Branch Research Articles

One-shot random forest model calibration for hand gesture decoding

Objective. Most existing machine learning models for myoelectric control require a large amount of data to learn user-specific characteristics of the electromyographic (EMG) signals, which is burdensome. Our objective is to develop an approach to enable the calibration of a pre-trained model with minimal data from a new myoelectric user. Approach. We trained a random forest (RF) model with EMG data from 20 people collected during the performance of multiple hand grips. To adapt the decision rules for a new user, first, the branches of the pre-trained decision trees were pruned using the validation data from the new user. Then new decision trees trained merely with data from the new user were appended to the pruned pre-trained model. Results. Real-time myoelectric experiments with 18 participants over two days demonstrated the improved accuracy of the proposed approach when compared to benchmark user-specific RF and the linear discriminant analysis models. Furthermore, the RF model that was calibrated on day one for a new participant yielded significantly higher accuracy on day two, when compared to the benchmark approaches, which reflects the robustness of the proposed approach. Significance. The proposed model calibration procedure is completely source-free, that is, once the base model is pre-trained, no access to the source data from the original 20 people is required. Our work promotes the use of efficient, explainable, and simple models for myoelectric control.

Coagulation, non-associative algebras and binary trees

We consider the classical Smoluchowski coagulation equation with a general frequency kernel. We show that there exists a natural deterministic solution expansion in the non-associative algebra generated by the convolution product of the coalescence term. The non-associative solution expansion is equivalently represented by binary trees. We demonstrate that the existence of such solutions corresponds to establishing the compatibility of two binary-tree generating procedures, by: (i) grafting together the roots of all pairs of order-compatible trees at preceding orders, or (ii) attaching binary branches to all free branches of trees at the previous order. We then show that the solution represents a linearised flow, and also establish a new numerical simulation method based on truncation of the solution tree expansion and approximating the integral terms at each order by fast Fourier transform. In particular, for general separable frequency kernels, the complexity of the method is linear-loglinear in the number of spatial modes/nodes.

Whole-Transcriptome Sequencing Reveals the Global Molecular Responses and NAC Transcription Factors Involved in Drought Stress in Dendrobium catenatum.

Dendrobium catenatum is a highly drought-tolerant herb, which usually grows on cliffs or in the branches of trees, yet the underlying molecular mechanisms for its tolerance remain poorly understood. We conducted a comprehensive study utilizing whole-transcriptome sequencing approaches to investigate the molecular response to extreme drought stress in D. catenatum. A large number of differentially expressed mRNAs, lncRNAs, and circRNAs have been identified, and the NAC transcription factor family was highly enriched. Meanwhile, 46 genes were significantly up-regulated in the ABA-activated signaling pathway. In addition to the 89 NAC family members accurately identified in this study, 32 members were found to have different expressions between the CK and extreme drought treatment. They may regulate drought stress through both ABA-dependent and ABA-independent pathways. Moreover, the 32 analyzed differentially expressed DcNACs were found to be predominantly expressed in the floral organs and roots. The ceRNA regulatory network showed that DcNAC87 is at the core of the ceRNA network and is regulated by miR169, miR393, and four lncRNAs. These investigations provided valuable information on the role of NAC transcription factors in D. catenatum's response to drought stress.

Assessment of biomass and carbon storage of a Populus simonii windbreak located in the Western Cape Province, South Africa

The integration of trees within agricultural systems delivers the opportunity to provide multiple benefits over those afforded by agriculture without trees. The use of windbreaks as a form of agroforestry, in water scarce environments, is primarily used to reduce windspeeds in order to decrease evapotranspiration. Quick growing poplar species such as Populus simonii ((Carrière) Wesm.) are frequently utilised within windbreak structures, but to date, few allometric equations are available to quantify biomass production and to make inferences about carbon storage potential of this species, and none outside the forest. To fill this knowledge gap, we destructively sampled 17 P. simonii growing within a windbreak on a wine estate in the Western Cape Provence, South Africa. Power functions were constructed to explain tree height, whole tree aboveground woody biomass, stem and branch biomass as a function of stem diameter at 1.3 m. Additional functions were developed to predict individual branch length and biomass based on branch stub diameter. The presented models explained each variable with high significance. The models could be used to estimate carbon stock per km of windbreak for the given example. Furthermore, bark percentage predicted by stem sectional diameter was modelled to provide a function that can separate wood and bark fractions as a further outlook for the species’ utilisation.

