Branching Structure Research Articles

Unveiling the role of differential growth in 3D morphogenesis: An inference method to analyze area expansion rate distribution in biological systems

The three-dimensional (3D) morphologies of many organs in organisms, such as the curved shapes of leaves and flowers, the branching structure of lungs, and the exoskeletal shape of insects, are formed through surface growth. Although differential growth, a mode of surface growth, has been qualitatively identified as 3D morphogenesis, a quantitative understanding of the mechanical contribution of differential growth is lacking. To address this, we developed a quantitative inference method to analyze the distribution of the area expansion rate, which governs the growth of surfaces into 3D morphology. To validate the accuracy of our method, we tested it on a basic 3D morphology that allowed for the theoretical derivation of the area expansion rate distribution, and then assessed the difference between the predicted outcome and the theoretical solution. We also applied this method to complex 3D shapes and evaluated its accuracy through numerical experiments. The findings of the study revealed a linear decrease in error on a log–log scale with an increase in the number of meshes in both evaluations. This affirmed the reliability of the predictions for meshes that are sufficiently refined. Moreover, we employed our methodology to analyze the developmental process of the Japanese rhinoceros beetle Trypoxylus dichotomus, which is characterized by differential growth regulating 3D morphogenesis. The results indicated a notably high rate of area expansion on the left and right edges of the horn primordium, which is consistent with the experimental evidence of a higher rate of cell division in these regions. Hence, these findings confirm the efficacy of the proposed method in analyzing biological systems.

Morphometric Analysis of the Left Main Coronary Truncus, Left Anterior Descending Artery, Circumflex Artery, and Intermediate Artery: Measurements of Length, Angle, and Diameter

Aim: The aim of our study was to group the left main coronary truncus (LMCT) according to its branching structure and to determine its length, angle and diameter measurements together with LMCT’s main branches which are left anterior descending artery (LAD), circumflex artery (Cx) and intermediate artery (IA).
 Material and Methods: Between June 2019 and June 2021, coronary angiographies of 150 (female-39%, male-61%) patients were analysed by digital subtraction angiography. For each patient, the measurements of the length and diameter of the LMCT, LAD (proximal-middle-distal parts), Cx (proximal-middle-distal parts), and IA were calculated. Measurements were performed with 2-dimensional measurement technique.
 Results: The LMCT showed bifurcation pattern in 90.7% and trifurcation pattern in 9.3% of cases. The mean LMCA length and diameter were 15.9±5.7 mm and 6.0±0.9 mm, respectively. The LAD-CX angle defined as the bifurcation angle was 75.8±25.5°. The results that differed significantly between the sexes were the LMCT-LAD angle (159.2±17.8°) and the LAD-distal diameter (2.5±0.5 mm) (p

Semi-supervised ensemble fault diagnosis method based on adversarial decoupled auto-encoder with extremely limited labels

Intelligent fault diagnosis can enhance the reliability of mechanical equipment. However, only a few labels are available in a large amount of fault data due to high labeling costs in practical engineering. The fault recognition capability of existing semi-supervised diagnosis methods is severely insufficient with limited labels, especially with extremely limited labels that only a single labeled sample available per fault type. To address this issue, a novel semi-supervised ensemble fault diagnosis framework termed ADAE-LFDM is proposed based on adversarial decoupled auto-encoder (ADAE) and low-dimensional feature distance metric (LFDM). Firstly, the locally selective combination in parallel outlier ensembles (LSCP) method is introduced to efficiently separate normal and fault samples. Subsequently, an ADAE with branching structure and latent space feature regularization strategy is proposed to decouple and capture the fault feature. Finally, a LFDM strategy that contains feature dimensionality reduction, and centroid-based metric is performed to achieve high-accuracy fault diagnosis. Experimental results based on two rotating machinery datasets have demonstrated that the proposed method achieves a diagnostic accuracy of over 97 % when there is only a single labeled sample available per fault type, and an average diagnostic accuracy of 85 % under cross-operating condition, showing the superiority compared to other methods.

