultural practices and environmental factors. This can change how we understand subsistence strategies as well as how we interpret dental caries rates. Am. J. Hum. Biol., 2016. © 2016 Wiley Periodicals, Inc. Am. J. Hum. Biol. 28:825-836, 2016. © 2016Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Estimating Aeroheating of a 3D Body Using a 2D Flow Solver

NASA Technical Reports Server (NTRS)

Scott, Carl D.; Brykina, Irina G.

2005-01-01

A method for rapidly estimating the aeroheating, shear stress, and other properties of hypersonic flow about a three-dimensional (3D) blunt body has been devised. First, the geometry of the body is specified in Cartesian coordinates. The surface of the body is then described by its derivatives, coordinates, and principal curvatures. Next, previously relatively simple equations are used to find, for each desired combination of angle of attack and meridional angle, a scaling factor and the shape of an equivalent axisymmetric body. These factors and equivalent shapes are entered as inputs into a previously developed computer program that solves the two-dimensional (2D) equations of flow in a non-equilibrium viscous shock layer (VSL) about an axisymmetric body. The coordinates in the output of the VSL code are transformed back to the Cartesian coordinates of the 3D body, so that computed flow quantities can be registered with locations in the 3D flow field of interest. In tests in which the 3D bodies were elliptic paraboloids, the estimates obtained by use of this method were found to agree well with solutions of 3D, finite-rate-chemistry, thin-VSL equations for a catalytic body.

Dynamic Stall Data for 2-D and 3-D Test Cases

DTIC Science & Technology

2000-10-01

CASES Professor R A McD Galbraith Dr F N Coton Dr R B Green Dr M Vezza University of Glasgow INTRODUCTION Background Although substantial work has...aerofoil shape, aspect ratio, surface finish , data reduction software and Mach number, all but the Mach number had no effect on the observed trends

Complex furrows in a 2D epithelial sheet code the 3D structure of a beetle horn.

PubMed

Matsuda, Keisuke; Gotoh, Hiroki; Tajika, Yuki; Sushida, Takamichi; Aonuma, Hitoshi; Niimi, Teruyuki; Akiyama, Masakazu; Inoue, Yasuhiro; Kondo, Shigeru

2017-10-24

The external organs of holometabolous insects are generated through two consecutive processes: the development of imaginal primordia and their subsequent transformation into the adult structures. During the latter process, many different phenomena at the cellular level (e.g. cell shape changes, cell migration, folding and unfolding of epithelial sheets) contribute to the drastic changes observed in size and shape. Because of this complexity, the logic behind the formation of the 3D structure of adult external organs remains largely unknown. In this report, we investigated the metamorphosis of the horn in the Japanese rhinoceros beetle Trypoxylus dichotomus. The horn primordia is essentially a 2D epithelial cell sheet with dense furrows. We experimentally unfolded these furrows using three different methods and found that the furrow pattern solely determines the 3D horn structure, indicating that horn formation in beetles occurs by two distinct processes: formation of the furrows and subsequently unfolding them. We postulate that this developmental simplicity offers an inherent advantage to understanding the principles that guide 3D morphogenesis in insects.

Facile fabrication of plate-shaped hydrohausmannite as electrode material for supercapacitors

NASA Astrophysics Data System (ADS)

Liang, Jun; Chai, Yao; Li, Deli; Li, Meng; Lu, Jiaxue; Li, Li; Luo, Min

2017-08-01

A simple and one-step solvothermal synthesis method has been developed to prepare two-dimensional (2-D) hydrohausmannite ((Mn4-2xMnx)Mn8O16-x(OH)x) nanoplates with radial length of 300 nm and thickness of about 25 nm in a binary ethanediamine/water solvent system. The formation mechanism of hydrohausmannite is suggested. As an anode material for electrochemical capacitors, the plate-shaped hydrohausmannite not only displays a high specific capacity (215 at 0.1 A g-1) and good rate capability, but also shows good stable performance along with 94% specific capacity retained after 3000 cycle tests. The method can be easily controlled and expected to be applicable for the large-scale preparation of the 2-D hydrohausmannite.

LETTER: Test of Te profile invariance by sensitivity studies

NASA Astrophysics Data System (ADS)

Becker, G.

1992-06-01

The response of the electron temperature profile shape to variations of the electron heating and density profiles is investigated in different confinement regimes. It is shown that the changes in rTe = -Te/(dTe/dr) exceed the measurement error if the shape of the electron heat diffusivity χe(r) is kept fixed. The observed constancy of rTe(r) in the outer half of the plasma is incompatible with such a fixed χe(r) shape, i.e., a Te profile constraining mechanism must be present. Local transport laws of the form χe varies as rTe-α with α gtrsim 4 and χe propto (dTe/dr)α with α >= 2 yield the experimental stiffness of the Te(r) shape but conflict with empirical χe scalings. These results support the model of a self-organizing and adjusting χe(r) causing Te profile invariance

Fast viscosity solutions for shape from shading under a more realistic imaging model

NASA Astrophysics Data System (ADS)

Wang, Guohui; Han, Jiuqiang; Jia, Honghai; Zhang, Xinman

2009-11-01

Shape from shading (SFS) has been a classical and important problem in the domain of computer vision. The goal of SFS is to reconstruct the 3-D shape of an object from its 2-D intensity image. To this end, an image irradiance equation describing the relation between the shape of a surface and its corresponding brightness variations is used. Then it is derived as an explicit partial differential equation (PDE). Using the nonlinear programming principle, we propose a detailed solution to Prados and Faugeras's implicit scheme for approximating the viscosity solution of the resulting PDE. Furthermore, by combining implicit and semi-implicit schemes, a new approximation scheme is presented. In order to accelerate the convergence speed, we adopt the Gauss-Seidel idea and alternating sweeping strategy to the approximation schemes. Experimental results on both synthetic and real images are performed to demonstrate that the proposed methods are fast and accurate.

Phase-field crystal simulation facet and branch crystal growth

NASA Astrophysics Data System (ADS)

Chen, Zhi; Wang, Zhaoyang; Gu, Xinrui; Chen, Yufei; Hao, Limei; de Wit, Jos; Jin, Kexin

2018-05-01

Phase-field crystal model with one mode is introduced to describe morphological transition. The relationship between growth morphology and smooth density distribution was investigated. The results indicate that the pattern selection of dendrite growth is caused by the competition between interface energy anisotropy and interface kinetic anisotropy based on the 2D phase diagram. When the calculation time increases, the crystal grows to secondary dendrite at the dimensionless undercooling equal to - 0.4. Moreover, when noise is introduced in the growth progress, the symmetry is broken in the growth mode, and there becomes irregular fractal-like growth morphology. Furthermore, the single crystal shape develops into polycrystalline when the noise amplitude is large enough. When the dimensionless undercooling is less than - 0.3, the noise has a significant effect on the growth shape. In addition, the growth velocity of crystal near to liquid phase line is slow, while the shape far away from the liquid adapts to fast growth. Based on the simulation results, the method was proved to be effective, and it can easily obtain different crystal shapes by choosing the different points in 2D phase diagram.

Technology opportunities in a restructured electric industry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gehl, S.

1995-12-31

This paper describes the Strategic Research & Development (SR&D) program of the Electric Power Research Institute (EPRI). The intent of the program is to anticipate and shape the scientific and technological future of the electricity enterprise. SR&D serves those industry R&D needs that are more exploratory, precompetitive, and longer-term. To this end, SR&D seeks to anticipate technological change and, where possible, shape that change to the advantage of the electric utility enterprise and its customers. SR&D`s response to this challenge is research and development program that addresses the most probable future of the industry, but at the same time ismore » robust against alternative futures. The EPRI SR&D program is organized into several vectors, each with a mission that relates directly to one or more EPRI industry goals, which are summarized in the paper. 1 fig., 2 tabs.« less

A Marked Poisson Process Driven Latent Shape Model for 3D Segmentation of Reflectance Confocal Microscopy Image Stacks of Human Skin.

PubMed

Ghanta, Sindhu; Jordan, Michael I; Kose, Kivanc; Brooks, Dana H; Rajadhyaksha, Milind; Dy, Jennifer G

2017-01-01

Segmenting objects of interest from 3D data sets is a common problem encountered in biological data. Small field of view and intrinsic biological variability combined with optically subtle changes of intensity, resolution, and low contrast in images make the task of segmentation difficult, especially for microscopy of unstained living or freshly excised thick tissues. Incorporating shape information in addition to the appearance of the object of interest can often help improve segmentation performance. However, the shapes of objects in tissue can be highly variable and design of a flexible shape model that encompasses these variations is challenging. To address such complex segmentation problems, we propose a unified probabilistic framework that can incorporate the uncertainty associated with complex shapes, variable appearance, and unknown locations. The driving application that inspired the development of this framework is a biologically important segmentation problem: the task of automatically detecting and segmenting the dermal-epidermal junction (DEJ) in 3D reflectance confocal microscopy (RCM) images of human skin. RCM imaging allows noninvasive observation of cellular, nuclear, and morphological detail. The DEJ is an important morphological feature as it is where disorder, disease, and cancer usually start. Detecting the DEJ is challenging, because it is a 2D surface in a 3D volume which has strong but highly variable number of irregularly spaced and variably shaped "peaks and valleys." In addition, RCM imaging resolution, contrast, and intensity vary with depth. Thus, a prior model needs to incorporate the intrinsic structure while allowing variability in essentially all its parameters. We propose a model which can incorporate objects of interest with complex shapes and variable appearance in an unsupervised setting by utilizing domain knowledge to build appropriate priors of the model. Our novel strategy to model this structure combines a spatial Poisson process with shape priors and performs inference using Gibbs sampling. Experimental results show that the proposed unsupervised model is able to automatically detect the DEJ with physiologically relevant accuracy in the range 10- 20 μm .

A Marked Poisson Process Driven Latent Shape Model for 3D Segmentation of Reflectance Confocal Microscopy Image Stacks of Human Skin

PubMed Central

Ghanta, Sindhu; Jordan, Michael I.; Kose, Kivanc; Brooks, Dana H.; Rajadhyaksha, Milind; Dy, Jennifer G.