Modeling a new taper curve and form factor of tree branches using terrestrial laser scanning

Abstract Modeling branch taper curve and form factor contributes to increasing the efficiency of tree crown reconstructions: the branch taper, defined as the sequential measure of diameters along the course of the branch, is pivotal to accurately estimate key branch variables such as biomass and volume. Branch diameters or volumes have commonly been estimated from terrestrial laser scanning (TLS) based on automatized voxelization or cylinder-fitting approaches, given the whole branch length is sufficiently covered by laser reflections. The results are, however, often affected by ample variations in point cloud characteristics caused by varying point density, occlusions, and noise. As these characteristics of TLS can hardly be sufficiently controlled or eliminated in automatized techniques, we proposed a new branch taper curve model and form factor, which can be employed directly from the laser reflections and under variable point cloud characteristics. In this paper, the approach is demonstrated on primary branches using a set of TLS-derived datasets from a sample of 20 trees (six species). The results showed an R2 of 0.86 and a mean relative absolute error of 1.03 cm (29%) when validated with field-measured diameters. The approach improved the accuracy of diameter estimates for the fine branch scales (<10 cm) as compared to the quantitative structural model (QSM). Our approach also allowed branch diameter estimation for a relatively larger number of manually recognized primary branches (>85%) from point clouds when validated with panoramic images acquired simultaneously with laser scanning. Frequently used automatized crown reconstructions from QSM, on the other hand, were affected by gaps in the point clouds due to obstruction, with the crown-tops and finer branches being the most critical. Our approach reports mean form factors across the examined species of 0.35 and 0.49, with the diameters determined at 5% and 10% of the total branch length, respectively. Our approach may have the potential to produce branch volume information with reasonable accuracy from only knowing the length and respective diameter of each branch. Our model delivers a first approximation for the taper curve and form factor for primary branches but was developed on a relatively small set of samples. We believe that our approach holds the potential to improve the accuracy of the assessment of branch diameter and volume from TLS data. The approach may also be extended to other branch orders. This could expand the horizon for volumetric calculations and biomass estimates from non-destructive TLS proxies in tree crowns.

Ontophylo: Reconstructing the evolutionary dynamics of phenomes using new ontology‐informed phylogenetic methods

Abstract Reconstructing ancestral states for discrete characters is essential for understanding trait evolution in organisms. However, most existing methods are limited to individual characters and often overlook the hierarchical and interactive nature of traits. Recent advances in phylogenetics now offer the possibility of integrating knowledge from anatomy ontologies to reconstruct multiple discrete character histories. Nonetheless, practical applications that fully harness the potential of these new approaches are still lacking. This paper introduces ontophylo, an R package that extends the PARAMO pipeline to address these limitations. Ontophylo enables the reconstruction of phenotypic entities composed of amalgamated characters, such as anatomical regions or entire phenomes. It offers three new applications: (1) reconstruction of evolutionary rates of amalgamated characters using phylogenetic non‐homogeneous Poisson process (pNHPP) that allows modelling rate variation across tree branches and time; (2) reconstruction of morphospace dynamics; and (3) visualization of evolutionary rates on vector images of organisms. Ontophylo incorporates ontological knowledge to facilitate these applications. Benchmarking confirms the accuracy of pNHPP in estimating character rates under different evolutionary scenarios, and example applications demonstrate the utility of ontophylo in studying morphological evolution in Hymenoptera using simulated data. Ontophylo can be easily integrated with other ontology‐oriented and general‐purpose R packages and offers new opportunities to examine morphological evolution on a phenomic scale using new and legacy data.

