Branching Shapes Research Articles

The 3D tree dataset: an artistic experiment using a voxel-based GAN

AbstractIn visual culture, Generative Adversarial Networks (GANs) have been used to generate two-dimensional images, video, and three-dimensional forms. Whilst there are a relatively large number of conditional datasets of two-dimensional images, there are fewer datasets of three-dimensional objects available for training, evaluation, and practical use. In this paper, we introduce a synthetic dataset of 3D trees that provide novel geometric challenges for machine learning and describe our use of this dataset in training and qualitative evaluation via a public exhibition and survey. The 3D Tree Dataset was made using random variations of 76 bespoke tree templates based on art historical references to favor interesting, beautiful, and varied trunk and branch shapes. In generating and experimenting with this dataset, we wanted to know how a geometrically complex series of organic forms would challenge voxel-GANs compared to existing datasets comprising industrial objects such as chairs and cars. As an interdisciplinary project between visual arts and computer science, we used 3D printing and animation to visualize and communicate our outputs to non-specialist audiences. In this paper, we describe and share the 3D Tree Dataset, outline the process of generating the dataset, describe the GAN architecture and application used to test the dataset and discuss the results relative to our artistic and cultural goals.

Reconfigurable DNA Nanocage for Protein Encapsulation and Regulation.

Creating nanomachines capable of precisely capturing, organizing, and regulating the activity of target biomolecules holds profound significance for advancing nanotechnology and therapeutics. Here, we develop a multistage reconfigurable DNA nanocage that can enclose and modulate proteins through multivalent interactions, activated by specific molecular signals. By strategically designing and manipulating the strut architecture of the DNA nanocages, we can achieve precise control over their reconfiguration among pyramid, square, and linear branch shapes. Additionally, we demonstrated its ability to capture thrombin and effectively inhibit its coagulation activity by incorporating two thrombin-targeting aptamers into the designed arms of the DNA nanocage. The activity of thrombin can be recovered by rearranging the conformation of the DNA nanocage and exposing the protein, thereby activating the coagulation process. This approach enriches the design toolbox for dynamic nanomachines and inspires a new strategy for protein encapsulation and regulation with potential future therapeutic applications.

Engineering Regulation of the Weird Branches in a Branching Estuary and its Mechanics: Using the North Branch of the Yangtze Estuary as an Example

Weird horizontal shapes of branches, in large branching estuaries, often cause significant flood risks and environment-related problems. People usually resort to engineering methods to improve the horizontal shape of the weird branches and solve related issues. The responses of the riverbed evolution of a branching estuary to anthropogenic activity are complicated because of complex estuarine hydrodynamics and sediment transports, especially when the project locates specially (e.g., at estuary outlets). The North Branch of the Yangtze Estuary has a narrow upper reach which is almost orthogonal to the South Branch and has a trumpet-shaped lower reach with a wide outlet. The weird horizontal shape of the North Branch brings significant flood risks to cities along this branch, the shrinkage of its entrance, and other problems. In this study, a regulation of the North Branch, which is launched at Guyuan Sand (GYS) just outside the exit of the North Branch, is taken as an example. The GYS regulation aims to improve the weird horizontal shape of the North Branch by building new layouts of outlets, by which people decrease the flood risk of the surrounding cities. The GYS regulation is studied using a 2D numerical model. The riverbed evolution of the Yangtze Estuary in a typical hydrological year is simulated, while the water/sediment fluxes at cross-sections of branches in the estuary during a spring/neap tide are quantitatively calculated. It is found that the regulation changes the rotational flows near the shore, and further reshapes the estuarine circulations of mass inside the outlets, especially exchanges of water/sediment between different branches. The regulation directly changes the riverbed evolution at the outlet of the North Branch, and meanwhile has significant indirect influences on the riverbed evolution of the entrance of the North Branch. The varying riverbed evolution at the entrance of the North Branch and the varying water/sediment fluxes, under different designs of regulations, are related and analyzed. An essential improvement for the weird horizontal shape of the North Branch by an engineering method is shown to be possible, while the regulation mechanism of the engineering method and the response of estuarine riverbed evolution to the regulation are clarified. This study provides a new insight for improving estuarine branches with weird horizontal shapes, by reshaping the tidal processes and the accompanying sediment transports in a branching estuary.