2016-01-01

Segmenting objects of interest from 3D datasets is a common problem encountered in biological data. Small field of view and intrinsic biological variability combined with optically subtle changes of intensity, resolution and low contrast in images make the task of segmentation difficult, especially for microscopy of unstained living or freshly excised thick tissues. Incorporating shape information in addition to the appearance of the object of interest can often help improve segmentation performance. However, shapes of objects in tissue can be highly variable and design of a flexible shape model that encompasses these variations is challenging. To address such complex segmentation problems, we propose a unified probabilistic framework that can incorporate the uncertainty associated with complex shapes, variable appearance and unknown locations. The driving application which inspired the development of this framework is a biologically important segmentation problem: the task of automatically detecting and segmenting the dermal-epidermal junction (DEJ) in 3D reflectance confocal microscopy (RCM) images of human skin. RCM imaging allows noninvasive observation of cellular, nuclear and morphological detail. The DEJ is an important morphological feature as it is where disorder, disease and cancer usually start. Detecting the DEJ is challenging because it is a 2D surface in a 3D volume which has strong but highly variable number of irregularly spaced and variably shaped “peaks and valleys”. In addition, RCM imaging resolution, contrast and intensity vary with depth. Thus a prior model needs to incorporate the intrinsic structure while allowing variability in essentially all its parameters. We propose a model which can incorporate objects of interest with complex shapes and variable appearance in an unsupervised setting by utilizing domain knowledge to build appropriate priors of the model. Our novel strategy to model this structure combines a spatial Poisson process with shape priors and performs inference using Gibbs sampling. Experimental results show that the proposed unsupervised model is able to automatically detect the DEJ with physiologically relevant accuracy in the range 10 – 20µm. PMID:27723590

Ultra-wide bandpass filter based on long-period fiber gratings and the evanescent field coupling between two fibers.

PubMed

Kim, Myoung Jin; Jung, Yong Min; Kim, Bok Hyeon; Han, Won-Taek; Lee, Byeong Ha

2007-08-20

We demonstrate a fiber-based bandpass filter with an ultra-wide spectral bandwidth. The ultra-wide band feature is achieved by inscribing a long-period fiber grating (LPG) in a specially-designed low index core single mode fiber. To get the bandpass function, the evanescent field coupling between two attached fibers is utilized. By applying strain, the spectral shape of the pass-band is adjusted to flat-top and Gaussian shapes. For the flat-top case, the bandwidth is obtained ~ 160 nm with an insertion loss of ~ 2 dB. With strain, the spectral shape is switched into a Gaussian one, which has ~ 120 nm FWHM and ~ 4.18 dB insertion loss at the peak.

3D conformal MRI-controlled transurethral ultrasound prostate therapy: validation of numerical simulations and demonstration in tissue-mimicking gel phantoms.

PubMed

Burtnyk, Mathieu; N'Djin, William Apoutou; Kobelevskiy, Ilya; Bronskill, Michael; Chopra, Rajiv

2010-11-21

MRI-controlled transurethral ultrasound therapy uses a linear array of transducer elements and active temperature feedback to create volumes of thermal coagulation shaped to predefined prostate geometries in 3D. The specific aims of this work were to demonstrate the accuracy and repeatability of producing large volumes of thermal coagulation (>10 cc) that conform to 3D human prostate shapes in a tissue-mimicking gel phantom, and to evaluate quantitatively the accuracy with which numerical simulations predict these 3D heating volumes under carefully controlled conditions. Eleven conformal 3D experiments were performed in a tissue-mimicking phantom within a 1.5T MR imager to obtain non-invasive temperature measurements during heating. Temperature feedback was used to control the rotation rate and ultrasound power of transurethral devices with up to five 3.5 × 5 mm active transducer elements. Heating patterns shaped to human prostate geometries were generated using devices operating at 4.7 or 8.0 MHz with surface acoustic intensities of up to 10 W cm(-2). Simulations were informed by transducer surface velocity measurements acquired with a scanning laser vibrometer enabling improved calculations of the acoustic pressure distribution in a gel phantom. Temperature dynamics were determined according to a FDTD solution to Pennes' BHTE. The 3D heating patterns produced in vitro were shaped very accurately to the prostate target volumes, within the spatial resolution of the MRI thermometry images. The volume of the treatment difference falling outside ± 1 mm of the target boundary was, on average, 0.21 cc or 1.5% of the prostate volume. The numerical simulations predicted the extent and shape of the coagulation boundary produced in gel to within (mean ± stdev [min, max]): 0.5 ± 0.4 [-1.0, 2.1] and -0.05 ± 0.4 [-1.2, 1.4] mm for the treatments at 4.7 and 8.0 MHz, respectively. The temperatures across all MRI thermometry images were predicted within -0.3 ± 1.6 °C and 0.1 ± 0.6 °C, inside and outside the prostate respectively, and the treatment time to within 6.8 min. The simulations also showed excellent agreement in regions of sharp temperature gradients near the transurethral and endorectal cooling devices. Conformal 3D volumes of thermal coagulation can be precisely matched to prostate shapes with transurethral ultrasound devices and active MRI temperature feedback. The accuracy of numerical simulations for MRI-controlled transurethral ultrasound prostate therapy was validated experimentally, reinforcing their utility as an effective treatment planning tool.

Configuration optimization of space structures

NASA Technical Reports Server (NTRS)

Felippa, Carlos; Crivelli, Luis A.; Vandenbelt, David

1991-01-01

The objective is to develop a computer aid for the conceptual/initial design of aerospace structures, allowing configurations and shape to be apriori design variables. The topics are presented in viewgraph form and include the following: Kikuchi's homogenization method; a classical shape design problem; homogenization method steps; a 3D mechanical component design example; forming a homogenized finite element; a 2D optimization problem; treatment of volume inequality constraint; algorithms for the volume inequality constraint; object function derivatives--taking advantage of design locality; stiffness variations; variations of potential; and schematics of the optimization problem.

Temporal multiplexing with adaptive optics for simultaneous vision

PubMed Central

Papadatou, Eleni; Del Águila-Carrasco, Antonio J.; Marín-Franch, Iván; López-Gil, Norberto

2016-01-01

We present and test a methodology for generating simultaneous vision with a deformable mirror that changed shape at 50 Hz between two vergences: 0 D (far vision) and −2.5 D (near vision). Different bifocal designs, including toric and combinations of spherical aberration, were simulated and assessed objectively. We found that typical corneal aberrations of a 60-year-old subject changes the shape of objective through-focus curves of a perfect bifocal lens. This methodology can be used to investigate subjective visual performance for different multifocal contact or intraocular lens designs. PMID:27867718

A 2D/3D image analysis system to track fluorescently labeled structures in rod-shaped cells: application to measure spindle pole asymmetry during mitosis.

PubMed

Schmitter, Daniel; Wachowicz, Paulina; Sage, Daniel; Chasapi, Anastasia; Xenarios, Ioannis; Simanis; Unser, Michael

2013-01-01

The yeast Schizosaccharomyces pombe is frequently used as a model for studying the cell cycle. The cells are rod-shaped and divide by medial fission. The process of cell division, or cytokinesis, is controlled by a network of signaling proteins called the Septation Initiation Network (SIN); SIN proteins associate with the SPBs during nuclear division (mitosis). Some SIN proteins associate with both SPBs early in mitosis, and then display strongly asymmetric signal intensity at the SPBs in late mitosis, just before cytokinesis. This asymmetry is thought to be important for correct regulation of SIN signaling, and coordination of cytokinesis and mitosis. In order to study the dynamics of organelles or large protein complexes such as the spindle pole body (SPB), which have been labeled with a fluorescent protein tag in living cells, a number of the image analysis problems must be solved; the cell outline must be detected automatically, and the position and signal intensity associated with the structures of interest within the cell must be determined. We present a new 2D and 3D image analysis system that permits versatile and robust analysis of motile, fluorescently labeled structures in rod-shaped cells. We have designed an image analysis system that we have implemented as a user-friendly software package allowing the fast and robust image-analysis of large numbers of rod-shaped cells. We have developed new robust algorithms, which we combined with existing methodologies to facilitate fast and accurate analysis. Our software permits the detection and segmentation of rod-shaped cells in either static or dynamic (i.e. time lapse) multi-channel images. It enables tracking of two structures (for example SPBs) in two different image channels. For 2D or 3D static images, the locations of the structures are identified, and then intensity values are extracted together with several quantitative parameters, such as length, width, cell orientation, background fluorescence and the distance between the structures of interest. Furthermore, two kinds of kymographs of the tracked structures can be established, one representing the migration with respect to their relative position, the other representing their individual trajectories inside the cell. This software package, called "RodCellJ", allowed us to analyze a large number of S. pombe cells to understand the rules that govern SIN protein asymmetry. (Continued on next page) (Continued from previous page). "RodCellJ" is freely available to the community as a package of several ImageJ plugins to simultaneously analyze the behavior of a large number of rod-shaped cells in an extensive manner. The integration of different image-processing techniques in a single package, as well as the development of novel algorithms does not only allow to speed up the analysis with respect to the usage of existing tools, but also accounts for higher accuracy. Its utility was demonstrated on both 2D and 3D static and dynamic images to study the septation initiation network of the yeast Schizosaccharomyces pombe. More generally, it can be used in any kind of biological context where fluorescent-protein labeled structures need to be analyzed in rod-shaped cells. RodCellJ is freely available under http://bigwww.epfl.ch/algorithms.html.

Direct measurement of proximal isovelocity surface area by real-time three-dimensional color Doppler for quantitation of aortic regurgitant volume: an in vitro validation.

