Branch Orientation Research Articles

Loss of a highly conserved sterile alpha motif domain gene (WEEP) results in pendulous branch growth in peach trees

Plant shoots typically grow upward in opposition to the pull of gravity. However, exceptions exist throughout the plant kingdom. Most conspicuous are trees with weeping or pendulous branches. While such trees have long been cultivated and appreciated for their ornamental value, the molecular basis behind the weeping habit is not known. Here, we characterized a weeping tree phenotype in Prunus persica (peach) and identified the underlying genetic mutation using a genomic sequencing approach. Weeping peach tree shoots exhibited a downward elliptical growth pattern and did not exhibit an upward bending in response to 90° reorientation. The causative allele was found to be an uncharacterized gene, Ppa013325, having a 1.8-Kb deletion spanning the 5' end. This gene, dubbed WEEP, was predominantly expressed in phloem tissues and encodes a highly conserved 129-amino acid protein containing a sterile alpha motif (SAM) domain. Silencing WEEP in the related tree species Prunus domestica (plum) resulted in more outward, downward, and wandering shoot orientations compared to standard trees, supporting a role for WEEP in directing lateral shoot growth in trees. This previously unknown regulator of branch orientation, which may also be a regulator of gravity perception or response, provides insights into our understanding of how tree branches grow in opposition to gravity and could serve as a critical target for manipulating tree architecture for improved tree shape in agricultural and horticulture applications.

Features of the Regional Economic Systems Development with a Mono-Branch Focus

Subject . The relevance of the study is explained by the need to develop regional economic systems based on the activation of innovative processes and the use of a differentiated approach depending on the level of economic development of the territory. The subject of this study is the regions of the national economy, characterized by a strong branch orientation. Purpose . The author of the article attempts to develop an approach to ensure innovative development of economy on the basis of determining the strategic direction of regions development with an industry focus, by targeting the key parameters of the system. Within the framework of the stated goal solution, the method of analytical hierarchical procedure was used, allowing to decompose the investigated problem and to carry out a paired comparison of the selected development strategies. Methodology . A grouping of indicators was carried out, the dynamics of which can be used to determine the stage of the industry life cycle, dominating in the region. Three strategic vectors of the region development were identified, taking into account the dynamics of innovative processes in the industry and contribution to the region economic development which is dominant in the economic activity, the indicators determining the stage of the industry life cycle were pointed out, the approach to identify strategic development priorities of the regional economy was proposed taking into account the most important factors. There is an approach to the prioritization of regional economic systems development strategies with paired comparisons of alternatives. Results . The calculations allow choosing development strategies for the regional economy development with a mono-branch focus depending on the relative importance of the selected criteria. Conclusions . The formulated provisions can be taken into account in the development of the strategy of the regional economy advanced development by enhancing innovative activity.

Anisotropic-Scale Junction Detection and Matching for Indoor Images.

Junctions play an important role in characterizing local geometrical structures of images, and the detection of which is a longstanding but challenging task. Existing junction detectors usually focus on identifying the location and orientations of junction branches while ignoring their scales, which, however, contain rich geometries of images. This paper presents a novel approach for junction detection and characterization, which especially exploits the locally anisotropic geometries of a junction and estimates its scales by relying on an a-contrario model. The output junctions are with anisotropic scales, saying that a scale parameter is associated with each branch of a junction and are thus named as anisotropic-scale junctions (ASJs). We then apply the new detected ASJs for matching indoor images, where there are dramatic changes of viewpoints and the detected local visual features, e.g., key-points, are usually insufficient and lack distinctive ability. We propose to use the anisotropic geometries of our junctions to improve the matching precision of indoor images. The matching results on sets of indoor images demonstrate that our approach achieves the state-of-the-art performance on indoor image matching.Junctions play an important role in characterizing local geometrical structures of images, and the detection of which is a longstanding but challenging task. Existing junction detectors usually focus on identifying the location and orientations of junction branches while ignoring their scales, which, however, contain rich geometries of images. This paper presents a novel approach for junction detection and characterization, which especially exploits the locally anisotropic geometries of a junction and estimates its scales by relying on an a-contrario model. The output junctions are with anisotropic scales, saying that a scale parameter is associated with each branch of a junction and are thus named as anisotropic-scale junctions (ASJs). We then apply the new detected ASJs for matching indoor images, where there are dramatic changes of viewpoints and the detected local visual features, e.g., key-points, are usually insufficient and lack distinctive ability. We propose to use the anisotropic geometries of our junctions to improve the matching precision of indoor images. The matching results on sets of indoor images demonstrate that our approach achieves the state-of-the-art performance on indoor image matching.