Dragging 3D printing technique controls pore sizes of tissue engineered blood vessels to induce spontaneous cellular assembly

To date, several off-the-shelf products such as artificial blood vessel grafts have been reported and clinically tested for small diameter vessel (SDV) replacement. However, conventional artificial blood vessel grafts lack endothelium and, thus, are not ideal for SDV transplantation as they can cause thrombosis. In addition, a successful artificial blood vessel graft for SDV must have sufficient mechanical properties to withstand various external stresses. Here, we developed a spontaneous cellular assembly SDV (S-SDV) that develops without additional intervention. By improving the dragging 3D printing technique, SDV constructs with free-form, multilayers and controllable pore size can be fabricated at once. Then, The S-SDV filled in the natural polymer bioink containing human umbilical vein endothelial cells (HUVECs) and human aorta smooth muscle cells (HAoSMCs). The endothelium can be induced by migration and self-assembly of endothelial cells through pores of the SDV construct. The antiplatelet adhesion of the formed endothelium on the luminal surface was also confirmed. In addition, this S-SDV had sufficient mechanical properties (burst pressure, suture retention, leakage test) for transplantation. We believe that the S-SDV could address the challenges of conventional SDVs: notably, endothelial formation and mechanical properties. In particular, the S-SDV can be designed simply as a free-form structure with a desired pore size. Since endothelial formation through the pore is easy even in free-form constructs, it is expected to be useful for endothelial formation in vascular structures with branch or curve shapes, and in other tubular tissues such as the esophagus.

Scavenger receptor endocytosis controls apical membrane morphogenesis in the Drosophila airways.

The acquisition of distinct branch sizes and shapes is a central aspect in tubular organ morphogenesis and function. In the Drosophila airway tree, the interplay of apical extracellular matrix (ECM) components with the underlying membrane and cytoskeleton controls tube elongation, but the link between ECM composition with apical membrane morphogenesis and tube size regulation is elusive. Here, we characterized Emp (epithelial membrane protein), a Drosophila CD36 homolog belonging to the scavenger receptor class B protein family. emp mutant embryos fail to internalize the luminal chitin deacetylases Serp and Verm at the final stages of airway maturation and die at hatching with liquid filled airways. Emp localizes in apical epithelial membranes and shows cargo selectivity for LDLr-domain containing proteins. emp mutants also display over elongated tracheal tubes with increased levels of the apical proteins Crb, DE-cad, and phosphorylated Src (p-Src). We show that Emp associates with and organizes the βH-Spectrin cytoskeleton and is itself confined by apical F-actin bundles. Overexpression or loss of its cargo protein Serp lead to abnormal apical accumulations of Emp and perturbations in p-Src levels. We propose that during morphogenesis, Emp senses and responds to luminal cargo levels by initiating apical membrane endocytosis along the longitudinal tube axis and thereby restricts airway elongation.

Large Duct Pancreatic Ductal Adenocarcinoma: A Morphological Variant of Pancreatic Ductal Adenocarcinoma With Distinct CT and MRI Characteristics.