Analysis of the properties of the topological Index using (analysis tools)

Graph G has two sets of information: the vertices, V(G), and the edges, E(G). The definitions for the Connectivity, Geometric Arithmetic, Atomic Bond, and Sum Connectivity Indices of G:
 
 were deg(u), deg(v) are a degree of vertices. Dendrimers are synthetic, man-made molecules that are composed of monomers organized in a branching structure. in this article, we calculate Connectivity, Geometric Arithmetic, Atom Bond Connectivity, and Sum Connectivity Index for the PAMAM, POPAM, and HACN1J dendrimers.

Simultaneous observations of equatorial plasma bubbles with an all-sky airglow imager and a HF Doppler sounding system in Taiwan

High-Frequency Doppler (HFD) sounders at low-latitudes often detect characteristic oblique spreading Doppler traces in the spectrogram, known as Oblique Spread Structure (OSS). OSS has been expected to be generated by the dispersion of radio wave reflection due to equatorial plasma bubbles (EPBs). However, it has not yet been confirmed whether OSS is surely a manifestation of EPB by conducting simultaneous observations of EPB and OSS with different observational techniques. Additionally, it remains unclear what kinds of properties of EPB are reflected in the fine structure of OSS. In this study, we investigated three cases of OSSs and EPBs simultaneously observed by a HFD sounding system and an all-sky airglow imager in Taiwan. For the three cases presented here, the timing of OSS occurrence in the HFD data well coincided with that of the EPB appearance in the airglow data. The frequency shift of OSS is quantitatively explained assuming a radio wave reflection at 250–300 km altitudes. These results strongly indicate that OSS is formed by electron density variations at F-region altitudes accompanying EPB; thus, OSS is a manifestation of EPB in the HFD observations. Furthermore, it was suggested that the fine structure of OSS reflected the branching structure of EPB when the multiple branches of EPB reached the intermediate reflection point of the HFD observation. The detection of EPB occurrence and its fine structure using HFD observation enables monitoring of EPB regardless of weather conditions, which will contribute to monitoring the space weather impact of EPBs, for example, on GNSS navigation, in a wide area.Graphical

Striking a Balance between Conservation and Development: A Geospatial Approach to Watershed Prioritisation in the Himalayan Basin

This study was undertaken in the Himalayan basin, in the river Lohawati, Uttarakhand, to study its hydro-morphological characteristics and prioritise the watersheds using geospatial tools. Advanced Spaceborne Thermal Emission and Reflection (ASTER-30 m) data and the Survey of India’s topographic sheets were used to analyse the study area comprehensively. Nine watersheds were identified within the basin in order to calculate the hydro-morphological characteristics in terms of basic, shape, texture, and relief aspects. The basin was identified as being elongated, with a total drainage area of 337.48 km2. The interaction between the terrain, rock formations, and precipitation levels produced a branching structure in the areas drainage system that ranged from dendritic to sub-dendritic. The basin had been classified as a fifth-order basin, comprising a network of 500 stream segments spanning a total length of 492.41 km. In each of the watersheds, the primary streams are of the first order, followed by those of the second order, and so forth. The physiography and lithology of the basin have a significant influence on this pattern. The calculated elongation ratio, circulatory ratio, form factor, shape index, and shape factor ranged from 0.57 to 0.80, 0.35 to 0.64, 0.26 to 0.50, 1.98 to 3.89, and 0.57 to 1.77, respectively. These values indicate that watersheds are elongated, suggesting moderate lag times. The parameters, including drainage density (0.98 to 1.62), stream frequency (1.07 to 1.59), infiltration number (1.04 to 2.59), drainage texture (0.67 to 2.82), and drainage intensity (0.93 to 1.12), pointed towards the coarser drainage texture, higher infiltration, and minimal runoff characteristics of the basin. In light of the relief characteristics of the basin, a higher basin relief, relief ratio, and relative relief were observed for the watersheds, indicating the possibility of higher erosion and deforestation rates. Using the Weighted Sum Analysis (WSA) method, the computed factors were utilised to rank the watersheds based on their potential for erosion. Based on the WSA approach, watersheds were classified into high-, moderate-, and low-prioritisation zones. This further indicates that 36.14% (121.95 km2) of watersheds are in the high-priority zone, and that 48.84% (164.91 km2) and 15.00% (50.62 km2) of watersheds are in the moderate- and low-priority zones, respectively. The WSA is a practical strategy to prioritise watersheds when making appropriate decisions.