Umbel convexity and the geometry of trees

For every p∈(0,∞), a new metric invariant called umbel p-convexity is introduced. The asymptotic notion of umbel convexity captures the geometry of countably branching trees, much in the same way as Markov convexity, the local invariant which inspired it, captures the geometry of bounded degree trees. Umbel convexity is used to provide a “Poincaré-type” metric characterization of the class of Banach spaces that admit an equivalent norm with Rolewicz's property (β). We explain how a relaxation of umbel p-convexity, called infrasup-umbel p-convexity, plays a role in obtaining compression rate bounds for coarse embeddings of countably branching trees. Local analogues of these invariants - fork p-convexity and infrasup-fork p-convexity - are introduced, and their relationship to Markov p-convexity and relaxations of the p-fork inequality is discussed. The metric invariants are estimated for a large class of Heisenberg groups, and in particular a parallelogram p-convexity inequality is proved for Heisenberg groups over p-uniformly convex Banach spaces. Finally, a new characterization of non-negative curvature is given.

Claude Chamber

Proto-photographic and proto-cinematic technologies are an unending source of inspiration for a visual artist. We want to consider the case of an eighteenth-century optical device, the Claude mirror, as a starting point for an artistic collaboration.
 The Claude mirror is a small black convex mirror named after the painter Claude Lorrain and used by late eighteenth-century and early nineteenth-century painters and travellers for viewing landscapes. The dark mirror surface produces an image with a limited tonal range, allowing the viewer to look at the environment as if it were a painting. A famous Thomas Gainsborough drawing shows a man seated on a bank with a sketchbook on his lap and holding an oval mirror propped against a tree branch (Gainsborough, 1750-55).
 In spring 2019, in a flash of joint inspiration, we conceived a method of combining aspects of our artistic processes: Salla’s moving image and Laura’s printmaking practice. For 18 months, we captured photographic time-lapse sequences of everyday views from the backyards of our studios, residencies, and homes as reflections on the surface of copper plates installed in the environment (Myllylä and Vainikka, 2021). In the resulting installation, titled Claude Chamber, we projected the video sequences on the gallery space, reflected via the same mirror surfaces, and the projected images became distorted and spatial.
 We were intrigued by this optical device, in which characteristics of photography and printmaking meet. One can think of a Claude glass as a predecessor of the camera viewfinder, an early photographic gesture. It can also be viewed as a printing plate, a matrix reflecting a view. In a traditional printing plate, the image is attached or fastens itself onto the surface of the plate; in our installation, the image is transient and moving.

Damage caused by singing cicadas (Hemiptera: Cicadidae) in the field protective forest belts in South Dobrudzha, Bulgaria

During the period 2020-2023, strong damage caused by singing cicadas (Hemiptera: Cicadidae) were registered on ash trees (Fraxinus spp.) in the field protective forest belts (FPFBs) in South Dobrudzha, northeastern Bulgaria. Bioacoustic studies have shown that the sounds are of Cicada orni. Many exuvia of the species were also found on the trunks and branches of ash trees. On the upper shoots and petioles, numerous oviposition holes were observed, which lead to leaf fall and drying of branch tips. In different FPFBs, tree crown damage ranges from a moderate (25-60% defoliation) to a severe (over 60% defoliation) degree. The attacks were stronger on Fraxinus excelsior and F. americana compared to F. angustifolia. The cicadas affect both old trees and young ash saplings. In young plantations, other tree species (Sophora japonica, Gleditsia triacanthos) were also affected. Imaginal activity of Cicada orni was recorded in July and August, and the peak of egg hatching occurred from early August to mid-September. The high number of Cicada orni necessitates the development of measures to control the pest in the FPFBs.