To investigate the imaging characteristics of large duct pancreatic ductal adenocarcinoma (LD-PDAC) on computed tomography (CT) and magnetic resonance imaging (MRI). Thirty-five patients with LD-PDAC (63.2 ± 9.7 years) were retrospectively evaluated. Tumor morphology on CT and MRI (predominantly solid mass vs. solid mass with prominent cysts vs. predominantly cystic mass) was evaluated. Additionally, the visibility, quantity, shape (oval vs. branching vs. irregular), and MRI signal intensity of neoplastic cysts within the LD-PDAC were investigated. The radiological diagnoses rendered for LD-PDAC in radiology reports were reviewed. LD-PDAC was more commonly observed as a solid mass with prominent cysts (45.7% [16/35] on CT and 37.1% [13/35] on MRI) or a predominantly cystic mass (20.0% [7/35] on CT and 40.0% [14/35] on MRI) and less commonly as a predominantly solid mass on CT (34.3% [12/35]) and MRI (22.9% [8/35]). The tumor morphology on imaging was significantly associated with the size of the cancer gland on histopathological examination (P = 0.020 [CT] and 0.013 [MRI]). Neoplastic cysts were visible in 88.6% (31/35) and 91.4% (32/35) of the LD-PDAC cases on CT and MRI, respectively. The cysts appeared as branching (51.6% [16/35] on CT and 59.4% [19/35] on MRI) or oval shapes (45.2% [14/35] on CT and 31.2% [10/35] on MRI) with fluid-like MRI signal intensity. In the radiology reports, 10 LD-PDAC cases (28.6%) were misinterpreted as diseases other than typical PDAC, particularly intraductal papillary mucinous neoplasms. LD-PDAC frequently appears as a solid mass with prominent cysts or as a predominantly cystic mass on CT and MRI. Radiologists should be familiar with the imaging features of LD-PDAC to avoid misdiagnosis.

Line-based deep learning method for tree branch detection from digital images

Preventive maintenance of power lines, including cutting and pruning of tree branches, is essential to avoid interruptions in the energy supply. Automatic methods can support this risky task and also reduce time-consuming. Here, we propose a method in which the orientation and the grasping positions of tree branches are estimated. The proposed method firstly predicts the straight line (representing the tree branch extension) based on a convolutional neural network (CNN). Secondly, a Hough transform is applied to estimate the direction and position of the line. Finally, we estimate the grip point as the pixel point with the highest probability of belonging to the line. We generated a dataset based on internet searches and annotated 1868 images considering challenging scenarios with different tree branch shapes, capture devices, and environmental conditions. Ten-fold cross-validation was adopted, considering 90% for training and 10% for testing. We also assessed the method under corruptions (gaussian and shot) with different severity levels. The experimental analysis showed the effectiveness of the proposed method reporting F1-score of 96.78%. Our method outperformed state-of-the-art Deep Hough Transform (DHT) and Fully Convolutional Line Parsing (F-Clip).

Phonon signatures in spectra of exciton polaritons in transition metal dichalcogenides

Embedding a monolayer of a transition metal dichalcogenide in a high-$Q$ optical cavity results in the formation of distinct exciton polariton modes. The polaritons are affected by the strong exciton-phonon interaction in the monolayer. We use a time convolutionless master equation to calculate the phonon influence on the spectra of the polaritons. We discuss the nontrivial dependence of the line shapes of both branches on temperature and detuning. The peculiar polariton dispersion relation results in a linewidth of the lower polariton being largely independent of the coupling to acoustic phonons. For the upper polariton, acoustic phonons lead to a low-energy shoulder of the resonance in the linear response. Furthermore, we analyze the influence of inhomogeneous broadening being the dominant contribution to the lower polariton linewidth at low temperatures. Our results point towards interesting phonon features in polariton spectra in transition metal dichalcogenides.

Variational problems for tree roots and branches

This paper studies two classes of variational problems introduced in [7], related to the optimal shapes of tree roots and branches. Given a measure $\mu$ describing the distribution of leaves, a sunlight functional $\S(\mu)$ computes the total amount of light captured by the leaves. For a measure $\mu$ describing the distribution of root hair cells, a harvest functional $\H(\mu)$ computes the total amount of water and nutrients gathered by the roots. In both cases, we seek a measure $\mu$ that maximizes these functionals subject to a rami?ed transportation cost, for transporting nutrients from the roots to the trunk or from the trunk to the leaves. Compared with [7], here we do not impose any a priori bound on the total mass of the optimal measure $\mu$, and more careful a priori estimates are thus required. In the unconstrained optimization problem for branches, we prove that an optimal measure exists, with bounded support and bounded total mass. In the unconstrained problem for tree roots, we prove that an optimal measure exists, with bounded support but possibly unbounded total mass. The last section of the paper analyzes how the size of the optimal tree depends on the parameters defining the various functionals.