Takeoff orientation of the major aortic arch branches irrespective of arch type: Ramifications for brachiocephalic interventions including carotid stenting.

Background:Our previous work demonstrating great ease and predictability of cannulation of the major aortic arch branches with an upwardly pointing 3DR catheter, irrespective of aortic arch type, led us to hypothesize that centering or “cresting” of these vessels must occur along the superior most aspect of the aortic arch in a curvilinear fashion.Methods:We retrospectively analyzed 111 computed tomographic scans of the chest and thoracic aorta with intravenous contrast performed at our hospital between April 2011 and May 2012 utilizing TeraRecon image reconstruction software. Four studies were excluded due to poor image quality and/or surgical changes to native aortic architecture.Results:Of the 107 studies included, 104 (97.2%) demonstrated centering of the major aortic arch branches on a curvilinear line “cresting” the superior most aspect of the aortic arch irrespective of arch type. Of the three studies that did not demonstrate this “cresting,” two were found to have aberrant right subclavian arteries associated with a type I aortic arch, and one had an aberrant right common carotid associated with a type II aortic arch.Conclusion:Operators engaging major aortic arch branches need to be mindful of the fact that these vessels are indeed centered on a line “cresting” along the superior most aspect of the aortic arch, and any algorithm that, by taking this information into account, reduces catheter manipulation in the aortic arch could potentially result in a reduction in distal atheroembolic events.

Soil moisture estimation in Ferlo region (Senegal) using radar (ENVISAT/ASAR) and optical (SPOT/VEGETATION) data

The sensitivity of the radar signal to the seasonal dynamics in the Sahel region is a considerable asset for monitoring surface parameters including soil moisture. Given the sensitivity of the radar signal to vegetation mass production, roughness and soil moisture, the main problem has been to estimate the contribution of these three parameters to the signal. This study aims to circumvent this problem by combining radar with optical data. The DMP (Dry Mater Product) extracted from SPOT data allowed to estimate vegetation mass production. Surface roughness was estimated from radar data during the dry season. Because during the dry season, radar signal is only conditioned by soil roughness in this region a Radiative Transfer Model (RTM) was used: it consists in a microwave scattering model of layered vegetation based on the first-order solution of the radiative transfer equation and it accounts for multiple scattering within the canopy, surface roughness of the soil, and the interaction between canopy surface and soil.This model was designed to account for the branch size distribution, leaf orientation distribution, and branch orientation distribution for each size. In this study, the RTM has been calibrated with ESCAT (European Radar Satellite Scatterometer) data, and has been used in order to estimate soil moisture.The results obtained have allowed to track the spatial and temporal dynamics of soil moisture on the one hand, and on the other hand the influence of geology and morphopedology on the spatial dynamics of the soil moisture variability. These results are promising despite the fact that the inversed RTM often faces difficulties to interpret the signal for saturated soils, giving an aberrant value of soil moisture more often than not.

Open snake model based on global guidance field for embryo vessel location

The development of vessels can provide important information about the growth status of animal embryos. It is, therefore, important to automatically locate the deformed vessel branches from the embryo images. However, very few vessel detectors can accurately locate all vessel branches when the captured images are low quality and the implied vessel shapes are complex. In this study, a new framework consisting of vessel region extraction and snake shape optimisation is proposed. The main contribution in this detector is a novel open snake model based on the global guidance field and deformation template initialisation. Experimental results on a specific application of an embryo vessel database [Database and source codes: https://github.com/wcxie/Egg‐embryro‐vessel‐location/.] demonstrate that the proposed algorithm not only locates the vessel shape properly but also obtains the orientations of embryo vessel branches accurately. Comparison to traditional guidance fields and the active appearance model illustrates the effectiveness and competitiveness of the proposed model.