Shape-driven confluent rigidity transition in curved biological tissues

Collective cell motions underlie structure formation during embryonic development. Tissues exhibit emergent multicellular characteristics such as jamming, rigidity transitions, and glassy dynamics, but there remain questions about how those tissue-scale dynamics derive from local cell-level properties. Specifically, there has been little consideration of the interplay between local tissue geometry and cellular properties influencing larger-scale tissue behaviors. Here, we consider a simple two-dimensional computational vertex model for confluent tissue monolayers, which exhibits a rigidity phase transition controlled by the shape index (ratio of perimeter to square root area) of cells, on surfaces of constant curvature. We show that the critical point for the rigidity transition is a function of curvature such that positively curved systems are likely to be in a less rigid, more fluid, phase. Likewise, negatively curved systems (saddles) are likely to be in a more rigid, less fluid, phase. A phase diagram we generate for the curvature and shape index constitutes a testable prediction from the model. The curvature dependence is interesting because it suggests a natural explanation for more dynamic tissue remodeling and facile growth in regions of higher surface curvature. Conversely, we would predict stability at the base of saddle-shaped budding structures without invoking the need for biochemical or other physical differences. This concept has potential ramifications for our understanding of morphogenesis of budding and branching structures.

Bifurcations and synchrony in a ring of delayed Wilson–Cowan oscillators

Ring structures are crucial in network neuroscience, enabling the integration of neural information through closed loop circuits within feedback systems. Here, we use numerical bifurcation analysis to explore time delay effects on a ring of delay-coupled Wilson–Cowan masses. Investigating a low-dimensional ‘self-coupled’ version of the aforementioned system, we uncover the bifurcation structure of the synchronization manifold, and unveil a diverse array of dynamic synchronization patterns that emerge as a consequence of Hopf branch crossings and subsequent higher-order bifurcations. Analysis of the full system reveals transverse instabilities in the synchronized state for large regions of parameter space, with the ring network architecture promoting various dynamics depending on the balance between coupling strength and delay time. Under weak coupling, emergent oscillations are generally synchronous or anti-phase synchronous, with transitions between them triggered by a torus bifurcation of a periodic orbit. Regions of synchronous and anti-phase synchronous solutions are delineated by weakly chaotic borders due to the breakdown of the torus. As coupling strength increases, the bifurcation diagram displays more overlapped branching structure, resulting in increasingly complicated, multistable dynamics.

Exploring pulse mitigation in heterogeneous granular metamaterials

Recognizing the need for effective control of vibration and sound propagation in various industries, this study investigates the potential of designing heterogeneous granular networks for vibroacoustic transmission mitigation. It introduces new models of granular systems: decorated, stepped, and tapered 2-level branching structures. The research assesses changes in particle size (5–10 mm radii) and material properties (density and Young's Modulus) to create finely-tuned composites that significantly modulate pulse waves. The discrete element method predicts wave propagation in these granular metamaterials, comparing monodispersed chains, conventional chain networks, and the proposed heterogeneous structures. Their pulse diffusion capacity is evaluated, showing how collective responses can be adjusted by altering physical parameters like particle size and composition. Preliminary findings underscore the utility of these configurations in advancing the development of elastic and acoustic metamaterials, demonstrating a peak amplitude reduction more than five times greater than an equivalent monomer system. With versatility across a wide frequency range, these metamaterials could pioneer a new direction in impact mitigation.

Microplastics Enhance the Prevalence of Antibiotic Resistance Genes in Anaerobic Sludge Digestion by Enriching Antibiotic-Resistant Bacteria in Surface Biofilm and Facilitating the Vertical and Horizontal Gene Transfer.