Influence of Surface Conductivity on Dispersion Curves, Mode Shapes, Stress, and Potential for Lamb Waves Propagating in Piezoelectric Plate.

Lamb waves propagating in piezoelectric plate covered by thin-film electrodes with arbitrary conductivity are investigated. The structure consists of three parts, piezoelectric plate, top and bottom thin films with arbitrary conductivities, and top and bottom free space. The governing equations in each part are first solved, and then, continuous conditions are used to form the propagating matrix. Finally, the dispersion equations are obtained by boundary conditions. Calculating the dispersion equations with different conductivities, the dispersion curves in high conductivity and zero conductivity are compared. The wave mode shapes of different branches are investigated, including the distributions of mechanical displacements and stresses in the piezoelectric plate and distributions of electrical displacement and potential in both plate and free space. The relationships between frequency difference and wave mode shapes in zero and high conductivity are investigated. Furthermore, the dispersion curves of general conductivity are calculated. The attenuation of waves is compared in different branches and different conductivities. The wave mode shapes are also calculated and compared with the cases in zero and high conductivities.

Shrubbery-shell inspired 3D model stylization

We propose a new method to automatically generate a shrub-branch-style shell (also called a hollow-branch sculpture) decorative pattern for an arbitrary 3D model along its surface curvature. Our method generates the branching pattern by using a particle-based model without requiring any basic tree-shape elements to be extracted from existing 2D images or 3D models. We modify the particle method by constraining the direction vectors for particle motion onto a given mesh surface so the branch structure grows along the surface to form a shell of the input object. The global and local branch shapes are changed by adjusting the growth space and growth factors, providing better controllability and diversity of the resulting patterns. In addition, the growth space for the branching pattern can be interactively assigned by a user’s brush to an arbitrary area of the mesh surface where the trajectory of the brush stroke is reflected in the branch-growth directions. The following control options are also considered: merging multiple branch clusters having different root locations, biasing the generation of strong main branches, and creating a windowed growth space for thin shapes. The versatility and effectiveness of our approach are demonstrated by generating various arborsculpture-inspired shapes.

Non-symmetric branching of fluid flows in 3D vessels

Nonsymmetric branching flow through a three-dimensional (3D) vessel is considered at medium-to-high flow rates. The branching is from one mother vessel to two or more daughter vessels downstream, with laminar steady or unsteady conditions assumed. The inherent 3D nonsymmetry is due to the branching shapes themselves, or the differences in the end pressures in the daughter vessels, or the incident velocity profiles in the mother. Computations based on lattice-Boltzmann methodology are described first. A subsequent analysis focuses on small 3D disturbances and increased Reynolds numbers. This reduces the 3D problem to a two-dimensional one at the outer wall in all pressure-driven cases. As well as having broader implications for feeding into a network of vessels, the findings enable predictions of how much swirling motion in the cross-plane is generated in a daughter vessel downstream of a 3D branch junction, and the significant alterations provoked locally in the shear stresses and pressures at the walls. Nonuniform incident wall-shear and unsteady effects are examined. A universal asymptotic form is found for the flux change into each daughter vessel in a 3D branching of arbitrary cross-section with a thin divider.

NONSYMMETRIC BRANCHING OF FLUID FLOWS IN 3D VESSELS

Nonsymmetric branching flow through a three-dimensional (3D) vessel is considered at medium-to-high flow rates. The branching is from one mother vessel to two or more daughter vessels downstream, with laminar steady or unsteady conditions assumed. The inherent 3D nonsymmetry is due to the branching shapes themselves, or the differences in the end pressures in the daughter vessels, or the incident velocity profiles in the mother. Computations based on lattice-Boltzmann methodology are described first. A subsequent analysis focuses on small 3D disturbances and increased Reynolds numbers. This reduces the 3D problem to a two-dimensional one at the outer wall in all pressure-driven cases. As well as having broader implications for feeding into a network of vessels, the findings enable predictions of how much swirling motion in the cross-plane is generated in a daughter vessel downstream of a 3D branch junction, and the significant alterations provoked locally in the shear stresses and pressures at the walls. Nonuniform incident wall-shear and unsteady effects are examined. A universal asymptotic form is found for the flux change into each daughter vessel in a 3D branching of arbitrary cross-section with a thin divider.