PubMed

Pirat, Bahar; Little, Stephen H; Igo, Stephen R; McCulloch, Marti; Nosé, Yukihiko; Hartley, Craig J; Zoghbi, William A

2009-03-01

The proximal isovelocity surface area (PISA) method is useful in the quantitation of aortic regurgitation (AR). We hypothesized that actual measurement of PISA provided with real-time 3-dimensional (3D) color Doppler yields more accurate regurgitant volumes than those estimated by 2-dimensional (2D) color Doppler PISA. We developed a pulsatile flow model for AR with an imaging chamber in which interchangeable regurgitant orifices with defined shapes and areas were incorporated. An ultrasonic flow meter was used to calculate the reference regurgitant volumes. A total of 29 different flow conditions for 5 orifices with different shapes were tested at a rate of 72 beats/min. 2D PISA was calculated as 2pi r(2), and 3D PISA was measured from 8 equidistant radial planes of the 3D PISA. Regurgitant volume was derived as PISA x aliasing velocity x time velocity integral of AR/peak AR velocity. Regurgitant volumes by flow meter ranged between 12.6 and 30.6 mL/beat (mean 21.4 +/- 5.5 mL/beat). Regurgitant volumes estimated by 2D PISA correlated well with volumes measured by flow meter (r = 0.69); however, a significant underestimation was observed (y = 0.5x + 0.6). Correlation with flow meter volumes was stronger for 3D PISA-derived regurgitant volumes (r = 0.83); significantly less underestimation of regurgitant volumes was seen, with a regression line close to identity (y = 0.9x + 3.9). Direct measurement of PISA is feasible, without geometric assumptions, using real-time 3D color Doppler. Calculation of aortic regurgitant volumes with 3D color Doppler using this methodology is more accurate than conventional 2D method with hemispheric PISA assumption.

Red blood cell thickness is evolutionarily constrained by slow, hemoglobin-restricted diffusion in cytoplasm.

PubMed

Richardson, Sarah L; Swietach, Pawel

2016-10-25

During capillary transit, red blood cells (RBCs) must exchange large quantities of CO 2 and O 2 in typically less than one second, but the degree to which this is rate-limited by diffusion through cytoplasm is not known. Gas diffusivity is intuitively assumed to be fast and this would imply that the intracellular path-length, defined by RBC shape, is not a factor that could meaningfully compromise physiology. Here, we evaluated CO 2 diffusivity (D CO2 ) in RBCs and related our results to cell shape. D CO2 inside RBCs was determined by fluorescence imaging of [H + ] dynamics in cells under superfusion. This method is based on the principle that H + diffusion is facilitated by CO 2 /HCO 3 - buffer and thus provides a read-out of D CO2 . By imaging the spread of H + ions from a photochemically-activated source (6-nitroveratraldehyde), D CO2 in human RBCs was calculated to be only 5% of the rate in water. Measurements on RBCs containing different hemoglobin concentrations demonstrated a halving of D CO2 with every 75 g/L increase in mean corpuscular hemoglobin concentration (MCHC). Thus, to compensate for highly-restricted cytoplasmic diffusion, RBC thickness must be reduced as appropriate for its MCHC. This can explain the inverse relationship between MCHC and RBC thickness determined from >250 animal species.

Human red blood cell recognition enhancement with three-dimensional morphological features obtained by digital holographic imaging

NASA Astrophysics Data System (ADS)

Jaferzadeh, Keyvan; Moon, Inkyu

2016-12-01

The classification of erythrocytes plays an important role in the field of hematological diagnosis, specifically blood disorders. Since the biconcave shape of red blood cell (RBC) is altered during the different stages of hematological disorders, we believe that the three-dimensional (3-D) morphological features of erythrocyte provide better classification results than conventional two-dimensional (2-D) features. Therefore, we introduce a set of 3-D features related to the morphological and chemical properties of RBC profile and try to evaluate the discrimination power of these features against 2-D features with a neural network classifier. The 3-D features include erythrocyte surface area, volume, average cell thickness, sphericity index, sphericity coefficient and functionality factor, MCH and MCHSD, and two newly introduced features extracted from the ring section of RBC at the single-cell level. In contrast, the 2-D features are RBC projected surface area, perimeter, radius, elongation, and projected surface area to perimeter ratio. All features are obtained from images visualized by off-axis digital holographic microscopy with a numerical reconstruction algorithm, and four categories of biconcave (doughnut shape), flat-disc, stomatocyte, and echinospherocyte RBCs are interested. Our experimental results demonstrate that the 3-D features can be more useful in RBC classification than the 2-D features. Finally, we choose the best feature set of the 2-D and 3-D features by sequential forward feature selection technique, which yields better discrimination results. We believe that the final feature set evaluated with a neural network classification strategy can improve the RBC classification accuracy.

The drag and terminal velocity of volcanic ash and lapilli with 3D shape obtained by X-ray microtomography

NASA Astrophysics Data System (ADS)

Dioguardi, Fabio; Mele, Daniela; Dellino, Pierfrancesco; Dürig, Tobias

2017-04-01

New experiments of falling volcanic particles were performed in order to define drag and terminal velocity models applicable in a wide range of Reynolds number Re. Experiments were carried out with fluids of various viscosities and with particles that cover a wide range of size, density and shape. Particle shape, which strongly influences fluid drag, was measured in 3D by High-resolution X-ray microtomography, by which sphericity and fractal dimension were obtained, the latter used for quantifying the aerodynamic drag of irregular particles for the first time. With this method, the measure of particle shape descriptors proved to be easier and less operator dependent than previously used 2D image particle analyses. Drag laws that make use of the new 3D parameters were obtained by fitting particle data to the experiments, and single-equation terminal velocity models were derived. They work well both at high and low Re (3x10-2 < Re < 104), while earlier formulations made use of different equations at different ranges of Re. The new drag laws are well suited for the modelling of particle transportation both in the eruptive column and pyroclastic density currents, where coarse and fine particles are present, and also in the distal part of the umbrella region, where fine ash is involved in the large-scale domains of atmospheric circulation. A table of the typical values of 3D sphericity and fractal dimension of particles from known plinian, subplinian and ash plume eruptions is presented. Graphs of terminal velocity as a function of grain size are proposed as tools to help volcanologists and atmosphere scientists to model particle transportation of explosive eruptions. Some volcanological application examples are finally presented.

3D surface parameterization using manifold learning for medial shape representation

NASA Astrophysics Data System (ADS)

Ward, Aaron D.; Hamarneh, Ghassan

2007-03-01

The choice of 3D shape representation for anatomical structures determines the effectiveness with which segmentation, visualization, deformation, and shape statistics are performed. Medial axis-based shape representations have attracted considerable attention due to their inherent ability to encode information about the natural geometry of parts of the anatomy. In this paper, we propose a novel approach, based on nonlinear manifold learning, to the parameterization of medial sheets and object surfaces based on the results of skeletonization. For each single-sheet figure in an anatomical structure, we skeletonize the figure, and classify its surface points according to whether they lie on the upper or lower surface, based on their relationship to the skeleton points. We then perform nonlinear dimensionality reduction on the skeleton, upper, and lower surface points, to find the intrinsic 2D coordinate system of each. We then center a planar mesh over each of the low-dimensional representations of the points, and map the meshes back to 3D using the mappings obtained by manifold learning. Correspondence between mesh vertices, established in their intrinsic 2D coordinate spaces, is used in order to compute the thickness vectors emanating from the medial sheet. We show results of our algorithm on real brain and musculoskeletal structures extracted from MRI, as well as an artificial multi-sheet example. The main advantages to this method are its relative simplicity and noniterative nature, and its ability to correctly compute nonintersecting thickness vectors for a medial sheet regardless of both the amount of coincident bending and thickness in the object, and of the incidence of local concavities and convexities in the object's surface.

Clinical anthropometrics and body composition from 3D whole-body surface scans.

PubMed

Ng, B K; Hinton, B J; Fan, B; Kanaya, A M; Shepherd, J A

2016-11-01

Obesity is a significant worldwide epidemic that necessitates accessible tools for robust body composition analysis. We investigated whether widely available 3D body surface scanners can provide clinically relevant direct anthropometrics (circumferences, areas and volumes) and body composition estimates (regional fat/lean masses). Thirty-nine healthy adults stratified by age, sex and body mass index (BMI) underwent whole-body 3D scans, dual energy X-ray absorptiometry (DXA), air displacement plethysmography and tape measurements. Linear regressions were performed to assess agreement between 3D measurements and criterion methods. Linear models were derived to predict DXA body composition from 3D scan measurements. Thirty-seven external fitness center users underwent 3D scans and bioelectrical impedance analysis for model validation. 3D body scan measurements correlated strongly to criterion methods: waist circumference R 2 =0.95, hip circumference R 2 =0.92, surface area R 2 =0.97 and volume R 2 =0.99. However, systematic differences were observed for each measure due to discrepancies in landmark positioning. Predictive body composition equations showed strong agreement for whole body (fat mass R 2 =0.95, root mean square error (RMSE)=2.4 kg; fat-free mass R 2 =0.96, RMSE=2.2 kg) and arms, legs and trunk (R 2 =0.79-0.94, RMSE=0.5-1.7 kg). Visceral fat prediction showed moderate agreement (R 2 =0.75, RMSE=0.11 kg). 3D surface scanners offer precise and stable automated measurements of body shape and composition. Software updates may be needed to resolve measurement biases resulting from landmark positioning discrepancies. Further studies are justified to elucidate relationships between body shape, composition and metabolic health across sex, age, BMI and ethnicity groups, as well as in those with metabolic disorders.

Hierarchically three-dimensional (3D) nanotubular sea urchin-shaped iron oxide and its application in heavy metal removal and solar-induced photocatalytic degradation.

PubMed

Lee, Soon Chang; Jeong, Yesul; Kim, Youn Jung; Kim, Hyeran; Lee, Hyun Uk; Lee, Young-Chul; Lee, Sang Moon; Kim, Hae Jin; An, Ha-Rim; Ha, Myoung Gyu; Lee, Go-Woon; Lee, Young-Seak; Lee, Gaehang

2018-04-23

In this study, hierarchically three-dimensional (3D) nanotubular sea urchin-shaped iron oxide nanostructures (3D-Fe 2 O 3 ) were synthesized by a facile and rapid ultrasound irradiation method. Additives, templates, inert gas atmosphere, pH regulation, and other complicated procedures were not required. Dense 3D-Fe 2 O 3 with a relatively large Brunauer-Emmett-Teller (BET) surface area of 129.4 m 2 /g was synthesized within 23 min, and the BET surface area was further improved to 282.7 m 2 /g by a post heat-treatment process. In addition, this post processing led to phase changes from maghemite (γ phase) to hematite (α phase) Fe 2 O 3 . Subsequent characterization suggested that the growth mechanism of the 3D-Fe 2 O 3 follows self-assembly and oriented attachment. The prepared 3D-Fe 2 O 3 was applied to wastewater purification. Ultrasound-irradiated 3D-Fe 2 O 3 can eliminate a As(V) and Cr(VI) from water with 25 times faster removal rate by using a one third smaller amount than commercial α-Fe 2 O 3 . This was attributed to the inter-particle pores and relatively positively charged surface of the nanostructure. In addition, post heat treatment on ultrasound-irradiated 3D-Fe 2 O 3 significantly influenced the photocatalytic degradation of methylene blue and phenol, with a 25 times higher removal efficiency than that of commercial α-Fe 2 O 3 , because of both high BET surface area and good crystallization of the prepared samples. Copyright © 2018 Elsevier B.V. All rights reserved.