Antibiotic resistance genes (ARGs) and microplastics (MPs) are recognized as emerging contaminants and threats to global human health. Despite both of them being significantly detected in their "hotspots", i.e., waste activated sludge (WAS), rare studies on how MPs affect ARGs and antibiotic-resistant bacteria (ARB) in anaerobic sludge digestion are available. Herein, the fate of ARGs and ARB after exposure to MPs of three dosages (10, 30, and 80 particles/g-TS), three polymer types (LDPE, PET, and PS), and three branching extents (LDPE, LLDPE, and HDPE) in anaerobic sludge digestion was investigated. Metagenomic results indicated that all variants of MPs resulted in an increase of the relative abundance of ARGs in the digester compared to the control. The abundance of ARGs demonstrated a dosage-dependent relationship within the range from 10 to 80 particles/g-TS, resulting in an increase from 4.5 to 27.9% compared to the control. Branching structure and polymer type influence ARG level in the sludge digester as well. Mechanism studies revealed that LDPE selectively enriched potential ARB and ARGs in the surface biofilm, possibly creating a favorable environment for ARB proliferation and ARG exchange. Furthermore, vertical transfer of ARGs was facilitated by LDPE through increasing bacterial cell proliferation accompanied by the enhancement of relevant functional genes. The elevated abundance of mobile genetic elements (MGEs) and ARGs-carrying plasmids also demonstrated that MGE-mediated horizontal transfer was promoted by LDPE at 80 particles/g-TS. This effect was compounded by increased oxidative stress, cell membrane permeability, and cell cohesion, collectively facilitating horizontal ARG transfer. Consequently, both vertical and horizontal transfer of ARGs could be concurrently promoted by LDPE an in anaerobic sludge digester.

Branching pomsets: Design, expressiveness and applications to choreographies

Choreographic languages describe possible sequences of interactions among a set of agents. Typical models are based on languages or automata over sending and receiving actions. Pomsets provide a more compact alternative by using a partial order to explicitly represent causality and concurrency between these actions. However, pomsets offer no representation of choices, thus a set of pomsets is required to represent branching behaviour. For example, if an agent Alice can send one of two possible messages to Bob three times, one would need a set of 2×2×2 distinct pomsets to represent all possible branches of Alice's behaviour. This paper proposes an extension of pomsets, named branching pomsets, with a branching structure that can represent Alice's behaviour using 2+2+2 ordered actions. We compare the expressiveness of branching pomsets with that of several forms of event structures from the literature. We encode choreographies as branching pomsets and show that the pomset semantics of the encoded choreographies are bisimilar to their operational semantics. Furthermore, we define well-formedness conditions on branching pomsets, inspired by multiparty session types, and we prove that the well-formedness of a branching pomset is a sufficient condition for the realisability of the represented communication protocol. Finally, we present a prototype tool that implements our theory of branching pomsets, focusing on its applications to choreographies.

The application advances of dendrimers in biomedical field

AbstractDendrimers are a family of nano‐sized three‐dimensional polymers with unique dendritic branching structures and compact spherical geometries. In recent years, dendrimers have made a series of breakthroughs in the biomedical field. In this review, we introduce the synthesis principles, modification methods, and new materials designed based on dendrimers; discuss the importance of cytotoxicity of dendrimers for applications; and elaborate on their applications in the field of molecular assembly and cancer diagnosis and treatment. We speculate that in the near future, more new materials based on dendrimers will be applied in the biomedical field.

Multispectral method combined with molecular modelling to investigate the binding mechanisms of DBP and DIBP on pepsin

The binding mechanisms of dibutyl phthalate (DBP) and diisobutyl phthalate (DIBP) with pepsin (PEP) were investigated by multispectral method and computational techniques (molecular docking, molecular dynamics, surface electrostatic potential), as well as cytotoxicity assay. Fluorescence studies revealed that both DBP and DIBP had a static bursting effect on PEP, forming a stable complex. Furthermore, the formation of PEP-DBP/DIBP complexes was observed to occur spontaneously (ΔG < 0), driven by the interactions of hydrogen bonding and van der Waals forces. PEP exhibits a higher binding constant Ka of DBP (3.30 × 104 L·mol−1) compared to that of DIBP (2.37 × 104 L·mol−1). The higher stability of PEP-DBP complexes can be attributed to the different branching structures of DBP and DIBP, this observation was further supported by the larger negative surface area of DBP (125.90 Å2) in the ESP analysis, and were aligned with the MD simulations results of more stable RMSD and lower Rg value in presence of DBP. Computational analysis revealed that both DBP and DIBP exhibited binding interactions with the fluorescent groups (Tyr 75, Phe 111, and Phe 117) by van der Waals forces. DBP/DIBP binds to the Asp 32 and Asp 215 motifs of the catalytic activity center of PEP. Combined with the lower Rg values, CD tests suggested that the addition of DBP/DIBP caused the rise of α-Helix content thereby compacted the conformation structure of PEP into a compact shape. In addition, DBP generated more hydrogen bonds with PEP compared to DIBP, also as evidence to the higher stability of EPE-DBP. Finally, the IC50 of DBP and DIBP on Caco-2 cells were determined to be 5.16 × 10-4 mol·L-1 and 1.37 × 10-3 mol·L-1, respectively confirming the higher level of toxicity of DBP. The present study elucidates the effect and binding mechanism of DBP/DIBP on PEP at the molecular level, providing fundamental data for the impact and potential risk assessment of PAEs on the human digestive system.

