Skeletonization of volumetric angiograms for display

The display of three-dimensional angiograms can benefit from the knowledge of quantitative shape features such as tangent and curvature of the centerline of vessels. These can be obtained from a curve-like skeleton representation. If connectivity and topology are preserved, and if geometrical constraints such as smoothness and centeredness are satisfied, it is possible to estimate length, orientation, curvature, and torsion. It is also required that no part of the original object be left unrepresented. An efficient method for the identification of such shape components is developed. First, a suitable representation is obtained using a voxel coding approach to yield connected and labeled unit-thick paths. The desired features are estimated from a smoothed version of the skeleton produced by a moving average filter. The computational cost is linear, of the order of N(object), the total number of object voxels contained in the binary volumetric data. The method is also shown to be robust to boundary noise. Examples are discussed.     

Elastic properties of the red blood cell membrane that determine echinocyte deformability

The natural biconcave shape of red blood cells (RBC) may be altered by injury or environmental conditions into a spiculated form (echinocyte). An analysis is presented of the effect of such a transformation on the resistance of RBC to entry into capillary sized cylindrical tubes. The analysis accounts for the elasticity of the membrane skeleton in dilation and shear, and the local and nonlocal resistance of the bilayer to bending, the latter corresponding to different area strains in the two leaflets of the bilayer. The shape transformation is assumed to be driven by the equilibrium area difference (A₀, the difference between the equilibrium areas of the bilayer leaflets), which also affects the energy of deformation. The cell shape is approximated by a parametric model. Shape parameters, skeleton shear deformation, and the skeleton density of deformed membrane relative to the skeleton density of undeformed membrane are obtained by minimization of the corresponding thermodynamic potential. Experimentally, A₀ is modified and the corresponding discocyte–echinocyte shape transition obtained by high-pressure aspiration into a narrow pipette, and the deformability of the resulting echinocyte is examined by whole cell aspiration into a larger pipette. We conclude that the deformability of the echinocyte can be accounted for by the mechanical behavior of the normal RBC membrane, where the equilibrium area difference A₀ is modified.     

Optimum DNA Curvature Using a Hybrid Approach Involving an Artificial Neural Network and Genetic Algorithm

Abstract

In the present paper, a hybrid technique involving artificial neural network (ANN) and genetic algorithm (GA) has been proposed for performing modeling and optimization of complex biological systems. In this approach, first an ANN approximates (models) the nonlinear relationship(s) existing between its input and output example data sets. Next, the GA, which is a stochastic optimization technique, searches the input space of the ANN with a view to optimize the ANN output. The efficacy of this formalism has been tested by conducting a case study involving optimization of DNA curvature characterized in terms of the R_L value. Using the ANN-GA methodology, a number of sequences possessing high R_L values have been obtained and analyzed to verify the existence of features known to be responsible for the occurrence of curvature. A couple of sequences have also been tested experimentally. The experimental results validate qualitatively and also near-quantitatively, the solutions obtained using the hybrid formalism. The ANN-GA technique is a useful tool to obtain, ahead of experimentation, sequences that yield high R_L values. The methodology is a general one and can be suitably employed for optimizing any other biological feature.     

Combined Metaheuristic Algorithm and Radiomics Strategy for the Analysis of Neuroanatomical Structures in Schizophrenia and Schizoaffective Disorders

ObjectivesSchizophrenia (SZ) is the most chronic disabling psychotic brain disorder. It is characterized by delusions and auditory hallucinations, as well as impairments in memory. Schizoaffective (SA) signs are co-morbid with SZ and are characterized by symptoms of SZ and mood disorder. Various researches suggest that SZ and SA share a number of equally severe cognitive deficits, but the pathophysiology has not yet been addressed in a comprehensive way. In this work, the heterogeneity in whole brain, ventricle and cerebellum region from psychotic MR brain images is examined using Machine learning and radiomic features.Materials and methodsT1 weighted MR brain images are obtained from Schizconnect database for the analysis. The shape prior level set method is used to segment the ventricle and cerebellum structures. The radiomic features which include shape and texture are extracted from these regions to discriminate the SZ and SA subjects. The performance of these features is evaluated with Binary Particle Swarm Optimization (BPSO) based Fuzzy Support Vector Machine (FSVM) classifier.ResultsThe shape constrained Level Set method is able to better segment ventricles and cerebellum regions from the images. The significant features that are extracted from whole brain, ventricle and cerebellum are identified by the BPSO based FSVM. The combination of radiomic features extracted from cerebellum region achieved high classification accuracy (90.09%) using metaheuristic algorithm. The extracted features from cerebellum are correlated with PANSS score. The causal analysis shows that there is an association been the tissue texture variation in identifying the disease severity. The symmetry analysis shows that left brain mean area is larger than the right side area. In particular SA has low cerebellum area compared to SZ. The radiomic features such as Hermite, Laws and tensor extracted from the left cerebellum show a significant texture variation in all the considered subjects (p<0.0001).ConclusionsThe results are clinically relevant in discriminating the pattern change in the structure, hence this biomarker and frame work could be used for the severity study of psychotic disorders.     