Structural diversity and photocatalytic properties of Cd(II) coordination polymers constructed by a flexible V-shaped bipyridyl benzene ligand and dicarboxylate derivatives.

PubMed

Liu, Lei-Lei; Yu, Cai-Xia; Ma, Feng-Ji; Li, Ya-Ru; Han, Jing-Jing; Lin, Lu; Ma, Lu-Fang

2015-01-28

Hydrothermal reactions of Cd(OAc)2·2H2O with a flexible V-shaped bipyridyl benzene ligand and five benzenedicarboxylic acid derivatives gave rise to five new coordination polymers i.e., [Cd(1,4-BDC)(bpmb)(H2O)]n (1), {[Cd(1,3-BDC)(bpmb)]·0.125H2O}n (2), [Cd2(5-Me-1,3-BDC)2(bpmb)2]n (3), [Cd(5-NO2-1,3-BDC)(bpmb)(H2O)]n (4) and [Cd(5-OH-1,3-BDC)(bpmb)(H2O)]n (5) (bpmb = 1,3-bis(pyridine-3-ylmethoxy)benzene, 1,4-H2BDC = 1,4-benzenedicarboxylic acid, 1,3-H2BDC = 1,3-benzenedicarboxylic acid, 5-Me-1,3-H2BDC = 5-methyl-1,3-benzenedicarboxylic acid, 5-NO2-1,3-H2BDC = 5-nitro-1,3-benzenedicarboxylic acid, 5-OH-1,3-H2BDC = 5-hydroxy-1,3-benzenedicarboxylic acid). Their structures have been determined by single-crystal X-ray diffraction analyses, elemental analyses, IR spectra, powder X-ray diffraction (PXRD) and thermogravimetric analyses (TGA). Compound 1 is a two-fold interpenetrating network showing the coexistence of polyrotaxane and polycatenane characters. Compounds 2 and 3 exhibit similar 2D (3,5)-connected (4(2)·6(7)·8)(4(2)·6) nets in which the bpmb ligands work as lockers in interlocking 1D [Cd(1,3-BDC/5-Me-1,3-BDC)]n chains. Compound 4 shows a 2D 4-connected (6(6)) sandwich-like structure with differently oriented [Cd(5-NO2-1,3-BDC)]n chains. Compound 5 is a 3D supramolecular pcu net based on a 1D ladder-shaped chain. These results suggest that the substituted positions of carboxylate groups and changes in substituted R groups in the 5-position of BDC ligands have significant effect on the final structures. These compounds exhibited relatively good photocatalytic activity towards the degradation of methylene blue (MB) in aqueous solution under UV irradiation. Moreover, solid-state photoluminescence properties of 1-5 were also investigated.

Quantifying temporal bone morphology of great apes and humans: an approach using geometric morphometrics.

PubMed

Lockwood, Charles A; Lynch, John M; Kimbel, William H

2002-12-01

The hominid temporal bone offers a complex array of morphology that is linked to several different functional systems. Its frequent preservation in the fossil record gives the temporal bone added significance in the study of human evolution, but its morphology has proven difficult to quantify. In this study we use techniques of 3D geometric morphometrics to quantify differences among humans and great apes and discuss the results in a phylogenetic context. Twenty-three landmarks on the ectocranial surface of the temporal bone provide a high level of anatomical detail. Generalized Procrustes analysis (GPA) is used to register (adjust for position, orientation and scale) landmark data from 405 adults representing Homo, Pan, Gorilla and Pongo. Principal components analysis of residuals from the GPA shows that the major source of variation is between humans and apes. Human characteristics such as a coronally orientated petrous axis, a deep mandibular fossa, a projecting mastoid process, and reduced lateral extension of the tympanic element strongly impact the analysis. In phenetic cluster analyses, gorillas and orangutans group together with respect to chimpanzees, and all apes group together with respect to humans. Thus, the analysis contradicts depictions of African apes as a single morphotype. Gorillas and orangutans lack the extensive preglenoid surface of chimpanzees, and their mastoid processes are less medially inflected. These and other characters shared by gorillas and orangutans are probably primitive for the African hominid clade.

Formation of Monocrystalline 1D and 2D Architectures via Epitaxial Attachment: Bottom-Up Routes through Surfactant-Mediated Arrays of Oriented Nanocrystals.

PubMed

Nakagawa, Yoshitaka; Kageyama, Hiroyuki; Oaki, Yuya; Imai, Hiroaki

2015-06-09

Monocrystalline architectures with well-defined shapes were achieved by bottom-up routes through epitaxial attachment of Mn3O4 nanocrystals. The crystallographically continuous 1D chains elongated in the a axis and 2D panels having large a or c faces were obtained by removal of the organic mediator from surfactant-mediated 1D and 2D arrays of Mn3O4 nanocrystals, respectively. Our basal approach indicates that the epitaxial attachment through the surfactant-mediated arrays is utilized for fabrication of a wide variety of micrometric architectures from nanometric crystalline units.

MBE Growth of InN/GaN(0001) and Shape Transitions of InN islands

NASA Astrophysics Data System (ADS)

Cao, Yongge; Xie, Maohai; Liu, Ying; Ng, Y. F.

2003-03-01

Plasma-assisted molecular-beam epitaxial growth of InN on GaN(0001) is investigated. Both layer-by-layer and Stranski-Krastanov (SK) growth modes are observed under different growth windows. Strain relaxation is studied by real-time recording of the in-plane lattice spacing evolutions on RHEED pattern, which suggest a gradual relaxation of the strain in InN film commenced during the first bilayer (BL) deposition and almost completed after 2-4 BLs. For SK growth, 3D islanding initiates after the strain has mostly been relieved, presumably by dislocations. Based on statistical analysis, the shape transitions of 3D islands are firstly observed in the III-nitrides system. The InN islands transform gradually from pyramids to platelets with increasing of In flux. Under In-rich growth condition, the reverse trend of island shape evolution dependence on volume size, compared with Equilibrium Crystal Shape (ECS) theory, is induced by the Indium self-surfactant effects, in which Indium adlayer on the top surface of InN islands will depress the thermodynamic driving force for the vertical growth of 3D islands. Lateral growth of 3D islands is not only the result of kinetic process but also favored by thermodynamics while Indium self-surfactant exist.

Mapping and genomic targeting of the major leaf shape gene (L) in Upland cotton (Gossypium hirsutum L.).

PubMed

Andres, Ryan J; Bowman, Daryl T; Kaur, Baljinder; Kuraparthy, Vasu

2014-01-01

A major leaf shape locus (L) was mapped with molecular markers and genomically targeted to a small region in the D-genome of cotton. By using expression analysis and candidate gene mapping, two LMI1 -like genes are identified as possible candidates for leaf shape trait in cotton. Leaf shape in cotton is an important trait that influences yield, flowering rates, disease resistance, lint trash, and the efficacy of foliar chemical application. The leaves of okra leaf cotton display a significantly enhanced lobing pattern, as well as ectopic outgrowths along the lobe margins when compared with normal leaf cotton. These phenotypes are the hallmark characteristics of mutations in various known modifiers of leaf shape that culminate in the mis/over-expression of Class I KNOX genes. To better understand the molecular and genetic processes underlying leaf shape in cotton, a normal leaf accession (PI607650) was crossed to an okra leaf breeding line (NC05AZ21). An F2 population of 236 individuals confirmed the incompletely dominant single gene nature of the okra leaf shape trait in Gossypium hirsutum L. Molecular mapping with simple sequence repeat markers localized the leaf shape gene to 5.4 cM interval in the distal region of the short arm of chromosome 15. Orthologous mapping of the closely linked markers with the sequenced diploid D-genome (Gossypium raimondii) tentatively resolved the leaf shape locus to a small genomic region. RT-PCR-based expression analysis and candidate gene mapping indicated that the okra leaf shape gene (L (o) ) in cotton might be an upstream regulator of Class I KNOX genes. The linked molecular markers and delineated genomic region in the sequenced diploid D-genome will assist in the future high-resolution mapping and map-based cloning of the leaf shape gene in cotton.

Optimal design of composite hip implants using NASA technology

NASA Technical Reports Server (NTRS)

Blake, T. A.; Saravanos, D. A.; Davy, D. T.; Waters, S. A.; Hopkins, D. A.

1993-01-01

Using an adaptation of NASA software, we have investigated the use of numerical optimization techniques for the shape and material optimization of fiber composite hip implants. The original NASA inhouse codes, were originally developed for the optimization of aerospace structures. The adapted code, which was called OPORIM, couples numerical optimization algorithms with finite element analysis and composite laminate theory to perform design optimization using both shape and material design variables. The external and internal geometry of the implant and the surrounding bone is described with quintic spline curves. This geometric representation is then used to create an equivalent 2-D finite element model of the structure. Using laminate theory and the 3-D geometric information, equivalent stiffnesses are generated for each element of the 2-D finite element model, so that the 3-D stiffness of the structure can be approximated. The geometric information to construct the model of the femur was obtained from a CT scan. A variety of test cases were examined, incorporating several implant constructions and design variable sets. Typically the code was able to produce optimized shape and/or material parameters which substantially reduced stress concentrations in the bone adjacent of the implant. The results indicate that this technology can provide meaningful insight into the design of fiber composite hip implants.

Parametric model of human body shape and ligaments for patient-specific epidural simulation.