The complete mitochondrial genome of the tropical sea urchin Tripneustes gratilla (Linnaeus, 1758) with two spine colors

The complete mitochondrial genomes of two spine-color individuals, red and white, of the tropical sea urchin species Tripneustes gratilla (Linnaeus, 1758) were sequenced on Illumina system platform. The red-spined species had a genome size of 15,774 bp, while the white-spined species had a genome size of 15,723 bp. Both genomes contained 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. The GC composition in both species was above 40%. In order to investigate the phylogenetic relationships of two different spine-color individuals, a comprehensive analysis was conducted using eight complete mitochondrial genomic sequences of the genus Tripneustes on the software MEGA X. It was observed that the two spine color types of T. gratilla species showed a high similarity of 98.91%. However, different color-spined species of T. gratilla were found in separate branches of the phylogenetic tree of the same sea urchin species.

New mermithid nematode-spider associations, along with a molecular phylogeny of mermithids hosted in spiders

Mermithid parasitoids are well known to infect spiders; however, their impact on hosts and their taxonomic identity are still poorly analyzed. We present the first record of a mermithid nematode infection in the spider genera Piratula (Lycosidae) and Coelotes (Agelenidae), and in the species Alopecosa pulverulenta and Pardosa paludicola (Lycosidae). We describe the maldevelopment of the spiders’ female genitalia induced by the parasitoid and summarize data on the impact of nematode parasitoids on spider development and behaviour. Phylogenetic analysis, based on the 18S rDNA, showed that spider parasitoidism arose independently in different branches of the phylogenetic tree of the family Mermithidae.

The complete chloroplast genome of Dendrocalamus liboensis Hsueh & D. Z. Li 1985 and its phylogenetic analysis

Dendrocalamus liboensis Hsueh & D. Z. Li 1985 is a unique member of the Bambusoideae subfamily found in Guizhou, China. The species has both economic importance and ornamental value. This study represents the first report of the sequencing and assembly of the complete chloroplast genome of D. liboensis. The total length of the genome was 139,483 bp, with a conventional quadripartite framework consisting of a large single-copy (LSC) region (83,001 bp in length), a small single-copy (SSC) region (12,896 bp in length), and two inverted repeats (IR) regions (both 21,793 bp in length). Overall, the D. liboensis chloroplast genome contained 128 functional genes, including 83 protein-coding genes, 37 tRNAs, and 8 rRNAs. Phylogenetic analysis showed that D. liboensis closely resembled D. sapidus, with both found on a strongly supported branch of the phylogenetic tree.

The Seismicity Rate Model for the 2022 Aotearoa New Zealand National Seismic Hazard Model

ABSTRACT A seismicity rate model (SRM) has been developed as part of the 2022 Aotearoa New Zealand National Seismic Hazard Model revision. The SRM consists of many component models, each of which falls into one of two classes: (1) inversion fault model (IFM); or (2) distributed seismicity model (DSM). Here we provide an overview of the SRM and a brief description of each of the component models. The upper plate IFM forecasts the occurrence rate for hundreds of thousands of potential ruptures derived from the New Zealand Community Fault Model version 1.0 and utilizing either geologic- or geodetic-based fault-slip rates. These ruptures are typically less than a couple of hundred kilometers long, but can exceed 1500 km and extend along most of the length of the country (albeit with very low probabilities of exceedance [PoE]). We have also applied the IFM method to the two subduction zones of New Zealand and forecast earthquake magnitudes of up to ∼Mw 9.4, again with very low PoE. The DSM combines a hybrid model developed using multiple datasets with a non-Poisson uniform rate zone model for lower seismicity regions of New Zealand. Forecasts for 100 yr are derived that account for overdispersion of the rate variability when compared with Poisson. Finally, the epistemic uncertainty has been modeled via the range of models and parameters implemented in an SRM logic tree. Results are presented, which indicate the sensitivity of hazard results to the logic tree branches and that were used to reduce the overall complexity of the logic tree.

Accurate Airway Tree Segmentation in CT Scans via Anatomy-aware Multi-class Segmentation and Topology-guided Iterative Learning.