FROM TLS POINT CLOUDS TO 3D MODELS OF TREES: A COMPARISON OF EXISTING ALGORITHMS FOR 3D TREE RECONSTRUCTION

Abstract. 3D models of tree geometry are important for numerous studies, such as for urban planning or agricultural studies. In climatology, tree models can be necessary for simulating the cooling effect of trees by estimating their evapotranspiration. The literature shows that the more accurate the 3D structure of a tree is, the more accurate microclimate models are. This is the reason why, since 2013, we have been developing an algorithm for the reconstruction of trees from terrestrial laser scanner (TLS) data, which we call TreeArchitecture. Meanwhile, new promising algorithms dedicated to tree reconstruction have emerged in the literature. In this paper, we assess the capacity of our algorithm and of two others -PlantScan3D and SimpleTree- to reconstruct the 3D structure of trees. The aim of this reconstruction is to be able to characterize the geometric complexity of trees, with different heights, sizes and shapes of branches. Based on a specific surveying workflow with a TLS, we have acquired dense point clouds of six different urban trees, with specific architectures, before reconstructing them with each algorithm. Finally, qualitative and quantitative assessments of the models are performed using reference tree reconstructions and field measurements. Based on this assessment, the advantages and the limits of every reconstruction algorithm are highlighted. Anyway, very satisfying results can be reached for 3D reconstructions of tree topology as well as of tree volume.

Chaetetes morphology, environment, and taxonomy

Chaetetes, a hypercalcified sponge, formed expansive biostromes in Atokan strata of the Hueco Mountains, West Texas, where they grew in very shallow water on a broad shallow carbonate shelf. The Chaetetes there have tabular, columnar, compound-columnar, and branching shapes, and grew to heights of greater than 1 m. In most cases, they grew from a point source with an axial growth style. The laminar growth style occurs rarely, overlying growth interruption surfaces and where initial growth was on a hard surface such as solitary rugose corals. From the analysis of these fossils in the context of their inferred paleoenvironment, and integrating observations and available data from other localities, we conclude that the morphology of Chaetetes—their shape and growth style—was determined primarily by sedimentation parameters concurrent with their growth. These parameters were substrate character—texture and firmness—and both overall rate of sediment accumulation and variations in the rate relative to the rate of Chaetetes growth. Six species of Chaetetes were described previously in North America. Four of these are too incompletely known to be of taxonomic value. The other two, Chaetetes milleporaceus and Chaetetes favosus, form a continuum of morphotypes that is interpreted here to represent a single species, C. milleporaceus by priority.

대구경 고압 T형 분기관의 지관 형상에 따른 내부 유동 영향성 해석

This study describes the effect of T branch shape on internal flow characteristics inside itself. Continuity and three-dimensional Reynolds-averaged Navier-Stokes equation have been used as governing equations for the numerical analysis. The T branch was modeled assuming that it is used for Alaska pipeline project which was planned to provide reliable transportation of natural gas from ANS to Alaska-Yukon border. Therefore the characteristics of T branch and operating condition of pipeline were from report of Alaska pipeline project. The nine T branch shapes were analyzed and the mass flow rate ratio between mainline and branch was assumed to be 0.95 : 0.05, 0.9 : 0.1, 0.85 : 0.15. The results shows that there are typical flow patterns in T branch and the shape of T branch makes some differences to the internal flow of branch rather than mainline.

The intersection of the extrinsic hedgehog and WNT/wingless signals with the intrinsic Hox code underpins branching pattern and tube shape diversity in the drosophila airways.