Structure and biocompatibility improvement mechanism of highly oriented poly(lactic acid) produced by solid die drawing

Highly oriented long-chain-branched poly(lactic acid) (LCB-PLA) was fabricated through solid die drawing technology for the purpose of further improving the mechanical properties and biocompatibility of PLA as bone fixation materials. Compared with neat PLA, higher draw ratio can be obtained for LCB-PLA during the drawing process, which led to the sharp increase of the mechanical properties of PLA samples. For LCB-PLA sample with 13.2 of draw ratio, the tensile strength and modulus reached up to 235.4MPa and 8.2GPa, respectively, which satisfied the requirement of the weight-bearing implant fixation. The MTT and ALP results suggested that the proliferation, differentiation and ALP activity of osteoblasts on the surface of PLA samples increased with draw ratio. In addition, cells with flat and extension morphology adhered and grew better, and the spreading area of cells on LCB-PLA samples was larger than that on PLA samples, which suggested that long chain branching and uniaxial orientation exhibited optimal role in promoting cell growth and maintaining their morphology. After orientation, due to the increase of crystallinity and CH3 content on the sample surface, the hydrophobicity increased, promoting the protein adsorption and thus the cell adhesion on it; moreover, cell adhered more stably on the CO enriched and grooved surfaces of the oriented samples, further improving the cell reproduction and aggregation.

Comparing structure and biomechanics of extant Carica papaya and Ochroma pyramidale stems allows re-evaluating the functional morphology of the fossil ‘seed fern’ Lyginopteris oldhamia

This study aims at assessing the mechanical importance of the conspicuous sclerenchymatous ‘Dictyoxylon’ cortex of the extinct gymnosperm Lyginopteris oldhamia by comparing the latter to the extant angiosperms Carica papaya and Ochroma pyramidale, both possessing a cortex composed of mechanically relevant wedges of phloem fibres. Our studies show that the anatomical structure of the cortex in L. oldhamia is very similar to C. papaya and O. pyramidale and that comparable variations occur in the cortex of L. oldhamia as found in C. papaya and O. pyramidale when reorienting oblique stems or branches. This similarity in (adaptable) anatomical structures leads to the conclusion that the cortex of L. oldhamia was also able to readjust the orientation of stem and branches as a reaction to mechanical stress, shown for C. papaya and O. pyramidale. This finding supports the hypothesis that L. oldhamia stems might well have been self-supporting in (very) young ontogenetic stages and became semi-self-supporting or climbing in older ontogenetic stages.

Detection of Anomalous Cervical Internal Carotid Artery Branches by Colour Duplex Ultrasound

Conventional anatomical descriptions of the cervical internal carotid artery (ICA) report that no branches arise from this segment. However reports of ICA branches exist. The study aim was to determine the prevalence of anomalous branches of the ICA using colour duplex ultrasound (CDU). Four hundred consecutive patients (800 carotid vessels) referred to a tertiary hospital vascular laboratory for investigation of carotid disease were included. A clear differentiation of a low resistive ICA and a high resistive external carotid artery (ECA) waveform was required. CDU was performed on a Philips IU22 ultrasound system with a 9-3MHz linear array transducer employing a standard carotid imaging protocol. The origin of each ICA branch was identified using B-mode and CDU. Anatomical orientation of ICA branches and distance from bifurcation was recorded and spectral CDU analysis was performed. Twenty ICA branches, tracking cephaladly, were detected in 16 patients (4%), or 2.5% (20/800) vessels. The median age was 73 years; 50% were female and 50% male. All patients demonstrated a single branch [unilateral anomaly (n=12 patients), bilateral anomaly (n=4) patients]. Eighty-five percent arose from the posterior wall of the ICA. The median distance from ICA bifurcation was 4mm (range 0-18mm). ICA branch diameters ranged from 1.2mm to 2.4mm (median 1.4mm, mean 1.6mm). Eighty percent of ICA branches had less than 50% stenosis. Spectral analysis revealed high resistive waveforms in all branches. Branches from the ICA exist and can be characterised with CDU. Prevalence in a tertiary hospital referral cohort is 4%. Given their potential clinical implications, standard carotid imaging protocols should consider routine assessment and reporting of ICA branches.