Intrathoracic airway segmentation in computed tomography is a prerequisite for various respiratory disease analyses such as chronic obstructive pulmonary disease, asthma and lung cancer. Due to the low imaging contrast and noises execrated at peripheral branches, the topological-complexity and the intra-class imbalance of airway tree, it remains challenging for deep learning-based methods to segment the complete airway tree (on extracting deeper branches). Unlike other organs with simpler shapes or topology, the airway's complex tree structure imposes an unbearable burden to generate the "ground truth" label (up to 7 or 3 hours of manual or semi-automatic annotation per case). Most of the existing airway datasets are incompletely labeled/annotated, thus limiting the completeness of computer-segmented airway. In this paper, we propose a new anatomy-aware multi-class airway segmentation method enhanced by topology-guided iterative self-learning. Based on the natural airway anatomy, we formulate a simple yet highly effective anatomy-aware multi-class segmentation task to intuitively handle the severe intra-class imbalance of the airway. To solve the incomplete labeling issue, we propose a tailored iterative self-learning scheme to segment toward the complete airway tree. For generating pseudo-labels to achieve higher sensitivity (while retaining similar specificity), we introduce a novel breakage attention map and design a topology-guided pseudo-label refinement method by iteratively connecting breaking branches commonly existed from initial pseudo-labels. Extensive experiments have been conducted on four datasets including two public challenges. The proposed method achieves the top performance in both EXACT'09 challenge using average score and ATM'22 challenge on weighted average score. In a public BAS dataset and a private lung cancer dataset, our method significantly improves previous leading approaches by extracting at least (absolute) 6.1% more detected tree length and 5.2% more tree branches, while maintaining comparable precision.

The degree of hydraulic vulnerability segmentation at the individual level is related to stomata sensitivity in seedlings of three oak species

AbstractIt is hypothesized that ‘hydraulic vulnerability segmentation’ (the vulnerability of expendable organs is higher compared to the vulnerability of nonexpendable organs) can enhance the drought‐tolerance of trees. However, prediction of positive segmentation (leaf minus branch) did not gain undisputed support in field observations. Further, the main organs of trees (leaf/trunk/root) are vital to test the hypothesis at the individual level. Unfortunately, most verifications of the hypothesis focus on the hydraulic vulnerabilities between leaves and terminal branches of mature trees. In this study, we grew three deciduous oak (Quercus mongolica, Q. variabilis and Q. aliena) seedlings (6 months old), and measured the hydraulic vulnerabilities of leaves (by rehydration method), main stems and main roots (by bench dehydration method). The sensitivity of stomata to water potential was obtained by monitoring the stomata conductance response to drought stress. The xylem anatomy of main stem and main root was also measured. It was found that the leaves of all three oak species exhibited greater vulnerability than the main stems and main roots. The leaf‐stem segmentation was more pronounced than the stem‐root one, and the stem‐root in Q. aliena even showed a reversed segmentation. Further, we found that higher stomatal sensitivity was associated with higher P50,leaf (water potential at 50% loss of leaf hydraulic conductivity), and narrower segmentation between leaf and the most embolism‐resistant organ. Collectively, our results support the ‘hydraulic vulnerability segmentation’ hypothesis at the individual level, and highlight the importance of stomatal regulation in hydraulic vulnerability segmentation.