PubMed

Vaughan, Neil; Dubey, Venketesh N; Wee, Michael Y K; Isaacs, Richard

2014-10-01

This work is to build upon the concept of matching a person's weight, height and age to their overall body shape to create an adjustable three-dimensional model. A versatile and accurate predictor of body size and shape and ligament thickness is required to improve simulation for medical procedures. A model which is adjustable for any size, shape, body mass, age or height would provide ability to simulate procedures on patients of various body compositions. Three methods are provided for estimating body circumferences and ligament thicknesses for each patient. The first method is using empirical relations from body shape and size. The second method is to load a dataset from a magnetic resonance imaging (MRI) scan or ultrasound scan containing accurate ligament measurements. The third method is a developed artificial neural network (ANN) which uses MRI dataset as a training set and improves accuracy using error back-propagation, which learns to increase accuracy as more patient data is added. The ANN is trained and tested with clinical data from 23,088 patients. The ANN can predict subscapular skinfold thickness within 3.54 mm, waist circumference 3.92 cm, thigh circumference 2.00 cm, arm circumference 1.21 cm, calf circumference 1.40 cm, triceps skinfold thickness 3.43 mm. Alternative regression analysis method gave overall slightly less accurate predictions for subscapular skinfold thickness within 3.75 mm, waist circumference 3.84 cm, thigh circumference 2.16 cm, arm circumference 1.34 cm, calf circumference 1.46 cm, triceps skinfold thickness 3.89 mm. These calculations are used to display a 3D graphics model of the patient's body shape using OpenGL and adjusted by 3D mesh deformations. A patient-specific epidural simulator is presented using the developed body shape model, able to simulate needle insertion procedures on a 3D model of any patient size and shape. The developed ANN gave the most accurate results for body shape, size and ligament thickness. The resulting simulator offers the experience of simulating needle insertions accurately whilst allowing for variation in patient body mass, height or age. Copyright © 2014 Elsevier B.V. All rights reserved.

Ultrafast responses of two V-shaped compounds with a reverse conjugated structural configuration: an investigation of the reason for the enhanced two-photon absorption cross-section

NASA Astrophysics Data System (ADS)

Wang, Yaochuan; Jiang, Yihua; Liu, Dajun; Wang, Yizhuo; Wang, Guiqiu; Hua, Jianli

2018-06-01

To study the effect of the conjugated structural configuration on the two-photon absorption (TPA) properties of V-shaped compounds, two 1,3,5-triazine-based compounds with the same electron donor (D) and acceptor (A) connected in a reverse-conjugated structural configuration ( T02: D-π-A-π-D; R02: A-π-D-π-A) were systematically investigated using steady-state and transient absorption spectroscopy, open-aperture Z-scan measurements, and two-photon fluorescence measurements. The TPA cross-section of compound R02 connected in a A-π-D-π-A-conjugated structural configuration with triphenylamine as the central core was 203 GM, which showed a 2.3-fold enhancement compared with compound T02 connected in a reverse D-π-A-π-D-conjugated structural configuration (90 GM, with 1,3,5-triazine as the central core). This result indicates that the conjugated structural configuration plays an important role in the TPA properties. A two-color pump-probe experiment was used to investigate the effect of the conjugated structural configuration on the excited state and intra-molecular charge transfer (ICT) properties of these V-shaped compounds. The formation and relaxation lifetimes of the ICT state were determined. The results indicate that the electron-donating/accepting strength of the central group, which serves as a communal group for two D-π-A subunits, was confirmed to be a key role to the overall effect of the ICT for V-shaped compounds. These ultrafast dynamic results are in agreement with the TPA properties.

Rydberg Excitation of a Single Trapped Ion.

PubMed

Feldker, T; Bachor, P; Stappel, M; Kolbe, D; Gerritsma, R; Walz, J; Schmidt-Kaler, F

2015-10-23

We demonstrate excitation of a single trapped cold (40)Ca(+) ion to Rydberg levels by laser radiation in the vacuum ultraviolet at a wavelength of 122 nm. Observed resonances are identified as 3d(2)D(3/2) to 51F, 52F and 3d(2)D(5/2) to 64F. We model the line shape and our results imply a large state-dependent coupling to the trapping potential. Rydberg ions are of great interest for future applications in quantum computing and simulation, in which large dipolar interactions are combined with the superb experimental control offered by Paul traps.

3D ultrasound Nakagami imaging for radiation-induced vaginal fibrosis

NASA Astrophysics Data System (ADS)

Yang, Xiaofeng; Rossi, Peter; Shelton, Joseph; Bruner, Debrorah; Tridandapani, Srini; Liu, Tian

2014-03-01

Radiation-induced vaginal fibrosis is a debilitating side-effect affecting up to 80% of women receiving radiotherapy for their gynecological (GYN) malignancies. Despite the significant incidence and severity, little research has been conducted to identify the pathophysiologic changes of vaginal toxicity. In a previous study, we have demonstrated that ultrasound Nakagami shape and PDF parameters can be used to quantify radiation-induced vaginal toxicity. These Nakagami parameters are derived from the statistics of ultrasound backscattered signals to capture the physical properties (e.g., arrangement and distribution) of the biological tissues. In this paper, we propose to expand this Nakagami imaging concept from 2D to 3D to fully characterize radiation-induced changes to the vaginal wall within the radiation treatment field. A pilot study with 5 post-radiotherapy GYN patients was conducted using a clinical ultrasound scanner (6 MHz) with a mechanical stepper. A serial of 2D ultrasound images, with radio-frequency (RF) signals, were acquired at 1 mm step size. The 2D Nakagami shape and PDF parameters were calculated from the RF signal envelope with a sliding window, and then 3D Nakagami parameter images were generated from the parallel 2D images. This imaging method may be useful as we try to monitor radiation-induced vaginal injury, and address vaginal toxicities and sexual dysfunction in women after radiotherapy for GYN malignancies.

Upgrades to the Mars Initial Reference Ionosphere (MIRI) Model Due to Observations from MAVEN, MEX and MRO.

NASA Astrophysics Data System (ADS)

Narvaez, C.; Mendillo, M.; Trovato, J.

2017-12-01

A semi-empirical model of the maximum electron density (Nmax) of the martian ionosphere [MIRI-mark-1](1) was derived from an initial set radar observations by the MEX/MARSIS instrument. To extend the model to full electron density profiles, normalized shapes of Ne(h) from a theoretical model(2) were calibrated by MIRI's Nmax. Subsequent topside ionosphere observations from MAVEN indicated that topside shapes from MEX/MARSIS(3) offered improved morphology. The MEX topside shapes were then merged to the bottomside shapes from the theoretical model. Using a larger set of MEX/MARSIS observations (07/31/2005 - 05/24/2015), a new specification of Nmax as a function of solar zenith angle and solar flux is now used to calibrate the normalized Ne(h) profiles. The MIRI-mark-2 model includes the integral with height of Ne(h) to form total electron content (TEC) values. Validation of the MIRI TEC was accomplished using an independent set of TEC derived from the SHARAD(4) experiment on MRO. (1) M. Mendillo, A. Marusiak, P. Withers, D. Morgan and D. Gurnett, A New Semi-empirical Model of the Peak Electron Density of the Martian Ionosphere, Geophysical Research Letters, 40, 1-5, doi:10.1002/2013GL057631, 2013. (2) Mayyasi, M. and M. Mendillo (2015), Why the Viking descent probes found only one ionospheric layer at Mars, Geophys. Res. Lett., 42, 7359-7365, doi:10.1002/2015GL065575 (3) Němec, F., D. Morgan, D. Gurnett, and D. Andrews (2016), Empirical model of the Martian dayside ionosphere: Effects of crustal magnetic fields and solar ionizing flux at higher altitudes, J. Geophys. Res. Space Physics, 121, 1760-1771, doi:10.1002/2015/A022060.(4) Campbell, B., and T. Watters (2016), Phase compensation of MARSIS subsurface sounding and estimation of ionospheric properties: New insights from SHARAD results, J.Geophys. Res. Planets, 121, 180-193, doi:10.1002/2015JE004917.

Numerical study of core formation of asymmetrically driven cone-guided targets

DOE PAGES

Sawada, Hiroshi; Sakagami, Hitoshi

2017-09-22

Compression of a directly driven fast ignition cone-sphere target with a finite number of laser beams is numerically studied using a three-dimensional hydrodynamics code IMPACT-3D. The formation of a dense plasma core is simulated for 12-, 9-, 6-, and 4-beam configurations of the GEKKO XII laser. The complex 3D shapes of the cores are analyzed by elucidating synthetic 2D x-ray radiographic images in two orthogonal directions. Finally, the simulated x-ray images show significant differences in the core shape between the two viewing directions and rotation of the stagnating core axis in the top view for the axisymmetric 9- and 6-beammore » configurations.« less

Numerical study of core formation of asymmetrically driven cone-guided targets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sawada, Hiroshi; Sakagami, Hitoshi

Compression of a directly driven fast ignition cone-sphere target with a finite number of laser beams is numerically studied using a three-dimensional hydrodynamics code IMPACT-3D. The formation of a dense plasma core is simulated for 12-, 9-, 6-, and 4-beam configurations of the GEKKO XII laser. The complex 3D shapes of the cores are analyzed by elucidating synthetic 2D x-ray radiographic images in two orthogonal directions. Finally, the simulated x-ray images show significant differences in the core shape between the two viewing directions and rotation of the stagnating core axis in the top view for the axisymmetric 9- and 6-beammore » configurations.« less

Visual shape perception as Bayesian inference of 3D object-centered shape representations.

PubMed

Erdogan, Goker; Jacobs, Robert A

2017-11-01

Despite decades of research, little is known about how people visually perceive object shape. We hypothesize that a promising approach to shape perception is provided by a "visual perception as Bayesian inference" framework which augments an emphasis on visual representation with an emphasis on the idea that shape perception is a form of statistical inference. Our hypothesis claims that shape perception of unfamiliar objects can be characterized as statistical inference of 3D shape in an object-centered coordinate system. We describe a computational model based on our theoretical framework, and provide evidence for the model along two lines. First, we show that, counterintuitively, the model accounts for viewpoint-dependency of object recognition, traditionally regarded as evidence against people's use of 3D object-centered shape representations. Second, we report the results of an experiment using a shape similarity task, and present an extensive evaluation of existing models' abilities to account for the experimental data. We find that our shape inference model captures subjects' behaviors better than competing models. Taken as a whole, our experimental and computational results illustrate the promise of our approach and suggest that people's shape representations of unfamiliar objects are probabilistic, 3D, and object-centered. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Palmitoylation regulates intracellular trafficking of β2 adrenergic receptor/arrestin/phosphodiesterase 4D complexes in cardiomyocytes.