Origin of an extensive network of non-tectonic synclines in Eocene limestones of the Western Desert, Egypt

Satellite images of the Western Desert of Egypt display conspicuous sinuous color patterning that previous workers have interpreted as erosional flutes formed by catastrophic flooding. Our work with high resolution satellite imagery shows that the patterning is not erosional but, rather, the result of a network of thousands of narrow synclines in the Eocene bedrock capping the Limestone Plateau. Synclines form as isolated, 200-400 meter-wide downwarps in otherwise flat-lying strata. Limb dips are shallow, and doubly plunging hinges form multiple basin closures along syncline lengths. Anticlines form “accidentally” in inter-syncline areas where two adjacent synclines lie close together. Synclines have two dominant orientations, WNW-ESE and NNW-SSE, parallel to two prominent joint and fault sets, and synclines branch, merge, and change orientation along their lengths. Synclines are all at the same scale with neither larger structures nor parasitic structures and are best described as non-tectonic sag synclines. An Egypt-wide inventory reveals that these synclines are both confined to Eocene limestones and developed, albeit it sporadically, over nearly 100,000 km2. The syncline network predates plateau gravels of the Katkut Formation, which have been interpreted as Oligocene or early Miocene in age, and the network is cut by faults related to Western Desert extension associated with Red Sea rifting. The mechanism that caused sag of overlying layers is not clear. Modern karst collapse, subsurface dissolution of evaporites, and collapse of paleokarst are all unlikely mechanisms given the timing of formation and the underlying stratigraphy. Silica diagenesis and downslope mobilization of underlying shales are possibilities, although uncertainty about the origin of silica in the limestones, plus the consistency of syncline orientations over large areas, make these models problematic. Hypogene karst, perhaps related to aggressive fluids associated with basaltic intrusions, may be the model most consistent with the admittedly limited data we currently have for the network.

Reformulation and extension of the thrust network analysis

We address the Thrust Network Analysis (TNA), i.e. the methodology for modeling masonry vaults as a discrete network of forces in equilibrium with gravitational loads, first contributed by O’Dwyer and fully developed by Block and coworkers. Reducing the bias by the quoted authors in favor of a graphical interpretation of the method, we reformulate the original version of the TNA by discarding the dual grid and focusing only on the primal grid, thus significantly enhancing the computational performances. The proposed reformulation of the TNA is also extended by including horizontal forces in the analysis as well as holes or free edges in the vault. Furthermore, the coefficient matrices entering the solution scheme are obtained by assembling the separate contribution of each branch, thus avoiding the ad hoc node numbering and branch orientation required by alternative implementations. Numerical examples, some of which referred to vaults having a particularly complex geometry, show the effectiveness and robustness of the proposed approach in assessing the safety conditions of existing masonry vaults or in designing new ones.

Branch Suppression and Orientation Control of Langmuir–Blodgett Patterning on Prestructured Surfaces

Branch Suppression and Orientation Control of Langmuir–Blodgett Patterning on Prestructured Surfaces

The shear stess profile of the pivotal fenestrated endograft at the level of the renal branches: A computational study for complex aortic aneurysms.

This study investigated the impact of the variant angulations on the values and distribution of wall shear stress on the renal branches and the mating vessels of a pivotal fenestrated design. An idealized endograft model of two renal branches was computationally reconstructed with variable angulations of the left renal branch. These ranged from the 1:30' to 3:30' o'clock position, corresponding from 45° to 105° with increments of 15°. A fluid-structure-interaction analysis was performed to estimate the wall shear stress. The proximal part of the renal branch preserved quite constant wall shear stress. The transition zone between its distal end and the renal artery showed the highest values compared to the proximal and middle segments, ranging from 8.9 to 12.4 Pa. The lowest stress values presented at 90° whereas the highest at 45°. The post-mating arterial segment showed constantly low stress values regardless of the pivotal branch angle (6.3 to 6.6 Pa). The 45° configuration showed a distribution of the highest stress posteriorly whereas the 105°-angulation anteriorly. The variant horizontal branch orientation influences the wall shear stress distribution across its length and affects its values only at its transition with the mating vessel. These findings and their potential association with adverse effects deserve further clinical validation.