Creep and stress relaxation of human red cell membrane

In contrast to most mechanical properties of the red cell, experimental information on stress relaxation (SR) of the membrane skeleton is scarce. On the other hand, many postulates or assumptions as to the value of the characteristic time of SR \((\tau _{\mathrm{SR}})\) can be found in the literature. Here, an experiment is presented that allows measurement of \(\tau _{\mathrm{SR}}\) up to values of about 10 h. The membrane skeleton was deformed passively by changing the spontaneous curvature of the bilayer thus transforming the natively biconcave red cells into echinocytes. This shape and the concomitant deformation of the skeleton were kept up to 4 h by incubation at 37 ℃. During this period, no plastic deformation (creep) was observed. After the incubation, the spontaneous curvature was returned to normal. The resulting shape was smooth showing no remnants of the echinocytic shape. Both observations indicate \(\tau _{\mathrm{SR}}\gtrapprox \) 10 h. This result is in gross disagreement to postulates or assumptions existing in the literature.     

Design and calibration of a semi-synthetic DNA phasing assay

Electrophoretic assays of intrinsic DNA shape and shape changes induced by ligand binding are extremely useful because of their convenience and simplicity. The development of calibrations and empirical quantitative relationships permits highly accurate measurement of DNA shape using electrophoresis. Many conventional analyses employ the unidirectional ligation of short DNA duplexes. However, many oligonucleotides (typically more than 20) must often be synthesized for a single experiment. Additionally, the length of the DNA duplex can become limiting, preventing the analysis of certain DNA sequences. We now describe a semi-synthetic electrophoretic phasing method that offers several advantages, including a reduced number of required synthetic oligonucleotides, the ability to analyze longer DNA duplexes and a simplified approach for data analysis. We characterize semi-synthetic DNA probes in electrophoretic phasing assays by ligation of synthetic duplexes containing A₅ tracts between two longer restriction fragments. Upon electrophoresis, the gel mobility is strongly correlated with the predicted DNA curvature provided by the reference A₅ tracts. Having obtained this calibration, we show that the semi-synthetic phasing assay can be readily and economically applied to analyze DNA curvature induced by DNA charge modifications and DNA bending due to peptide binding.     

Theoretical study of structural patterns in CH<Subscript>2</Subscript>OP<Subscript>2</Subscript> isomers

DFT calculations have been performed on the derivatives of formula CH₂OP₂ to determine their total energy, the relative energy between the isomers and their geometry. Among compounds with a P-C-P linkage, the most stable one is the 2-hydroxy-1,2-diphosphirene II.1, a three-membered heterocycle with a P=C unsaturation. The phosphavinylidene(oxo)phosphorane HP=C=P(O)H IV.5 (which has the same skeleton as the experimentally obtained Mes*P=C=P(O)Mes*) lies 36.30 kcal mol^-1 above it. The least stable compounds are carbenes; the singlet carbenes are more stable than the triplet ones.     

Visual shape representation with geometrically characterized contour partitions

This paper proposes a biologically plausible matching method to recognize general shapes based on contour curvature information. The human visual system recognizes general shapes flexibly in real-world scenes through the ventral pathway. The pathway is typically modeled using artificial neural networks. These network models, however, do not construct a shape representation that satisfies the following required constraints: (1) The original shape should be represented by a group of partitioned contours in order to retrieve the whole shape (global information) from the partial contours (local information). (2) Coarse and fine structures of the original shapes should be individually represented in order for the visual system to respond to shapes as quickly as possible based on the least number of their features, and to discriminate between shapes based on detailed information. (3) The shape recognition realized with an artificial visual system should be invariant to geometric transformation such as expansion, rotation, or shear. In this paper, we propose a visual shape representation with geometrically characterized contour partitions described on multiple spatial scales.     

Panamonon A and B,a pair of novel tetrahydrobenzofuran derivatives from Litsea panamonja (Nees) Hook. f.

A pair of novel tetrahydrobenzofuran derivatives with a unique C₁₈ carbon skeleton, panamonon A (1) and B (2), was isolated from the leaves and twigs of Litsea panamonja (Nees) Hook. f. These new compounds contain an unprecedented C₁₈ carbon skeleton consisting of a characteristic tetrahydrobenzofuran-2,5(3H,6H)-dione core with a biosynthetically extended geranyl side chain, designated as “panamonane”.