PubMed

Liu, Ruijie; Wang, Dayong; Shi, Qian; Fu, Qin; Hizon, Steven; Xiang, Yang K

2012-01-01

β(2) adrenergic receptor (β(2)AR) is a prototypical G-protein coupled receptor that stimulates the classic cAMP-protein kinase A (PKA) signaling pathway. Recent studies indicate that the cAMP-PKA activities are spatiotemporally regulated in part due to dynamic association of β(2)AR with phosphodiesterase 4D (PDE4D), a group of cAMP degradation enzymes. Here, we demonstrate that in cardiomyocytes, palmitoylation of β(2)AR, the covalent acylation of cysteine residue 341, plays a critical role in shaping subcellular cAMP-PKA activities in cardiomyocytes via regulating β(2)AR association with arrestin/PDE4D. Replacing cysteine 341 on β(2)AR with alanine (C341A) leads to an impaired binding to β arrestin 2. Surprisingly, the C341A mutant is able to internalize via an arrestin-independent pathway at saturated concentration of agonist stimulation; the internalization becomes caveolae-dependent and requires dynamin GTPase. However, the impaired binding to β arrestin 2 also leads to an impaired recruitment of PDE4D to the C341A mutant. Thus, the mutant C341A β(2)AR is transported alone from the plasma membrane to the endosome without recruiting PDE4D. This alteration leads to an enhanced cytoplasmic cAMP signal for PKA activation under β(2)AR stimulation. Functionally, Mutation of the C341 residue or inhibition of palmitoylation modification of β(2)AR enhances the receptor-induced PKA activities in the cytoplasm and increases in myocyte contraction rate. Our data reveal a novel function of palmitoylation in shaping subcellular cAMP-PKA signaling in cardiomyocytes via modulating the recruitment of β arrestin 2-PDE4D complexes to the agonist-stimulated β(2)AR.

Palmitoylation Regulates Intracellular Trafficking of β2 Adrenergic Receptor/Arrestin/Phosphodiesterase 4D Complexes in Cardiomyocytes

PubMed Central

Liu, Ruijie; Wang, Dayong; Shi, Qian; Fu, Qin; Hizon, Steven; Xiang, Yang K.

2012-01-01

β2 adrenergic receptor (β2AR) is a prototypical G-protein coupled receptor that stimulates the classic cAMP-protein kinase A (PKA) signaling pathway. Recent studies indicate that the cAMP-PKA activities are spatiotemporally regulated in part due to dynamic association of β2AR with phosphodiesterase 4D (PDE4D), a group of cAMP degradation enzymes. Here, we demonstrate that in cardiomyocytes, palmitoylation of β2AR, the covalent acylation of cysteine residue 341, plays a critical role in shaping subcellular cAMP-PKA activities in cardiomyocytes via regulating β2AR association with arrestin/PDE4D. Replacing cysteine 341 on β2AR with alanine (C341A) leads to an impaired binding to β arrestin 2. Surprisingly, the C341A mutant is able to internalize via an arrestin-independent pathway at saturated concentration of agonist stimulation; the internalization becomes caveolae-dependent and requires dynamin GTPase. However, the impaired binding to β arrestin 2 also leads to an impaired recruitment of PDE4D to the C341A mutant. Thus, the mutant C341A β2AR is transported alone from the plasma membrane to the endosome without recruiting PDE4D. This alteration leads to an enhanced cytoplasmic cAMP signal for PKA activation under β2AR stimulation. Functionally, Mutation of the C341 residue or inhibition of palmitoylation modification of β2AR enhances the receptor-induced PKA activities in the cytoplasm and increases in myocyte contraction rate. Our data reveal a novel function of palmitoylation in shaping subcellular cAMP-PKA signaling in cardiomyocytes via modulating the recruitment of β arrestin 2-PDE4D complexes to the agonist-stimulated β2AR. PMID:22912718

Asphyxia causes ultrasonographic D-shaping of the left ventricle--an experimental porcine study.

PubMed

Sørensen, A H; Wemmelund, K B; Møller-Helgestad, O K; Sloth, E; Juhl-Olsen, P

2016-02-01

In critical care, early diagnosis and correct treatment are of the utmost importance. Focused ultrasonography has gained acceptance as a pivotal tool for this by elucidating the underlying pathology. For example, massive pulmonary embolism is characterised by right ventricular dilatation. However, theoretically these characteristics might also be generated by asphyxia and the consequent hypoxia. We aimed to evaluate the ultrasonographic characteristics of asphyxia in a porcine model. Nineteen (13 intervention, 6 control) piglets were subjected to asphyxia until cardiac arrest, by disconnecting the ventilator tube. Ultrasonographic short-axis cine loops of the left ventricle were obtained every 30 seconds. The left ventricular (LV) eccentricity index (index of LV D-shaping) was quantified along with LV end-diastolic/end-systolic areas. Invasive pressures were measured throughout. The LV eccentricity index increased from 1.14 (1.10-1.31) to 1.86 (1.48-2.38), (P = 0.002), after 1.5 min, receded thereafter to baseline levels followed by a second increase after 5.5 min. LV end-diastolic area decreased from 11.6 cm(2) (11.1-13.2) to 6.3 cm(2) (3.3 -11.0) after 2.0 min (P = 0.009). Subsequently, values returned to the baseline level. The early and transient acute dilatation of the RV, coinciding with D-shaping of the LV and decrease in LV end-diastolic area seen in our study represent a combination of ultrasonographic characteristics normally attributed to pulmonary embolism. Early changes in ventricular chamber sizes and shape with septal flattening related to asphyxia can occur, but appear to be transient and disappear as circulatory collapse progresses, in an animal model. Despite this, asphyxia may represent a cause of ultrasonographic misinterpretation. © 2015 The Acta Anaesthesiologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

Performance evaluation for 120 four-layer DOI block detectors of the jPET-D4.

PubMed

Inadama, Naoko; Murayama, Hideo; Ono, Yusuke; Tsuda, Tomoaki; Hamamoto, Manabu; Yamaya, Taiga; Yoshida, Eiji; Shibuya, Kengo; Nishikido, Fumihiko; Takahashi, Kei; Kawai, Hideyuki

2008-01-01

The jPET-D4 is a brain positron emission tomography (PET) scanner that we have developed to meet user demands for high sensitivity and high spatial resolution. For this scanner, we developed a four-layer depth-of-interaction (DOI) detector. The four-layer DOI detector is a key component for the jPET-D4, its performance has great influence on the overall system performance. Previously, we reported the original technique for encoding four-layer DOI. Here, we introduce the final design of the jPET-D4 detector and present the results of an investigation on uniformity in performance of the detector. The performance evaluation was done over the 120 DOI crystal blocks for the detectors, which are to be assembled into the jPET-D4 scanner. We also introduce the crystal assembly method, which is simple enough, even though each DOI crystal block is composed of 1,024 crystal elements. The jPET-D4 detector consists of four layers of 16 x 16 Gd(2)SiO(5) (GSO) crystals and a 256-channel flat-panel position-sensitive photomultiplier tube (256ch FP-PMT). To identify scintillated crystals in the four-layer DOI detector, we use pulse shape discrimination and position discrimination on the two-dimensional (2D) position histogram. For pulse shape discrimination, two kinds of GSO crystals that show different scintillation decay time constants are used in the upper two and lower two layers, respectively. Proper reflector arrangement in the crystal block then allows the scintillated crystals to be identified in these two-layer groupings with two 2D position histograms. We produced the 120 DOI crystal blocks for the jPET-D4 system, and measured their characteristics such as the accuracy of pulse shape discrimination, energy resolution, and the pulse height of the full energy peak. The results show a satisfactory and uniform performance of the four-layer DOI crystal blocks; for example, misidentification rate in each GSO layer is <5% based on pulse shape discrimination, the averaged energy resolutions for the central four crystals of the first (farthest from the FP-PMT), second, third, and 4th layers are 15.7 +/- 1.0, 15.8 +/- 0.6, 17.7 +/- 1.2, and 17.3 +/- 1.4%, respectively, and variation in pulse height of the full energy peak among the four layers is <5% on average.

Assessing breathing motion by shape matching of lung and diaphragm surfaces

NASA Astrophysics Data System (ADS)

Urschler, Martin; Bischof, Horst

2005-04-01

Studying complex thorax breating motion is an important research topic for accurate fusion of functional and anatomical data, radiotherapy planning or reduction of breathing motion artifacts. We investigate segmented CT lung, airway and diaphragm surfaces at several different breathing states between Functional Residual and Total Lung Capacity. In general, it is hard to robustly derive corresponding shape features like curvature maxima from lung and diaphragm surfaces since diaphragm and rib cage muscles tend to deform the elastic lung tissue such that e.g. ridges might disappear. A novel registration method based on the shape context approach for shape matching is presented where we extend shape context to 3D surfaces. The shape context approach was reported as a promising method for matching 2D shapes without relying on extracted shape features. We use the point correspondences for a non-rigid thin-plate-spline registration to get deformation fields that describe the movement of lung and diaphragm. Our validation consists of experiments on phantom and real sheep thorax data sets. Phantom experiments make use of shapes that are manipulated with known transformations that simulate breathing behaviour. Real thorax data experiments use a data set showing lungs and diaphragm at 5 distinct breathing states, where we compare subsets of the data sets and qualitatively and quantitatively asses the registration performance by using manually identified corresponding landmarks.

Static sign language recognition using 1D descriptors and neural networks

NASA Astrophysics Data System (ADS)

Solís, José F.; Toxqui, Carina; Padilla, Alfonso; Santiago, César

2012-10-01

A frame work for static sign language recognition using descriptors which represents 2D images in 1D data and artificial neural networks is presented in this work. The 1D descriptors were computed by two methods, first one consists in a correlation rotational operator.1 and second is based on contour analysis of hand shape. One of the main problems in sign language recognition is segmentation; most of papers report a special color in gloves or background for hand shape analysis. In order to avoid the use of gloves or special clothing, a thermal imaging camera was used to capture images. Static signs were picked up from 1 to 9 digits of American Sign Language, a multilayer perceptron reached 100% recognition with cross-validation.