The tubular networks of the Drosophila respiratory system and our vasculature show distinct branching patterns and tube shapes in different body regions. These local variations are crucial for organ function and organismal fitness. Organotypic patterns and tube geometries in branched networks are typically controlled by variations of extrinsic signaling but the impact of intrinsic factors on branch patterns and shapes is not well explored. Here, we show that the intersection of extrinsic hedgehog(hh) and WNT/wingless (wg) signaling with the tube-intrinsic Hox code of distinct segments specifies the tube pattern and shape of the Drosophila airways. In the cephalic part of the airways, hh signaling induces expression of the transcription factor (TF) knirps (kni) in the anterior dorsal trunk (DTa1). kni represses the expression of another TF spalt major (salm), making DTa1 a narrow and long tube. In DTa branches of more posterior metameres, Bithorax Complex (BX-C) Hox genes autonomously divert hh signaling from inducing kni, thereby allowing DTa branches to develop as salm-dependent thick and short tubes. Moreover, the differential expression of BX-C genes is partly responsible for the anterior-to-posterior gradual increase of the DT tube diameter through regulating the expression level of Salm, a transcriptional target of WNT/wg signaling. Thus, our results highlight how tube intrinsic differential competence can diversify tube morphology without changing availabilities of extrinsic factors.

TAU LEPTON HADRONIC DECAYS AT BABAR AND BELLE

The BaBar and Belle experiments together recorded a total sample of some 3 ×109 tau lepton decays between the years 2000 and 2010. This enabled many new and improved measurements of tau hadronic decays to be made, and resulted in lower limits for branching fractions to rare and forbidden hadronic modes, such as those mediated by second-class weak currents which are sensitive to the u–d quark mass difference. Better measurements of strange decays have contributed to more precise data on the CKM matrix element, |Vus|. However, only limited progress has been made in measurements that feed into knowledge of the value of the strong coupling constant, αs, and the strange quark mass. This is largely due to the dominance of systematic uncertainties on branching fractions and shapes of mass spectra (spectral functions) for some of the important hadronic tau decay modes.

Congressional Power over Executive Branch Policy Making: Limitations on Bureaucratic Regulations, 1989‐2009

Research on American political institutions correctly emphasizes the ascendency of presidential power over the last century. Nevertheless, Congress possesses tools to influence how the executive branch shapes public policy. I examine how the use of limitation riders in appropriations laws allows Congress to affect the substance of bureaucratic decisions when Congress otherwise would not have much traction with the bureaucracy: under divided government. In examining the history of limitation riders that forbade the issuance of bureaucratic regulations from 1989 to 2009, I find support for this perspective. The findings suggest that, although Congress may be at a disadvantage in shaping law and policy relative to the president in many cases, its constitutionally protected spending authority continues to promote its ability to influence the executive branch.

Shape effects of CdS photocatalysts on hydrogen production

Granular and lamellar structured cadmium sulfide (CdS) with the shapes of branches, cauliflower and nanorods, were synthesized via a hydrothermal process. During the synthesis, ethylenediamine (EN) was used as a template and deionized water (DIW) as a coordination agent. Experimental results show that the morphology of CdS nanoparticles was controlled by EN concentration, CdS precursor concentration and molar ratio of Cd(NO3)2·4H2O to thiourea (NH2CSNH2). It was found that the key shape-controlling step is the formation of CdS nuclei via the decomposition of the cadmium-ethylenediamine complex. Various shapes of CdS nanoparticles were obtained based on the concentrations of EN in water. CdS particles synthesized in pure water show granular and lamellar shapes with a mixture of hexagonal and cubic crystal structures. When EN concentration was increased to 30%, branched morphology of CdS particles was observed. Further increasing EN concentration to 70% CdS catalyst particles resulted in a cauliflower-like shape. Finally, CdS nanorod particles with a hexagonal structure were developed when synthesized in a pure EN solution. Although EN concentration plays an important role in the shapes of CdS particles, experimental observation showed that the diameter and aspect ratio of as prepared CdS nanorods were determined by concentrations of CdS precursors. In the course of photocatalytic hydrogen production, nearly 2577 μmol H2 was produced over 0.05 g CdS nanorods in 4.0 h. The rate of hydrogen evolution over the CdS nanorods based photocatalyst was approximately 42.6 times higher than that over granular and agglomerated lamellar CdS.