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Highlights? A pair of novel tetrahydrobenzofuran derivatives with a unique C₁₈ carbon skeleton was isolated. ? The new compounds possess an unprecedented C₁₈ carbon skeleton and are designated as “panamonane”. ? They are featured with a tetrahydrobenzofuran-2,5(3H,6H)-dione moiety and a geranyl side chain. ? The plausible biosynthetic pathways of them were discussed.     

基于主成分分析的双对比光学投影断层成像

目的 本文提出了一种基于主成分分析（PCA）的双对比光学投影断层成像（DC-OPT）方法,以获得活体中血流网络和骨骼的三维可视化。方法 使用主成分分析方法来提取吸收图像和血流图像,原始图像序列的第一主成分用于获取吸收图像;通过计算每个像素的调制深度来获得流动图像。不同投影位置的流动和吸收对比图像被用于三维血流网络和骨骼的同步重建。结果 采用PCA和OPT相结合的方法,通过将动态血流信号和静态背景信号分离,实现了对微生物样本的血流网络和骨骼的三维成像。结论 本文研究的新颖之处在于通过同一光学系统获得了快速、同步、双对比的血流网络和骨骼三维图像。实验结果可用于活体生物的生理发育研究。     

Simaba guianensis subsp. huberi, a new Venezuelan taxon of Simaroubaceae

Simaba guianensis subsp.huberi (Simaroubaceae), restricted to the savannas of the Venezuelan State of Amazonas, is described and illustrated. The new subspecies is distinguished from the other two subspecies ofS. guianensis by its smaller size, characteristics of the leaflets (size, texture, apex shape, and margin curvature), and fruit color.     

Intrinsic curvature properties of photosynthetic proteins in chromatophores

In purple bacteria, photosynthesis is carried out on large indentations of the bacterial plasma membrane termed chromatophores. Acting as primitive organelles, chromatophores are densely packed with the membrane proteins necessary for photosynthesis, including light harvesting complexes LH1 and LH2, reaction center (RC), and cytochrome bc₁. The shape of chromatophores is primarily dependent on species, and is typically spherical or flat. How these shapes arise from the protein-protein and protein-membrane interactions is still unknown. Now, using molecular dynamics simulations, we have observed the dynamic curvature of membranes caused by proteins in the chromatophore. A membrane-embedded array of LH2s was found to relax to a curved state, both for LH2 from Rps. acidophila and a homology-modeled LH2 from Rb. sphaeroides. A modeled LH1-RC-PufX dimer was found to develop a bend at the dimerizing interface resulting in a curved shape as well. In contrast, the bc₁ complex, which has not been imaged yet in native chromatophores, did not induce a preferred membrane curvature in simulation. Based on these results, a model for how the different photosynthetic proteins influence chromatophore shape is presented.     

On the use of size functions for shape analysis

According to a recent mathematical theory a shape can be represented by size functions, which convey information on both the topological and metric properties of the viewed shape. In this paper the relevance of the theory of size functions to visual perception is investigated. An algorithm for the computation of the size functions is presented, and many theoretical properties of the theory are demonstrated on real images. It is shown that the representation of shape in terms of size functions (1) can be tailored to suit the invariance of the problem at hand and (2) is stable against small qualitative and quantitative changes of the viewed shape. A distance between size functions is used as a measure of similarity between the representations of two different shapes. The results obtained indicate that size functions are likely to be very useful for object recognition. In particular, they seem to be well suited for the recognition of natural and articulated objects.     

The Structure-taste Relationships of Aspartyl Dipeptide Esters

The molecular features common to sweet-tasting dipeptide esters are described. The molecular features of sweet amino acids were represented by the Fischer projection formulas and sweet peptides were related to the sweet amino acids through the Fischer projection formulas of the peptides. It was concluded that a peptide is sweet when it takes the formula 5a, whereas when it takes the formula 5b it is not sweet. It was also concluded that a third binding site (R₁ in 5a) besides the postulated AH–B system in a sweet molecule is necessary for an intense sweetness potency. The location of the site in the molecule relative to the AH–B system is important, as well as the shape and size of this site, because the third binding site is considered to participate in hydrophobic interaction with a similar binding site on the taste receptor. Increased sweetness is observed when these requirements are satisfied.     

Approximation and characterization of molecular surfaces

The representation and characterization of molecular surfaces are important in many areas of molecular modeling. Parametric representations of protein molecular surfaces are a compact way to describe a surface, and are useful for the evaluation of surface properties such as the normal vector, principal curvatures, and principal curvature directions. Simplified representations of molecular surfaces are useful for efficient rendering and for the display of large-scale surface features. Several techniques for representing surfaces by expansions of spherical harmonic functions have been reported, but these techniques require that the radius function is single valued, that is, each ray from an origin inside the surface intersects the surface at one and only one point. A new technique is described that removes this limitation and can be used to compute surface shape properties. © 1993 John Wiley & Sons, Inc.     

