Suffix Tree Research Articles

Birch sap exudation: influence of tree position in a forest stand on birch sap production, trunk wood anatomy and radial bending strength

It is commonly accepted that the period of early-spring xylem sap exudation marks a stage during which a positive pressure builds inside the tree trunks. This state changes when leaves appear, initiating water transport within the trunk. It is unknown, however, how the wood anatomical structure and its mechanical resistance influences the sap. We present the results of research on the relationship between exudation of sap from Roth trees from the interior of a forest stand and from its edge, and the anatomical structure of the trunk wood and its bending strength. During the period between March 21 and April 18, we performed five sets of measurements of sap exudation from trees at the edge of the stand and from the forest interior. The resulting radial wood samples were tested for bending strength using a fractometer. We tested the sap for electrolytic conductivity and sugars content. For the anatomical analysis of the wood, we determined the number of vessels per 1 mm, average vessel lumen area and potential conductivity index. We found that the trees along the edge of the stand exude more sap, but it is less concentrated than the sap from the trees from the interior. Bending strength perpendicular to wood fibres is higher in the trees from the stand edge and in the western side of the trunk, where the number of vessels per 1 mm2 and conductivity index are smaller. Seemingly, this is the result of western winds, which are dominant in Poland.Betula pendula2

Data collection methods for forest inventory: a comparison between an integrated conventional equipment and terrestrial laser scanning

This study aims to present a comparison analysis of two data collection methods that can be used in order to obtain reference ground truth data for forestry – a conventional method that uses specific equipment such as Field Map system, caliper and vertex inclinometer and a modern method based on terrestrial laser scanning (TLS) technology. The research was conducted in six circular Permanent Plots (PPs) with an area of 500 square meters each, within thinning and selected cuttings stands of sessile oak (Quercus petraea (Matt.) Liebl.), common beech (Fagus sylvatica L.) and Norway spruce (Picea abies L. Karst.), all situated in the Southern Carpathians (Mihaești, Mușeteși and Vidraru Forest Districts). Using the conventional method, the dendrometric tree characteristics such as height, diameter at breast height (dbh) and tree position were directly recorded in the field. As a modern method for data collection, a Faro Focus3D X 130 HDR terrestrial laser scanning device was used to scan each plot and to extract the dbh and height of the trees. In this regard, two scanning approaches were used - single scan (SS) and multiple scan (MS). In order to compare the two data acquisitions methods, we applied a Strengths, Weaknesses, Opportunities, Threats (SWOT) analysis on the basis of which we could establish the pros and cons of using the two methods. Therefore, one can choose the most advantageous method for obtaining the reference data for forestry, in terms of equipment acquisition cost, personnel skills and qualifications, data collection working time, accuracy of the data recorded, post processing time, labor costs. Although the use of TLS in forest inventory is a technology with high potential, further investigations need to be done, especially in the case of automatic extraction of the tree height. For accurate reference ground data for forest inventory purposes, we still recommend using the conventional methods although they are time consuming.

Effect of forest structure on stand productivity in Central European forests depends on developmental stage and tree species diversity

Recently, many studies have found positive biodiversity–productivity relationships in forests. In contrast, different types of correlations have been identified in the analyses of tree diversity–structure–productivity relationships. We suspect that these conflicting conclusions might result from the different developmental stages of the investigated forest stands. We therefore analyzed the development of tree diversity–structure–productivity relationships at the stand level and individual tree level in 192 long-term experimental plots in Central Europe. As a measure of stand productivity, we analyzed stand volume growth (m3 ha−1 year−1). Tree species diversity was quantified by the Shannon index and structural heterogeneity was represented by the Gini coefficient of basal area. For a more detailed analysis at the tree level using a smaller portion of the dataset, the tree position–dependent indices, diameter differentiation index, and aggregation index were used. Whether the effect of structural heterogeneity on stand productivity was positive or negative depended on the stand development stage. In early developmental stages, high structural heterogeneity lowered productivity. In later developmental stages, however, stand structural heterogeneity had a positive effect on productivity. Our study might provide insights regarding the mechanisms underlying the contradictory findings obtained in recent studies dealing with tree diversity–structure–productivity relationships. This knowledge is vital for the adaptation of forest management to meet future demands on forest ecosystems.