Integrated design algorithm for branching structures

Branching structures comprise slender beam members that may cause the buckling of entire structures due to compression. An intelligent design algorithm for branching structures is proposed to facilitate the design of branching structures. The branching can be automatically generated by giving loads and truss position. This algorithm consists of three parts, namely, form-finding algorithm, buckling optimization algorithm, and topology optimization algorithm. With this intelligent design algorithm, the moment of the branching members can be removed; the geometrical length of members can be optimized according to the buckling constraints; and the effective members can be automatically selected from the ground structures and the sectional size can be automatically determined simultaneously. This work can be efficiently utilized for the engineering in the design of branching structures.

An extracellular polysaccharide is involved in the aluminum tolerance of Pullulanibacillus sp. CA42, a newly isolated strain from the Chinese water chestnut growing in an actual acid sulfate soil area in Vietnam.

A novel aluminum-tolerant bacterial strain CA42 was isolated from the aquatic plant Eleocharis dulcis, which grows in a highly acidic swamp in Vietnam. Inoculation with CA42 allowed Oryza sativa to grow in the presence of 300 μM AlCl3 at pH 3.5, and biofilms were observed around the roots. Using 16S rRNA gene sequencing analysis, the strain was identified as Pullulanibacillus sp. CA42. This strain secreted large amounts of an extracellular polysaccharide (CA42 EPS). Results from structural analyses on CA42 EPS, namely methylation analysis and nuclear magnetic resonance (NMR), indicated that the chemical structure of CA42 EPS was a glycogen-like α-glucan. Purified CA42 EPS and the commercially available oyster glycogen adsorbed aluminum ions up to 15-30 μmol/g dry weight. Digestion treatments with α-amylase and pullulanase completely attenuated the aluminum ion-adsorbing activity of purified CA42 EPS and oyster glycogen, suggesting that the glycogen-like structure adsorbed aluminum ions and that its branching structure played an important role in its aluminum adsorbing activity. Furthermore, the aluminum tolerance of CA42 cells was attenuated by pullulanase treatment directly on the live CA42 cells. These results suggest that CA42 EPS adsorbs aluminum ions and is involved in the aluminum tolerance mechanism of Pullulanibacillus sp. CA42. Thus, this strain may be a potential plant growth-promoting bacterium in acidic soils. In addition, this study is the first to report a glycogen-like polysaccharide that adsorbs aluminum ions.

Bronchial tree of the human embryo: Examination based on a mammalian model.

The symmetry of the right and left bronchi, proposed in a previous comparative anatomical study as the basic model of the mammalian bronchial tree, was examined to determine if it applied to the embryonic human bronchial tree. Imaging data of 41 human embryo specimens at Carnegie stages (CS) 16-23 (equivalent to 6-8 weeks after fertilization) belonging to the Kyoto collection were obtained using phase-contrast X-ray computed tomography. Three-dimensional bronchial trees were then reconstructed from these images. Bronchi branching from both main bronchi were labeled as dorsal, ventral, medial, or lateral systems based on the branching position with numbering starting cranially. The length from the tracheal bifurcation to the branching point of the labeled bronchus was measured, and the right-to-left ratio of the same labeled bronchus in both lungs was calculated. In both lungs, the human embryonic bronchial tree showed symmetry with an alternating pattern of dorsal and lateral systems up to segmental bronchus B9 as the basic shape, with a more peripheral variation. This pattern is similar to that described in adult human lungs. Bronchial length increased with the CS in all labeled bronchi, whereas the right-to-left ratio was constant at approximately 1.0. The data demonstrated that the prototype of the human adult bronchial branching structure is formed and maintained in the embryonic stage. The morphology and branching position of all lobar bronchi and B6, B8, B9, and the subsegmental bronchus of B10 may be genetically determined. On the other hand, no common structures between individual embryos were found in the peripheral branches after the subsegmental bronchus of B10, suggesting that branch formation in this region is influenced more by environmental factors than by genetic factors.