Student construction of phylogenetic trees in an introductory biology course

Phylogenetic trees have become increasingly essential across biology disciplines. Consequently, learning about phylogenetic trees has become an important component of biology education and an area of interest for biology education research. Construction tasks, in which students generate phylogenetic trees from some type of data, are often used for instruction. However, the impact of these exercises on student learning is uncertain, in part due to our fragmented knowledge of what students construct during the tasks. The goal of this project was to develop a more robust method for describing student-generated phylogenetic trees, which will support future investigations that attempt to link construction tasks with student learning. Through iterative examination of data from an introductory biology course, we developed a method for describing student-generated phylogenetic trees in terms of style, conventionality, and accuracy. Students used the diagonal style more often than the bracket style for construction tasks. The majority of phylogenetic trees were constructed conventionally, and variable orientation of branches was the most common unconventional feature. In addition, the majority of phylogenetic trees were generated correctly (no errors) or adequately (minor errors only) in terms of accuracy. Suggesting extant taxa are descended from other extant taxa was the most common major error, while empty branches and extra nodes were very common minor errors. The method we developed to describe student-constructed phylogenetic trees uncovered several trends that warrant further investigation. For example, while diagonal and bracket phylogenetic trees contain equivalent information, student preference for using the diagonal style could impact comprehension. In addition, despite a lack of explicit instruction, students generated phylogenetic trees that were largely conventional and accurate. Surprisingly, accuracy and conventionality were also dependent on each other. Our method for describing phylogenetic trees constructed by students is based on data from one introductory biology course at one institution, and the results are likely limited. We encourage researchers to use our method as a baseline for developing a more generalizable tool, which will support future investigations that attempt to link construction tasks with student learning.

Symmetry-Dependent Optical Properties of Stellated Nanocrystals

Stellated metal nanostructures are a class of plasmonic colloids in which large electric field enhancements can occur at their sharp tips, making them excellent candidates for surface-enhanced Raman spectroscopy (SERS) and surface-enhanced infrared spectroscopy (SE-IRS) platforms. Shape-dependent rules for convex polyhedra such as cubes, nanorods, or octahedra exist, which describe far-field scattering and near-field enhancements. However, such rules are lacking for their concave counterparts, which include stellated structures. Here, the optical response of stellated Au nanocrystals with Oh, D4h, D3h, C2v, and Td symmetry were modeled to systematically investigate the role of symmetry, branching, and particle orientation with respect to excitation source using finite difference time domain (FDTD) calculations. Furthermore, these results are compared to experimentally obtained localized surface plasmon bands determined by UV–visible (UV–vis) spectroscopy for ensembles of similarly shaped metallic nanostru...

Spatial structure and development of Paspalum vaginatum (Poaceae): an architectural approach

Paspalum vaginatum Sw. is a perennial grass originating from tropical and subtropical regions worldwide that plays important ecological and utilitarian roles such as dune stabilisation and erosion control, and is used as a lawn and forage plant. The vegetative morphology of shoots was studied using an architectural approach with the aim of identifying constant features that characterise the architectural unit of this species, describing its developmental dynamics, and exploring the morphological basis of its extraordinary plasticity and adaptability to multiple ecological conditions. Plants of two ecotypes were cultivated in pots outdoors during two consecutive summers, and axes of different branching order were marked for periodical observations. Leaf typology, orientation and position of branches and occurrence and position of reproductive axes were considered. The basic growth pattern arises as a result of extensive plagiotropic growth of axes up to fourth branching order, which initially behave as stolons but can become rhizomes insofar the soil cover increases. Orthotropic floriferous axes up to fifth order develop at the axils of stolons, which can form ‘daughter’ clumps by basal tillering. Despite quantitative differences, both ecotypes share similar architectural features. Architectural analysis provides the basis to predict space occupation dynamics under different environmental conditions of growth.