Study of flow around model of cooling tower by means of 2D Particle Image Velocimetry measurement

NASA Astrophysics Data System (ADS)

Barraclough, Veronika; Novotný, Jan; Šafařík, Pavel

This paper deals with flow around a bluff body of hyperboloid shape. It combines results gathered in the course of research by means of Particle Image Velocimetry (PIV). The experiments were carried out by means of low-frequency 2D PIV and the Reynolds number was 43 000.

Experimental investigation for cavity dimensions of highly porous small bodies

NASA Astrophysics Data System (ADS)

Okamoto, T.; Nakamura, A.; Hasegawa, S.

2014-07-01

Small bodies were probably very porous during the formation of the solar system. In order to understand the surface evolution of highly porous bodies, it is necessary to investigate the impact process for targets with such high porosity. In this study, impact experiments with sintered glass-bead targets of 87 and 94 % porosities were conducted. Growth of cavities with time and the final cavity dimensions were analyzed and compared with previous studies of porous targets. Impact experiments were conducted using a two-stage light-gas gun at ISAS, Japan. The projectiles of a few millimeters were composed of titanium, aluminum, nylon, and basalt. The impact velocities ranged from 1.8 to 7.2 km s^{-1}. In order to observe the inside of the targets, we used a flash X-ray system and a micro-X-ray tomography instrument. The track shape was found to be divided into two types, elongated 'carrot' shape and short 'bulb' shape [1]. The figures on the left and right present a transmission image of the bulb shape track and a sketch of a cross section of the cavity, respectively. The results of the final maximum diameter, D_max and the final entrance-hole diameter, D_ent show that both dimensions tend to increase with impact velocity and decrease with target porosity. We adopted the scaling law of crater diameter [2] for our analysis of D_max and D_ent. The following empirical relations are obtained for targets with porosity ≥ 87 %: {D_max}/{d_p}(ρ_t/ρ_p)^{0.4} =10^{-1.52±0.27} ({Y}/ρ_t{v_0^2})^{-0.49 ± 0.07}, {D_ent}/{d_p}(ρ_t/ρ_p)^{0.4} =10^{-2.12±0.39} ({Y}/ρ_t{v_0^2})^{-0.53 ± 0.11}, where d_p, ρ_t, ρ_p, Y, and v_0 are the projectile diameter, target density, projectile density, target compressive strength, and the impact velocity, respectively. The results of the depth from the entrance hole to the maximum diameter of the cavity, L_max, shows that L_max decreases with impact velocity and increases with target porosity. If we assume that a projectile decelerates by inertial drag [1], the characteristic length L_0, which is the depth from the surface where the kinetic energy of the projectile becomes 1/e of the initial energy, is described as follows: L_0={2ρ_p}/{3C_dρ_t}d_p, where C_d is the drag coefficient that increases with dynamic pressure normalized by tensile strength of the projectile [1]. We found that L_max/d_p increases with L_0/d_p. It indicates that L_max depends on the degree of projectile deformation or disruption through the drag coefficient and also depends on the projectile-target density ratio. We will also discuss the growth of the cavity volume, maximum diameter, and depth of the cavity with time using dimensionless parameters of crater scaling [3].

Spreading dynamics of 2D dipolar Langmuir monolayer phases.

PubMed

Heinig, P; Wurlitzer, S; Fischer, Th M

2004-07-01

We study the spreading of a liquid 2D dipolar droplet in a Langmuir monolayer. Interfacial tensions (line tensions) and microscopic contact angles depend on the scale on which they are probed and obey a scaling law. Assuming rapid equilibration of the microscopic contact angle and ideal slippage of the 2D solid/liquid and solid/gas boundary, the driving force of spreading is merely expressed by the shape-dependent long-range interaction integrals. We obtain good agreement between experiment and numerical simulations using this theory.

The effect of intrinsic attenuation correction methods on the stationarity of the 3-D modulation transfer function of SPECT.

PubMed

Glick, S J; Hawkins, W G; King, M A; Penney, B C; Soares, E J; Byrne, C L

1992-01-01

The application of stationary restoration techniques to SPECT images assumes that the modulation transfer function (MTF) of the imaging system is shift invariant. It was hypothesized that using intrinsic attenuation correction (i.e., methods which explicitly invert the exponential radon transform) would yield a three-dimensional (3-D) MTF which varies less with position within the transverse slices than the combined conjugate view two-dimensional (2-D) MTF varies with depth. Thus the assumption of shift invariance would become less of an approximation for 3-D post- than for 2-D pre-reconstruction restoration filtering. SPECT acquisitions were obtained from point sources located at various positions in three differently shaped, water-filled phantoms. The data were reconstructed with intrinsic attenuation correction, and 3-D MTFs were calculated. Four different intrinsic attenuation correction methods were compared: (1) exponentially weighted backprojection, (2) a modified exponentially weighted backprojection as described by Tanaka et al. [Phys. Med. Biol. 29, 1489-1500 (1984)], (3) a Fourier domain technique as described by Bellini et al. [IEEE Trans. ASSP 27, 213-218 (1979)], and (4) the circular harmonic transform (CHT) method as described by Hawkins et al. [IEEE Trans. Med. Imag. 7, 135-148 (1988)]. The dependence of the 3-D MTF obtained with these methods, on point source location within an attenuator, and on shape of the attenuator, was studied. These 3-D MTFs were compared to: (1) those MTFs obtained with no attenuation correction, and (2) the depth dependence of the arithmetic mean combined conjugate view 2-D MTFs.(ABSTRACT TRUNCATED AT 250 WORDS)

Fabrication of custom-shaped grafts for cartilage regeneration.

PubMed

Koo, Seungbum; Hargreaves, Brian A; Gold, Garry E; Dragoo, Jason L

2010-10-01

to create a custom-shaped graft through 3D tissue shape reconstruction and rapid-prototype molding methods using MRI data, and to test the accuracy of the custom-shaped graft against the original anatomical defect. An iatrogenic defect on the distal femur was identified with a 1.5 Tesla MRI and its shape was reconstructed into a three-dimensional (3D) computer model by processing the 3D MRI data. First, the accuracy of the MRI-derived 3D model was tested against a laser-scan based 3D model of the defect. A custom-shaped polyurethane graft was fabricated from the laser-scan based 3D model by creating custom molds through computer aided design and rapid-prototyping methods. The polyurethane tissue was laser-scanned again to calculate the accuracy of this process compared to the original defect. The volumes of the defect models from MRI and laser-scan were 537 mm3 and 405 mm3, respectively, implying that the MRI model was 33% larger than the laser-scan model. The average (±SD) distance deviation of the exterior surface of the MRI model from the laser-scan model was 0.4 ± 0.4 mm. The custom-shaped tissue created from the molds was qualitatively very similar to the original shape of the defect. The volume of the custom-shaped cartilage tissue was 463 mm3 which was 15% larger than the laser-scan model. The average (±SD) distance deviation between the two models was 0.04 ± 0.19 mm. This investigation proves the concept that custom-shaped engineered grafts can be fabricated from standard sequence 3-D MRI data with the use of CAD and rapid-prototyping technology. The accuracy of this technology may help solve the interfacial problem between native cartilage and graft, if the grafts are custom made for the specific defect. The major source of error in fabricating a 3D custom-shaped cartilage graft appears to be the accuracy of a MRI data itself; however, the precision of the model is expected to increase by the utilization of advanced MR sequences with higher magnet strengths.

Damage methodology approach on a composite panel based on a combination of Fringe Projection and 2D Digital Image Correlation

NASA Astrophysics Data System (ADS)

Felipe-Sesé, Luis; Díaz, Francisco A.

2018-02-01

The recent improvement in accessibility to high speed digital cameras has enabled three dimensional (3D) vibration measurements employing full-field optical techniques. Moreover, there is a need to develop a cost-effective and non-destructive testing method to quantify the severity of damages arising from impacts and thus, enhance the service life. This effect is more interesting in composite structures since possible internal damage has low external manifestation. Those possible damages have been previously studied experimentally by using vibration testing. Namely, those analyses were focused on variations in the modal frequencies or, more recently, mode shapes variations employing punctual accelerometers or vibrometers. In this paper it is presented an alternative method to investigate the severity of damage on a composite structure and how the damage affects to its integrity through the analysis of the full field modal behaviour. In this case, instead of punctual measurements, displacement maps are analysed by employing a combination of FP + 2D-DIC during vibration experiments in an industrial component. In addition, to analyse possible mode shape changes, differences between damaged and undamaged specimens are studied by employing a recent methodology based on Adaptive Image Decomposition (AGMD) procedure. It will be demonstrated that AGMD Image decomposition procedure, which decompose the displacement field into shape descriptors, is capable to detect and quantify the differences between mode shapes. As an application example, the proposed approach has been evaluated on two large industrial components (car bonnets) made of short-fibre reinforced composite. Specifically, the evolution of normalized AGMD shape descriptors has been evaluated for three different components with different damage levels. Results demonstrate the potential of the presented approach making it possible to measure the severity of a structural damage by evaluating the mode shape based in the analysis of its shape descriptors.

A novel verification method using a plastic scintillator imagining system for assessment of gantry sag in radiotherapy.