TManual: Assistant for manually measuring length development in structures built by animals.

Structures built by animals are extended phenotypes, and animal behavior can be better understood by recording the temporal development of structure construction. For most subterranean and wood-boring animals, these structures consist of gallery systems, such as burrows made by mice, tunnel foraging by termites, and nest excavation in ants. Measurement of the length development of such structures is often performed manually. However, it is time-consuming and cognitively costly to track length development in nested branching structures, hindering the quantitative determination of temporal development. Here, I introduce TManual, which aids the manual measurement of structure length development using a number of images. TManual provides a user interface to draw gallery structures and take over all other processes handling input datasets (e.g., zero-adjustment, scaling the units, measuring the length, assigning gallery identities, and extracting network structures). Thus, users can focus on the measuring process without interruptions. As examples, I provide the results of the analysis of a dataset of tunnel construction by three termite species after successfully processing 1125 images in ~3 h. The output datasets clearly visualized the interspecific variation in tunneling speed and branching structures. Furthermore, I applied TManual to a complex gallery system by another termite species and extracted network structures. Measuring the lengths of objects from images is an essential task in biological observation. TManual helps users handle many images in a realistic time scale, enabling a comparative analysis across a wide array of species. TManual does not require programming skills and outputs a tidy data frame in CSV format. Therefore, it is suitable for any user who wants to perform image analysis for length measurements.

Ecosystem size and complexity as extrinsic drivers of food chain length in branching ecosystems

AbstractUnderstanding the drivers of food chain length in natural communities has intrigued ecologists since Elton publicized “food cycles” in the early 20th century. Proposed drivers of food chain length have included productivity, disturbance regime, ecosystem size, and trophic omnivory. However, current theories have largely assumed simple, two‐dimensional habitat architectures and may not be adequate to predict food chain length in ecosystems with a complex, branching structure. Here, we develop a spatially explicit theoretical model that provides an integrated framework for understanding variation in food chain length in branching networks. We show independent, positive influences of ecosystem size and complexity (as indicated by branching properties) on food chain length. However, the effects of ecosystem size and complexity were contingent upon other factors, appearing more clearly in high‐disturbance and high‐productivity regimes. Our results suggest that ecosystem complexity is an important yet overlooked driver of food chain length that may increase the resilience to anthropogenic environmental changes.

Rhizomorph: The Coordinated Function of Shoots and Roots

Computer graphics has dedicated a considerable amount of effort to generating realistic models of trees and plants. Many existing methods leverage procedural modeling algorithms - that often consider biological findings - to generate branching structures of individual trees. While the realism of tree models generated by these algorithms steadily increases, most approaches neglect to model the root system of trees. However, the root system not only adds to the visual realism of tree models but also plays an important role in the development of trees. In this paper, we advance tree modeling in the following ways: First, we define a physically-plausible soil model to simulate resource gradients, such as water and nutrients. Second, we propose a novel developmental procedural model for tree roots that enables us to emergently develop root systems that adapt to various soil types. Third, we define long-distance signaling to coordinate the development of shoots and roots. We show that our advanced procedural model of tree development enables - for the first time - the generation of trees with their root systems.

Structural characterization of exopolysaccharide produced by Streptococcus thermophilus and rheology of mixed protein-polysaccharide systems

This study determined the constituents and structural properties of extracellular polysaccharides of Streptococcus thermophilus (STEP) and investigated the rheological properties of the blended system of STEP and whey protein (STEP/WP). Two STEP, neutral polysaccharides (STEP-1) and acidic polysaccharides (STEP-2), were isolated and purified from S. thermophilus. Their molecular weights were 2197.74 and 141.99 kDa, respectively. STEP-1 were mainly composed of galactose, glucose, and rhamnose, whereas STEP-2 were mainly composed of galactose, mannose, and glucose. Methylation and NMR analyses confirmed that the STEP structural backbone included α- and β-type pyranose residues and many branching structures. The rheological results revealed that the apparent viscosity of STEP/WP was higher than that of STEP, while STEP/WP mainly acted as a viscous liquid under the influence of dairy processing parameters. These findings may be useful for STEP/WP application in the production of dairy products such as fermented milk and cheese.