Influence of Canopy Architecture on Stemflow in Agroforestry Trees in Western Himalayas

Rainfall event on a tree can be partitioned into throughfall, interception loss and stemflow. In this study, stemflow was measured for 39 rainfall events in 5-year-old plantations of 3 trees each, belonging to Morus alba and Grewia optiva in Dehradun, India. Diameter of selected Morus and Grewia trees varies from 7 to 9.3 and 8.12 to 10 cm respectively, whereas height varies from 4 to 4.5 and 5.5 to 6.5 m respectively. The minimum and maximum rainfall events recorded during the study period were 1.01 and 121.70 mm per day respectively. When the rainfall magnitude was less than or equal to 50 mm and more than 50 mm, stemflow volume from Morus was approximately 2.72 and 1.85 fold higher respectively, compared to Grewia . Maximum stemflow volume recorded for Morus and Grewia was 48,065 and 30,633 ml with respect to rainfall magnitude of 109.58 and 121.70 mm respectively. The generation of higher stemflow volume in case of Morus is due to concave orientation of branches and leaves. Results showed that a significant amount of nutrients leached from Grewia and Morus through stemflow process.

Vectorization of line drawing image based on junction analysis

Converting a scanned or shot line drawing image into a vector graph can facilitate further edit and reuse, making it a hot research topic in computer animation and image processing. Besides avoiding noise influence, its main challenge is to preserve the topological structures of the original line drawings, such as line junctions, in the procedure of obtaining a smooth vector graph from a rough line drawing. In this paper, we propose a vectorization method of line drawings based on junction analysis, which retains the original structure unlike done by existing methods. We first combine central line tracking and contour tracking, which allows us to detect the encounter of line junctions when tracing a single path. Then, a junction analysis approach based on intensity polar mapping is proposed to compute the number and orientations of junction branches. Finally, we make use of bending degrees of contour paths to compute the smoothness between adjacent branches, which allows us to obtain the topological structures corresponding to the respective ones in the input image. We also introduce a correction mechanism for line tracking based on a quadratic surface fitting, which avoids accumulating errors of traditional line tracking and improves the robustness for vectorizing rough line drawings. We demonstrate the validity of our method through comparisons with existing methods, and a large amount of experiments on both professional and amateurish line drawing images.

Auxin levels and MAX1–4 and TAC1 gene expression in different growth habits of peach

Branch orientation and distribution determine tree architecture that can influence orchard design and management. Peach [Prunus persica L. (Batch)] trees with three different branching genotypes were evaluated: fewer, nearly vertical branches (pillar), less vertical and more spreading branches (upright), and more abundant, least vertical branches (standard). Auxin concentrations and expression of genes that regulate branch development in herbaceous species, MAX1, 2, 3, 4 and TAC1 were determined. Shoots and roots of peach trees in the field and greenhouse were studied following pruning and during periods of growth when bud break and branch spatial orientation develop. Expression of MAX3 and MAX4 decreased in stems of field-grown peach trees that remained on the tree following pruning. In the greenhouse elevated auxin concentrations and higher gene expression of MAX3 in roots and MAX4 in stems were found in pillar rather than standard trees. Upright trees had auxin and MAX1–4 expression that was intermediate between pillar and standard trees. Temporal differences were found with MAX1–4 expression being greater in April or May but auxin concentrations were greater only in shoots in May. Expression of TAC1 was inversely related with auxin concentrations in shoots and was greatest in standard and least in pillar trees. The current work indicates that in stems, auxin, MAX3–4 genes, and TAC1 genes may influence regulatory processes that affect growth and development of peach trees with different growth habits. In addition to breeding, new plant growth regulators that affect the modes of action of root-originating signals may provide new cultural tools for managing tree growth and development.

Numerical study of a cylinder model of the diffusion MRI signal for neuronal dendrite trees

We study numerically how the neuronal dendrite tree structure can affect the diffusion magnetic resonance imaging (dMRI) signal in brain tissue. For a large set of randomly generated dendrite trees, synthetic dMRI signals are computed and fitted to a cylinder model to estimate the effective longitudinal diffusivity DL in the direction of neurites. When the dendrite branches are short compared to the diffusion length, DL depends significantly on the ratio between the average branch length and the diffusion length. In turn, DL has very weak dependence on the distribution of branch lengths and orientations of a dendrite tree, and the number of branches per node. We conclude that the cylinder model which ignores the connectivity of the dendrite tree, can still be adapted to describe the apparent diffusion coefficient in brain tissue.