Marker-free coregistration of UAV and backpack LiDAR point clouds in forested areas

Unmanned aerial vehicle Laser Scanning (ULS) and Backpack Laser Scanning (BLS) are two emerging mobile mapping technologies applicable for monitoring forested environments in unprecedented detail from complementary perspectives. Although ground-based backpack techniques provide detailed information about the forest understory and terrain, the measured point clouds based on SLAM techniques are stitched together gradually and normally expressed in a less-accurate arbitrary coordinate system. Conversely, ULS point clouds are acquired from above and usually georeferenced, yet the point density and penetrability near the ground may still suffer from dense overstory despite the low attitude operation. Coregistering the ground and aerial point clouds in the ULS coordinate system therefore provides a method for fusing understory and overstory information at single tree level without the time consuming procedure of applying ground control points. Since the ULS and BLS acquisition viewpoints differ greatly, standard coregistration methods requiring 3D point-level correspondences are likely to fail. This paper presents an object-level coregistration approach which instead operates on two sets of tree positions, with the goal of finding the optimal 3D transformation (consisting of rotation, translation and scaling) between the respective coordinate systems. The entire task is decomposed into separate problems of computing the common Z axis, estimating the scale, and 2D coregistration. In contrast to existing methods, our approach does not require additional information such as tree diameters or heights. We evaluated our method on real test plots involving diverse stem densities and tree species situated in forest farm of the eastern coastal region of Jiangsu, China. The tree positions for ground and aerial data were obtained respectively by cylinder fitting and tree segmentation. On 3 coniferous (dawn redwood) plots, 46–81% trees were matched with a distance below 50 cm, and mean position deviation of 27–36 cm. For 4 broadleaf (poplar) plots, no more than 50% trees were matched below a 1 m threshold and mean error of 54–67 cm, which can be attributed to the broadleaf trees’ more irregular shape and lack of a well defined tree top. Moreover, we show that the introduction of scaling into the transform can increase the matched tree count by up to 20 percentage points and decrease the mean matched distance by up to 13% compared to a strictly rigid transform.

Pollen flow and paternity in an isolated and non-isolated black walnut (Juglans nigra L.) timber seed orchard.

Artificial pollination of black walnut (Juglans nigra L.) is not practical and timber breeders have historically utilized only open-pollinated half-sib families. An alternate approach called “breeding without breeding,” consists of genotyping open-pollinated progeny using DNA markers to identify paternal parents and then constructing full-sib families. In 2014, we used 12 SSR markers to genotype 884 open-pollinated half-sib progeny harvested from two clonal orchards containing 206 trees, comprised of 52 elite timber selections. Seed was harvested in 2011 from each of two ramets of 23 clones, one upwind and one downwind, based on prevailing wind direction from the west—southwest. One orchard was isolated from wild black walnut and composed of forward selections while the other orchard was adjacent to a natural forest containing mature black walnut composed of backward selections. Isolation significantly increased within-orchard pollination (85%) of the progeny from the isolated orchard compared to 42% from the non-isolated orchard. Neither prevailing wind direction nor seed tree position in the orchard affected paternity patterns or wild pollen contamination. Genetic diversity indices revealed that progeny from both orchards were in Hardy–Weinberg equilibrium with very little inbreeding and no selfing. A significant level of inbreeding was present among the forward selected parents, but not the first generation (backward selected) parents. Some orchard clones failed to sire any progeny while other clones pollinated upwards of 20% of progeny.

Canopy attachment position influences metabolism and peel constituency of European pear fruit

BackgroundInconsistent pear fruit ripening resulting from variable harvest maturity within tree canopies can contribute to postharvest losses through senescence and spoilage that would otherwise be effectively managed using crop protectant and storage regimes. Because those inconsistencies are likely based on metabolic differences, non-targeted metabolic profiling peel of ‘d’Anjou’ pears harvested from the external or internal canopy was used to determine the breadth of difference and link metabolites with canopy position during long-term controlled atmosphere storage.ResultsDifferences were widespread, encompassing everything from expected distinctions in flavonol glycoside levels between peel of fruit from external and internal canopy positions to increased aroma volatile production and sucrose hydrolysis with ripening. Some of the most substantial differences were in levels of triterpene and phenolic peel cuticle components among which acyl esters of ursolic acid and fatty acyl esters of p-coumaryl alcohol were higher in the cuticle of fruit from external tree positions, and acyl esters of α-amyrin were elevated in peel of fruit from internal positions. Possibly the most substantial dissimilarities were those that were directly related to fruit quality. Phytosterol conjugates and sesquiterpenes related to elevated superficial scald risk were higher in pears from external positions which were to be potentially rendered unmarketable by superficial scald. Other metabolites associated with fruit aroma and flavor became more prevalent in external fruit peel as ripening progressed and, likewise, with differential soluble solids and ethylene levels, suggesting the final product not only ripens differentially but the final fruit quality following ripening is actually different based on the tree position.ConclusionsGiven the impact tree position appears to have on the most intrinsic aspects of ripening and quality, every supply chain management strategy would likely lead to diverse storage outcomes among fruit from most orchards, especially those with large canopies. Metabolites consistently associated with peel of fruit from a particular canopy position may provide targets for non-destructive pre-storage sorting used to reduce losses contributed by this inconsistency.