DNA barcode shows discordant cases among morphological and molecular species identification in Isbrueckerichthys (Siluriformes: Loricariidae)

Abstract Isbrueckerichthys is a genus of armored catfish (Siluriformes: Loricariidae) with five species in the lowlands from the Ribeira de Iguape basin and in the uplands of the Tibagi River basin. Despite the validation of the morphological species, molecular data to investigate gene flow and species delimitation have not been completed for all species. For this purpose, we compared sequences of COI region associated with barcoding molecular identification, aiming for a species delimitation analysis and generating population data of I. alipionis, I. epakmos, I. duseni, I. cf. duseni, I. saxicola, and I. calvus. The K2P genetic distance, molecular species delimitation analysis, and well-sustained branches in the phylogenetic tree validate I. alipionis, I. epakmos, and I. duseni, and suggest I. cf. duseni as a valid molecular operational taxonomic unit. However, no differences were detected between I. saxicola and I. calvus. The discordance between molecular and morphological species may be due to the recent dispersal of some Isbrueckerichthys representatives at the border between the Ribeira de Iguape and Tibagi basins. The isolation features of the mountainous region of Ribeira de Iguape basin and headwaters captures to uplands are presented to explain the dispersion and the cases of incipient speciation in Isbrueckerichthys lineages.

ОПТИМІЗАЦІЯ АЛГОРИТМУ ПАКЕТНОЇ ВЕЙВЛЕТ-ФІЛЬТРАЦІЇ СИГНАЛІВ

A wavelet packet filtering algorithm has been developed, which includes cyclic movement along the branches of the wavelet packet tree with a constraint on each branch of the approximation and detail coefficients until the minimum root-mean-square error is attained, with the optimal parameters of the wavelet threshold and threshold function. To calculate the root-mean-square error of filtering, after each cycle of processing the wavelet decomposition coefficients, the signal is reconstructed in the time domain. In the next cycle, the received signal is decomposed into approximation and detail coefficients until the root-mean-square error reaches a minimum for all possible values of the basic wavelet-threshold and the threshold function. The study was conducted with twenty of the most commonly used signals, including signals with linear and non-linear frequencies. To confirm the efficiency of packet wavelet filtering, a comparative analysis with the known methods based on a common threshold of detail coefficients at all levels of wavelet decomposition is given. Keywords: wavelet analysis, packet wavelet filtering, entropy, threshold function, threshholding.

Characterization of the length and the distance of insertion of the branches of apple trees

The current study focused on the branches Cherry Gala variety of apple in Azrouregion.The objective is to characterize the length and the insertion distance of different structures of apple trees based on nondestructive and exhaustive measurements of the branches. In total 2982 branches were identified and measured in the two stages (stage 1, stage 2) on different 6 levels present at each stage known as A, B, C, D, E, and F. The length of the branches in each stage and level was classified into 1 to 5 homogeneous classes. The length of vegetative branch variation was not significant between stages 1 and 2 but the insertion distance was significant for level D and not for levels A, B, and C. For five different length structures bearing fruit, the variation was significantly different for B, C, and D levels between stages 1 and 2 (length of fruiting spurs/ Dard/ Bourse; insertion distance of Dard and Bourse). The analysis showed that the length of the branches decreases while passing from one first stage to the second. The average branch length for stage 1 is 4,84 cm against 4,05 cm for stage 2. In each stage, the length decreases progressively while passing from one level to a higher level, except for level E of stage 1 and levels E and F of stage 2.

ПОВЫШЕНИЕ ЭФФЕКТИВНОСТИ УПРАВЛЕНИЕ ПРОЦЕССАМИ ПЕРЕВОЗОК СЕТЕВОЙ ДОСТАВКИ ГРУЗА АВТОМОБИЛЬНЫМ ТРАНСПОРТОМ

A methodology for designing a routing problem using the method of fictitious nodes and branches, taking into account restrictions, is given. The constraints are taken into account when reciprocating through the branches of the decision tree to block the cell with the maximum estimate. The results of the application of the developed methodology are presented, using the example of cargo transportation from the administrative center located in the Penza region to retail outlets in Penza per shift.

Long-Term Impacts of Tree Architectures and Branch Configurations on Tree Growth, Yield, Fruit Quality Attributes, and Leaf Minerals in “Aztec Fuji” Apple

Long-Term Impacts of Tree Architectures and Branch Configurations on Tree Growth, Yield, Fruit Quality Attributes, and Leaf Minerals in “Aztec Fuji” Apple