A Human Skeleton From The Pryor Creek Burial, 24YL404, Yellowstone County,Montana

Abstract

An adult human skeleton, found associated with artifacts of both Indian and White manufacture near Billings, Yellowstone County, Montana, is thought on the basis of cranial measurements and morphological features to be a prehistoric Crow Indian.     

Regional dependency of the vascular smooth muscle cell contribution to the mechanical properties of the pig ascending aortic tissue

BackgroundDilation and dissection of aneurysmal ascending aortic tissues occur preferentially at the outer curvature of the vessel. In this study we hypothesize that the density and contractile properties of the vascular smooth muscle cells (VSMCs) of the pig ascending aorta (AA) are heterogeneous and could explain the non-uniform remodeling and weakening of the AA during aneurysm formation.MethodsEleven pig AA rings were collected. Two square samples of 15×15 mm were taken from each ring from the inner and outer curvature of the AA. Each sample was subjected to equi-biaxial tensile testing in Krebs–Ringer solution maintained at 37 °C. Each test consisted of 8 cycles of preconditioning followed by one experimental run from 0% to 30% strain. Phenylephrine (10^?5 M) was added to contract VSMCs. After biaxial testing, samples were paraffin-embedded and stained with hematoxylin–phloxine–saffron (HPS) to quantify VSMC density.ResultsSignificant differences in cell density, maximum contractile stress resultant magnitude (MCSRM) and orientation (θ_MCSR) were found between the inner and outer curvature. The inner curvature had the greatest contraction. The outer curvature had the highest VSMC density with the maximum contraction stress resultant oriented towards the axial direction.ConclusionVSMC activation with phenylephrine had a significant effect on the stiffness of the pig AA. This effect was independent of location and direction. However, cell orientation, density and contractile properties were dependent on location and suggest variations in the remodeling capabilities, tissue strain and cell phenotype between locations.     

Membrane Curvature Induced by Aggregates of LH2s and Monomeric LH1s

The photosynthetic apparatus of purple bacteria is contained within organelles called chromatophores, which form as extensions of the cytoplasmic membrane. The shape of these chromatophores can be spherical (as in Rhodobacter sphaeroides), lamellar (as in Rhodopseudomonas acidophila and Phaeospirillum molischianum), or tubular (as in certain Rb. sphaeroides mutants). Chromatophore shape is thought to be influenced by the integral membrane proteins Light Harvesting Complexes I and II (LH1 and LH2), which pack tightly together in the chromatophore. It has been suggested that the shape of LH2, together with its close packing in the membrane, induces membrane curvature. The mechanism of LH2-induced curvature is explored via molecular dynamics simulations of multiple LH2 complexes in a membrane patch. LH2s from three species—Rb. sphaeroides, Rps. acidophila, and Phsp. molischianum—were simulated in different packing arrangements. In each case, the LH2s pack together and tilt with respect to neighboring LH2s in a way that produces an overall curvature. This curvature appears to be driven by a combination of LH2's shape and electrostatic forces that are modulated by the presence of well-conserved cytoplasmic charged residues, the removal of which inhibits LH2 curvature. The interaction of LH2s and an LH1 monomer is also explored, and it suggests that curvature is diminished by the presence of LH1 monomers. The implications of our results for chromatophore shape are discussed.     

Turning maneuvers in sharks: Predicting body curvature from axial morphology

Given the diversity of vertebral morphologies among fishes, it is tempting to propose causal links between axial morphology and body curvature. We propose that shape and size of the vertebrae, intervertebral joints, and the body will more accurately predict differences in body curvature during swimming rather than a single meristic such as total vertebral number alone. We examined the correlation between morphological features and maximum body curvature seen during routine turns in five species of shark: Triakis semifasciata, Heterodontus francisci, Chiloscyllium plagiosum, Chiloscyllium punctatum, and Hemiscyllium ocellatum. We quantified overall body curvature using three different metrics. From a separate group of size‐matched individuals, we measured 16 morphological features from precaudal vertebrae and the body. As predicted, a larger pool of morphological features yielded a more robust prediction of maximal body curvature than vertebral number alone. Stepwise linear regression showed that up to 11 features were significant predictors of the three measures of body curvature, yielding highly significant multiple regressions with r² values of 0.523, 0.537, and 0.584. The second moment of area of the centrum was always the best predictor, followed by either centrum length or transverse height. Ranking as the fifth most important variable in three different models, the body's total length, fineness ratio, and width were the most important non‐vertebral morphologies. Without considering the effects of muscle activity, these correlations suggest a dominant role for the vertebral column in providing the passive mechanical properties of the body that control, in part, body curvature during swimming. J. Morphol., 2009. © 2009 Wiley‐Liss, Inc.