Bidirectional Variable-Order de Bruijn Graphs

Compressed suffix trees and bidirectional FM-indexes can store a set of strings and support queries that let us explore the set of substrings they contain, adding and deleting characters on both the left and right, but they can use much more space than a de Bruijn graph for the strings. Bowe et al.’s BWT-based de Bruijn graph representation (Proc. Workshop on Algorithms for Bioinformatics, pp. 225–235, 2012) can be made bidirectional as well, at the cost of increasing its space usage by a small constant, but it fixes the length of the substrings. Boucher et al. (Proc. Data Compression Conference, pp. 383–392, 2015) generalized Bowe et al.’s representation to support queries about variable-length substrings, but at the cost of bidirectionality. In this paper we show how to make Boucher et al.’s variable-order implementation of de Bruijn graphs bidirectional.

Slenderness of pedunculate oak (Quercus robur L.) according to biosocial position

The paper presents results of an analysis of pedunculate oak slenderness. The dependence between slenderness of the oak tree and dimensions of the trunk and the crown dimensions of a single tree were examined. The biosocial position of each tree was determined based on the Kraft’s classification criteria. Following dimensions were measured for each tree: height, height of base of live crown, crown radius, diameter at breast height. The following crown parameters related to the growth space of a single tree were determined: crown length, crown width, crown projection area, space of a single tree, Seebach’s growth space number, crown projection area to basal area ratio, crown spread. Based on the obtained results, the following was found: biosocial position of the oak tree in vertical structure of the stand has significant impact on the size of the tree slenderness; the slenderness increases with deterioration of the biosocial position of the tree, but it decreases with the increase in the value of the tree’s measurement characteristics and the measures of its crown.

Estimating Tree Position, Diameter at Breast Height, and Tree Height in Real-Time Using a Mobile Phone with RGB-D SLAM

Accurate estimation of tree position, diameter at breast height (DBH), and tree height measurements is an important task in forest inventory. Mobile Laser Scanning (MLS) is an important solution. However, the poor global navigation satellite system (GNSS) coverage under the canopy makes the MLS system unable to provide globally-consistent point cloud data, and thus, it cannot accurately estimate the forest attributes. SLAM could be an alternative for solutions dependent on GNSS. In this paper, a mobile phone with RGB-D SLAM was used to estimate tree position, DBH, and tree height in real-time. The main aims of this paper include (1) designing an algorithm to estimate the DBH and position of the tree using the point cloud from the time-of-flight (TOF) camera and camera pose; (2) designing an algorithm to measure tree height using the perspective projection principle of a camera and the camera pose; and (3) showing the measurement results to the observer using augmented reality (AR) technology to allow the observer to intuitively judge the accuracy of the measurement results and re-estimate the measurement results if needed. The device was tested in nine square plots with 12 m sides. The tree position estimations were unbiased and had a root mean square error (RMSE) of 0.12 m in both the x-axis and y-axis directions; the DBH estimations had a 0.33 cm (1.78%) BIAS and a 1.26 cm (6.39%) root mean square error (RMSE); the tree height estimations had a 0.15 m (1.08%) BIAS and a 1.11 m (7.43%) RMSE. The results showed that the mobile phone with RGB-D SLAM is a potential tool for obtaining accurate measurements of tree position, DBH, and tree height.

Multi-pattern matching with variable-length wildcards using suffix tree

Multi-pattern matching with variable-length wildcards using suffix tree

Influence of toposequence position of Stryphnodendron adstringens trees on discrimination of samples based on spectroscopy

Influence of toposequence position of Stryphnodendron adstringens trees on discrimination of samples based on spectroscopy

Multi-pattern matching with variable-length wildcards using suffix tree

Multi-pattern matching with variable-length wildcards is an interesting and important problem in bioinformatics, information retrieval and other domains. Most of the previously developed multi-pattern matching methods, such as famous Aho–Corasick and Wu–Manber algorithms, aimed to solve some classical string matching problems. However, these algorithms are not efficient for patterns with flexible wildcards or do-not-care characters. In this paper, we propose two efficient algorithms for multi-pattern matching with variable-length wildcards based on suffix tree, called MMST-L and MMST-S, according to the length of exact characters in a pattern. Experimental results show that the two MMST algorithms, in most cases, outperform other various versions of comparing algorithms.