PubMed

Tsuneda, Masato; Nishio, Teiji; Saito, Akito; Tanaka, Sodai; Suzuki, Tatsuhiko; Kawahara, Daisuke; Matsushita, Keiichiro; Nishio, Aya; Ozawa, Shuichi; Karasawa, Kumiko; Nagata, Yasushi

2018-06-01

High accuracy of the beam-irradiated position is required for high-precision radiation therapy such as stereotactic body radiation therapy (SBRT), volumetric modulated arc therapy (VMAT), and intensity modulated radiation therapy (IMRT). Users generally perform the verification of the mechanical and radiation isocenters using the star shot test and the Winston Lutz test that allow evaluation of the displacement at the isocenter. However, these methods are unable to evaluate directly and quantitatively the sagging angle that is caused by the weight of the gantry itself along the gantry rotation axis. In addition, the verification of the central axis of the irradiated beam that is not dependent at the isocenter is needed for the mechanical quality assurance of a nonisocentric irradiation technique. In this study, we have developed a prototype system for the verification of three-dimensional (3D) beam alignment and we have verified the system concept for 3D isocentricity. Our system allows detection of the central axis in 3D coordinates and evaluation of the irradiated oblique angle to the gantry rotation axis, i.e., the sagging angle. In order to measure the central axis of the irradiated beam in 3D coordinates, we constructed the prototype verification system consisting of a column-shaped plastic scintillator (CoPS), a truncated cone-shaped mirror (TCsM), and a cooled charged-coupled device (CCD) camera. This verification system was irradiated with 6-MV photon beams and the scintillation light was measured using the CCD camera. The central axis on the axial plane (two-dimensional (2D) central axis) was acquired from the integration of the scintillation light along the major axis of the CoPS, and the central axis in 3D coordinates (3D central axis) was acquired from two curve-shaped profiles which were reflected by the TCsM. We verified the calculation accuracy of the gantry rotation axis, θ z . Additionally, we calculated the 3D central axis and the sagging angle at each gantry angle. We acquired the measurement images composed of the 2D central axis and the two curve-shaped profiles. The relationship between the irradiated and measured angles with respect to the gantry rotation axis had good linearity. The mean and standard deviation of the difference between the irradiated and measured angles were 0.012 and 0.078 degrees, respectively. The size of the 2D and 3D radiation isocenters were 0.470 and 0.652 mm on the axial plane and in 3D coordinates, respectively. The sagging angles were -0.31, 0.39, and 0.38 degrees at the gantry angles of 0, 180, and 180E degrees, respectively. We developed a novel verification system, designated as the "kompeito shot test system," to verify the 3D beam alignment. This system concept works for both verification of the 3D isocentricity and the direct evaluation of the sagging angle. Next, we want to improve the aspects of this system, such as the shape and the type of scintillator, to increase the system accuracy and nonisocentric beam alignment performance. © 2018 American Association of Physicists in Medicine.

Aging preserves the ability to perceive 3D object shape from static but not deforming boundary contours.

PubMed

Norman, J Farley; Bartholomew, Ashley N; Burton, Cory L

2008-09-01

A single experiment investigated how younger (aged 18-32 years) and older (aged 62-82 years) observers perceive 3D object shape from deforming and static boundary contours. On any given trial, observers were shown two smoothly-curved objects, similar to water-smoothed granite rocks, and were required to judge whether they possessed the "same" or "different" shape. The objects presented during the "different" trials produced differently-shaped boundary contours. The objects presented during the "same" trials also produced different boundary contours, because one of the objects was always rotated in depth relative to the other by 5, 25, or 45 degrees. Each observer participated in 12 experimental conditions formed by the combination of 2 motion types (deforming vs. static boundary contours), 2 surface types (objects depicted as silhouettes or with texture and Lambertian shading), and 3 angular offsets (5, 25, and 45 degrees). When there was no motion (static silhouettes or stationary objects presented with shading and texture), the older observers performed as well as the younger observers. In the moving object conditions with shading and texture, the older observers' performance was facilitated by the motion, but the amount of this facilitation was reduced relative to that exhibited by the younger observers. In contrast, the older observers obtained no benefit in performance at all from the deforming (i.e., moving) silhouettes. The reduced ability of older observers to perceive 3D shape from motion is probably due to a low-level deterioration in the ability to detect and discriminate motion itself.

3D Printing of a Thermoplastic Shape Memory Polymer using FDM

NASA Astrophysics Data System (ADS)

Zhao, Zhiyang; Weiss, R. A.; Vogt, Bryan

Shape memory polymers (SMPs) change from a temporary shape to its permanent shape when exposed to an external stimulus. The shape memory relies on the presence of two independent networks. 3D printing provides a facile method to fabricate complex shapes with high degrees of customizability. The most common consumer 3D printing technology is fused deposition modeling (FDM), which relies on the extrusion of a thermoplastic filament to build-up the part in a layer by layer fashion. The material choices for FDM are limited, but growing. The generation of an SMP that is printable by FDM could open SMPs to many new potential applications. In this work, we demonstrate printing of thermally activated SMP using FDM. Partially neutralized poly(ethylene-co-r-methacrylic acid) ionomers (Surlyn by Dupont) was extruded into filaments and used as a model thermoplastic shape memory material. The properties of the SMP part can be readily tuned by print parameters, such as infill density or infill direction without changing the base material. We discuss the performance and characteristics of 3D printed shapes compared to their compression molded analogs.

Fully optimized shaped pupils: preparation for a test at the Subaru Telescope

NASA Astrophysics Data System (ADS)

Carlotti, Alexis; Kasdin, N. Jeremy; Martinache, Frantz; Vanderbei, Robert J.; Young, Elizabeth J.; Che, George; Groff, Tyler D.; Guyon, Olivier

2012-09-01

The SCExAO instrument at the Subaru telescope, mainly based on a PIAA coronagraph can benefit from the addition of a robust and simple shaped pupil coronagraph. New shaped pupils, fully optimized in 2 dimensions, make it possible to design optimal apodizers for arbitrarily complex apertures, for instance on-axis telescopes such as the Subaru telescope. We have designed several masks with inner working angles as small as 2.5 λ / D, and for high-contrast regions with different shapes. Using Princeton University nanofabrication facilities, we have manufactured two masks by photolithography. These masks have been tested in the laboratory, both in Princeton and in the facilities of the National Astronomical Observatory of Japan (NAOJ) in Hilo. The goal of this work is to prepare tests on the sky of a shaped pupil coronagraph in 2012.

Competition between quasi-planar and cage-like structures in the B29- cluster: photoelectron spectroscopy and ab initio calculations.

PubMed

Li, Hai-Ru; Jian, Tian; Li, Wei-Li; Miao, Chang-Qing; Wang, Ying-Jin; Chen, Qiang; Luo, Xue-Mei; Wang, Kang; Zhai, Hua-Jin; Li, Si-Dian; Wang, Lai-Sheng

2016-10-26

Size-selected boron clusters have been found to be predominantly planar or quasi-planar (2D) in the small size regime with the appearance of three-dimensional (3D) borospherene cages of larger sizes. A seashell-like B 28 - cluster was previously shown to be the smallest borospherene, which competes with a quasi-planar isomer for the global minimum. Here we report a study on the structures and bonding of the B 29 - and B 29 clusters using photoelectron spectroscopy (PES) and first-principles calculations and demonstrate the continued competition between the 2D and borospherene structures. The PES spectrum of B 29 - displays a complex pattern with evidence of low-lying isomers. Global-minimum searches and extensive theoretical calculations revealed a complicated potential energy surface for B 29 - with five low-lying isomers, among which the lowest three were shown to contribute to the experimental spectrum. A 3D seashell-like C s (2, 1 A') isomer, featuring two heptagons on the waist and one octagon at the bottom, is the global minimum for B 29 - , followed by a 2D C 1 (3, 1 A) isomer with a hexagonal hole and a stingray-shaped 2D C s (1, 1 A') isomer with a pentagonal hole. However, by taking into account the entropic effects, the stingray-shaped isomer 1 was shown to be the lowest in energy at room temperature and was found to dominate the PES spectrum. Isomers 2 and 3, which have lower electron binding energies, were also found to be present in the experiment. Chemical bonding analyses showed that isomer 1 is an all-boron analogue of benzo[ghi]fluoranthene (C 18 H 10 ), whereas the borospherene isomer 2 possesses 18π electrons, conforming to the 2(N + 1) 2 electron counting rule for spherical aromaticity. For the B 29 neutral cluster, the seashell-like borospherene isomer is the global minimum, significantly lower in energy than the stingray-shaped quasi-planar structure.

Hybrid Shape Memory Alloy Composites for Extreme Environments

DTIC Science & Technology

2011-10-01

Shape Memory Alloys in Oil Well Applications,” Sintef Petroleum Research, 1999, Trondheim, Norway. 5. Hartl , D. J., Lagoudas, D., Mabe , J., Calkins...Materials and Structures, Vol. 19, No. 1., 2009. 6. Hartl , D. J., Lagoudas, D., Mabe , J., Calkins, F., and Mooney, J., “Use of Ni60Ti Shape Memory...hydraulic actuators) and can thus be located in environments not previously accessible. SMA actuators can also be found in the aerospace ( Hartl and

The decomposition of deformation: New metrics to enhance shape analysis in medical imaging.

PubMed

Varano, Valerio; Piras, Paolo; Gabriele, Stefano; Teresi, Luciano; Nardinocchi, Paola; Dryden, Ian L; Torromeo, Concetta; Puddu, Paolo E

2018-05-01

In landmarks-based Shape Analysis size is measured, in most cases, with Centroid Size. Changes in shape are decomposed in affine and non affine components. Furthermore the non affine component can be in turn decomposed in a series of local deformations (partial warps). If the extent of deformation between two shapes is small, the difference between Centroid Size and m-Volume increment is barely appreciable. In medical imaging applied to soft tissues bodies can undergo very large deformations, involving large changes in size. The cardiac example, analyzed in the present paper, shows changes in m-Volume that can reach the 60%. We show here that standard Geometric Morphometrics tools (landmarks, Thin Plate Spline, and related decomposition of the deformation) can be generalized to better describe the very large deformations of biological tissues, without losing a synthetic description. In particular, the classical decomposition of the space tangent to the shape space in affine and non affine components is enriched to include also the change in size, in order to give a complete description of the tangent space to the size-and-shape space. The proposed generalization is formulated by means of a new Riemannian metric describing the change in size as change in m-Volume rather than change in Centroid Size. This leads to a redefinition of some aspects of the Kendall's size-and-shape space without losing Kendall's original formulation. This new formulation is discussed by means of simulated examples using 2D and 3D platonic shapes as well as a real example from clinical 3D echocardiographic data. We demonstrate that our decomposition based approaches discriminate very effectively healthy subjects from patients affected by Hypertrophic Cardiomyopathy. Copyright © 2018 Elsevier B.V. All rights reserved.