On overabundant words and their application to biological sequence analysis

The observed frequency of the longest proper prefix, the longest proper suffix, and the longest infix of a word w in a given sequence x can be used for classifying w as avoided or overabundant. The definitions used for the expectation and deviation of w in this statistical model were described and biologically justified by Brendel et al. (1986) [1]. We have very recently introduced a time-optimal algorithm for computing all avoided words of a given sequence over an integer alphabet (2017) [2]. In this article, we extend this study by presenting an O(n)-time and O(n)-space algorithm for computing all overabundant words in a sequence x of length n over an integer alphabet. Our main result is based on a new non-trivial combinatorial property of the suffix tree T of x: the number of distinct factors of x whose longest infix is the label of an explicit node of T is no more than 3n−4. We further show that the presented algorithm is time-optimal by proving that O(n) is a tight upper bound for the number of overabundant words. Finally, we present experimental results, using both synthetic and real data, which justify the effectiveness and efficiency of our approach in practical terms.

INTEGRATION OF TREE DATABASE DERIVED FROM SATELLITE IMAGERY AND LIDAR POINT CLOUD DATA

Abstract. 3D tree database provides essential information of tree species abundance, spatial distribution and tree height for forest mapping, sustainable urban planning and 3D city modelling. Fusion of passive optical satellite imagery and active Lidar data can potentially be exploited for operational forest inventory. However, such fusion requires very high geometric accuracy for both data sets. This paper proposes an approach for 3D tree information extracted from passive and active data integrating into existing tree database by effectively using geometric information of satellite camera model and laser scanner scanning geometry. The paper also presents the individual methods for tree crown identification and delineation from satellite images and lidar point cloud data respectively, the geometric correction of tree position from tree top to tree base. The ground truth accuracy assessment for the tree extracted is also present.

Creating improvisations on chord progressions using suffix trees

Technology nowadays takes an increasing part of “creativity” in live music software such as the OMax-ImproteK-Djazz improvisation environment. Specifically, Djazz implements techniques for indexing and creating improvisations using a given chord progression. It relies on a database that we call a dictionary, storing musical sequences (audio or MIDI) associated with known chord changes. We define an improvisation on a given chord progression x as a sequence obtained by concatenating musical phrases identified with factors of x that can be found in the dictionary. Given a query sequence x and a dictionary D, we present an algorithm that finds an improvisation on x with respect to D. We use the suffix tree data structure to index D and then produce a graph formulation of the problem in order to find a suitable improvisation in linear time, with respect to the length of x.

Growth strain in straight and inclined Populus × euramericana cv. ‘74/76’ trees, and its relationship with selected wood properties

Growth stress is important to achieve upright growth and avoid exterior influence on living trees. However, many problems are also triggered by the release of growth stress during wood processing, such as end split of log, distortion of board and inaccurate sawing. In order to evaluate the possibility of these problems to occur in poplar clone 107, a new breeding poplar clone in China, surface longitudinal growth strain (SLGS) and internal longitudinal growth strain (ILGS) both of straight and inclined trees were measured for depicting distributing patterns of growth strain both in peripheral and radial directions. Besides that, according to one-way ANOVA analysis, individual tree and peripheral position have a significant effect on SLGS in inclined trees, whereas such effect is insignificant in straight trees. Fiber morphology and shrinkage of wood sample beneath the SLGS testing positions were determined to illustrate the relationships between these properties with SLGS. The results suggested that growth stress is a poor indicator of fiber morphology and wood shrinkage properties for straight trees but a good one for inclined trees. Both the positive SLGS and ILGS are unexpectedly found at the opposite wood side of inclined trees. It is speculated that when the reorientation of inclined trees is insufficiently supported by exerting tensile stress at tension wood side, compressive stress will be formed at the opposite wood side as a complement.

Finding Parallel Passages in Cultural Heritage Archives

It is of great interest to researchers and scholars in many disciplines (particularly those working on cultural heritage projects) to study parallel passages (i.e., identical or similar pieces of text describing the same thing) in digital text archives. Although there exist a few software tools for this purpose, they are restricted to a specific domain (e.g., the Bible) or a specific language (e.g., Hebrew). In this article, we present in detail how we build a digital infrastructure that can facilitate the search and discovery of parallel passages for any domain in any language. It is at the core of our Samtla (Search And Mining Tools with Linguistic Analysis) system designed in collaboration with historians and linguists. The system has already been used to support research on five large text corpora that span a number of different domains and languages. The key to such a domain-independent and language-independent digital infrastructure is a novel combination of a character-based n -gram language model, space-optimized suffix tree, and generalized edit distance. A comprehensive evaluation through crowdsourcing shows that the effectiveness of our system’s search functionality is on par with the human-level performance.

Conifer Regeneration After Experimental Shelterwood and Seed-Tree Treatments in Boreal Forests: Finding Silvicultural Alternatives.

Forest regeneration is a key element in achieving sustainable forest management. Partial harvest methods have been used extensively in temperate broadleaf and mixedwood ecosystems to promote regeneration on poorly stocked sites and to maintain forest composition and productivity. However, their effectiveness in promoting conifer establishment has yet to be demonstrated in unmanaged boreal forests, especially those dominated by black spruce (Picea mariana (Mill.) BSP) where constraints for regeneration differ from those found in more meridional regions. We aimed to evaluate conifer seedling density and dimensions, 10 years after the onset of a gradient of silvicultural treatments varying in harvesting intensities, and to identify the critical factors driving the regeneration process. Study blocks of even-aged black spruce stands in the eastern Canadian boreal forest were submitted to three variants of shelterwood harvesting: a seed-tree harvest, a clear-cut and an untreated control. Shelterwood and seed-tree harvesting were combined with spot scarification to promote regeneration. Shelterwood and seed-tree harvesting produced a density of conifer regeneration sufficient to maintain forest productivity, but they did not promote seedling growth. Black spruce was the predominant species in terms of regeneration density, with proportions 3–5× higher than that for balsam fir (Abies balsamea (L.) Mill.). Ten years after treatment, seed-origin black spruce seedlings were abundant in skidding trails, while layers dominated the residual strips. Balsam fir density was not influenced by treatment nor by tree position relative to skidding trails. Balsam fir and black spruce had different responses to treatment in terms of height and diameter, the former exhibiting a better growth performance and larger diameter in the residual strips. Spot scarification created micro-sites that had a significant impact on the regeneration process. Overall, our results support that shelterwood and seed-tree harvesting combined with scarification enable adequate regeneration in black spruce stands, confirming these treatments as viable silvicultural alternatives to clear-cutting when required by sustainable forest management objectives.

Extraction of Sample Plot Parameters from 3D Point Cloud Reconstruction Based on Combined RTK and CCD Continuous Photography

Enriching forest resource inventory is important to ensure the sustainable management of forest ecosystems. Obtaining forest inventory data from the field has always been difficult, laborious, time consuming, and expensive. Advances in integrating photogrammetry and computer vision have helped researchers develop some numeric algorithms and methods that can turn 2D (images) into 3D (point clouds) and are highly applicable to forestry. This paper aimed to develop a new, highly accurate methodology that extracts sample plot parameters based on continuous terrestrial photogrammetry. For this purpose, we designed and implemented a terrestrial observation instrument combining real-time kinematic (RTK) and charge-coupled device (CCD) continuous photography. Then, according to the set observation plan, three independent experimental plots were continuously photographed and the 3D point cloud of the plot was generated. From this 3D point cloud, the tree position coordinates, tree DBHs, tree heights, and other plot characteristics of the forest were extracted. The plot characteristics obtained from the 3D point cloud were compared with the measurement data obtained from the field to check the accuracy of our methodology. We obtained the position coordinates of the trees with the positioning accuracy (RMSE) of 0.162 m to 0.201 m. The relative root mean square error (rRMSE) of the trunk diameter measurements was 3.07% to 4.51%, which met the accuracy requirements of traditional forestry surveys. The hypsometrical measurements were due to the occlusion of the forest canopy and the estimated rRMSE was 11.26% to 11.91%, which is still good reference data. Furthermore, these image-based point cloud data also have portable observation instruments, low data collection costs, high field measurement efficiency, automatic data processing, and they can directly extract tree geographic location information, which may be interesting and important for certain applications such as the protection of registered famous trees. For forest inventory, continuous terrestrial photogrammetry with its unique advantages is a solution that deserves future attention in the field of tree detection and ecological construction.

New molecular sequences for two genera of marine planarians facilitate determination of their position in the phylogenetic tree, with new records for two species (Platyhelminthes, Tricladida, Maricola)

For the first time, molecular sequences of the 18S ribosomal DNA were generated for representatives of the genera Obrimoposthia Sluys & Ball, 1989 and Paucumara Sluys, 1989 of the suborder of the marine triclads, or Maricola, by analyzing the species Obrimoposthiawandeli (Hallez, 1906) and Paucumaratrigonocephala (Ijima & Kaburaki, 1916). On the basis of this molecular data the phylogenetic position of these two genera in the phylogenetic tree of the Maricola was determined and compared with their position in the phylogeny based on the analysis of anatomical features. New records for these two species are documented and their taxonomic status is determined on the basis of histological studies.