Many types of banana (Musa spp.)—one of the most economically important horticultural crops—exist, and their ploidy (diploid, triploid, and tetraploid, usually) and genome types (containing A or/and B genome in most cases) differ. At present, observation and genome type detection are commonly used to identify banana germplasm resources. However, the former is tedious, while the latter cannot distinguish categories below genome types. It is therefore urgent that a simple and effective method for identifying banana germplasm resources is established. We sequenced and analyzed the ribosomal DNA internal transcribed spacer (ITS) sequences of 62 banana germplasm and found that the sequencing peaks, especially the 20 bp region near the 420 bp position (referred to as the “420 bp region”), exhibited relatively recognizable and repeatable polymorphism characteristics. Using the “420 bp region” as a marker, we were able to quickly distinguish bananas belonging to different genome type groups (comprising the AA, AB, AAA, ABB, AAB, ABBB, AAAB, and AAAA groups) or different subgroups in the same genome type group (for example, the Cavendish, Gros Michel, Red, Lakatan, and Ibota Bota subgroups in the AAA group; and the Pisang Raja, Plantain, Pome and Silk subgroups in the AAB group). Moreover, it appeared that Sanger sequencing of ITS could be used for identifying banana hybrid offspring. These results demonstrated that the banana ITS region contains rich genetic information that is useful for genotyping. In general, ITS sequencing simplifies the classification of banana germplasm resources and has potential application in several areas of Musa improvement.

This study was designed for the first time to improve phenolic yield and antioxidant activity of ultrasonic-assisted extraction from Acer truncatum leaves (ATL) using response surface methodology, and phenolic composition in ATL extracted under the optimized condition were characterized by UPLC-QTOF-MS/MS. Solvent and extraction time were selected based on preliminary experiments, and a four-factors-three-levels central composite design was conducted to optimize solvent concentration (X₁), material-to-liquid ratio (X₂), ultrasonic temperature (X₃) and power (X₄) for an optimal total phenol yield (Y₁) and DPPH• antioxidant activity (Y₂). The results showed that the optimal combination was ethanol: water (v:v) 66.21%, material-to-liquid ratio 1:15.31 g/mL, ultrasonic temperature 60 °C, power 267.30 W, and time 30 min with three extractions, giving a maximal total phenol yield of 7593.62 mg gallic acid equivalent /100 g d.w. and a maximal DPPH• antioxidant activity of 74241.61 μmol Trolox equivalent/100 g d.w.. Furthermore, 22 phenolics were first identified in ATL extract obtained under the optimized conditions, indicating that gallates, gallotannins, quercetin, myricetin and chlorogenic acid derivatives were the main phenolic composition in ATL. What’s more, a gallotannins pathway existing in ATL from gallic acid to penta-O-galloyl-glucoside was interpreted. All these results provided practical information aiming at full utilization of phenolics in ATL, together with fundamental knowledge for further research.

Understanding morphological and genetic diversity of forest trees is essential to facilitate their conservation, sustainable management and genetic improvement for addressing the economic and environmental demands and challenges. We have examined variation in morphometric seed and pod traits and seed germination of multipurpose and widely distributed forest tree Albizia lebbek (Indian siris) from 12 provenances covering the species’ range in northern India and its relationships with bioclimatic factors. Highly significant inter-provenance variation was observed in seed size (seed length (SL), seed width (SW), SW/SL, SL×SW), seed mass (1000 seed weight), pod size (pod length (PL), pod width (PW), PW/PL), seed germination, number of seeds per pod, and insect infected seeds (IIS). The provenance effect contributed a major portion to the total phenotypic variance. Morphometric variation in all traits except for IIS was not clinal related to longitude, latitude, altitude or rainfall. There was an indication of the presence of ecotypic variation. IIS showed clinal variation with significant negative correlation with latitude. Most seed size and pod size traits showed positive correlations with several temperature bioclimatic factors and negative correlations with several precipitation bioclimatic factors. Our results have significance for genetic improvement, population genetics and genomics studies and conservation and sustainable management of A. lebbek genetic resources.

In Tunisia, olive is the most cultivated fruit crop while in the north where rainfall exceeded 400mm.year-1, the olive growing area is in widely extension in marginal soil with high slope gradient. Thus, the inclusion of cover crops is a sustainable solution to increase the ecosystem productivity, improve the soil fertility and oil yields. But, in Tunisia a few study were investigated the effect of legumes cover crop on the olive productivity. Therefore, the aim of this study was to evaluate the short-term (two cropping seasons s 2021 and 2022) effects of different seeded cover crops and soil management practices on the cover crops and soil characteristics, as well as enzymes activities and related microbial diversity. Six intercropping were tested in rainfed olive orchards (cv.Chétoui): Spontaneous vegetation (Spont), Wheat, Vetch, Oat, Fenugreek, mixture Vetch-Oat and compared to control (3 periodic tillage/year without intercropping). During the first cropping season, cover crops were cut as animal feed and only residues were incorporated into the soil. While, during the second year, all cover crops biomass were incorporated into the soil. Results indicate that the dry biomass and carbon uptake were significantly higher in grasses species (Wheat and Oat). But, highest level of nitrogen was found in Fenugreek cover crops. As compared to control, all cover crops including spontaneous vegetation increased soil organic matter and macronutrient level, mainly phosphorus. The most activity of β-glucosidase, phosphatase and arysulphatase was found in the cover crops plot of wheat and oat. In addition, this study improve that the utilization of the carbon sources was dominated by amides, amine and amino-acids in the fenugreek plot; while it was dominated by polymers and carboxylic acids in the case of wheat and oat.

A new pterygosomatid mite species, Neopterygosoma robertmertensi sp. n. (Acariformes: Pterygosomatidae) was collected from two specimens of Liolaemus robertmertensi (Liolaemidae) from Argentina. This new species is described based on active stages: adults (female and male) and juveniles (deutonymphs, protonymphs, larvae), and quiescent stages (nymphchrysalis, deutochrysalis and imagochrysalis). The changes in morphological characters during the ontogeny of N. robertmertensi have been analyzed in detail. A difference in larval sex morphology was observed for the first time in the family Pterygosomatidae (female larvae differ from male larvae by the shape and size of the idiosoma and position of the genital area). This new mite species is most similar to N. cyanogasteri but can be distinguished by the presence of different leg chaetotaxy patterns of genua IV and femora IV, four to six genital setae, three to five dorsomedial setae and two to three ventromedial setae. Phylogenetic analysis was conducted based on 120 morphological characters of all Neopterygosoma spp. and four outgroup species using the maximum parsimony approach. The results indicated that this species is nested within mites of the chilensis group of Neopterygosoma associated with host species of the section chiliensis of Liolaemus s. str. An updated diagnosis of the chilensis group of Neopterygosoma and an identification key for all species of this genus has been provided.

Molecular markers, including Simple Sequence Repeat (SSR), Single Nucleotide Polymorphism (SNP), and Intron Length Polymorphism (ILP), are widely utilized in crop improvement and population genetics studies. However, these marker resources remain insufficient for Musa species. In this study, we developed genome-wide SSR, SNP, and ILP markers from Musa and its sister species, creating a comprehensive molecular marker repository for the improvement of Musa species. This database contains 2115474 SSR, 63588 SNP, and 91547 ILP markers developed from thirteen Musa species and two of its relative species. We found that 77% of the SSR loci are suitable for marker development; 38% of SNP markers originated from the genic region, and transition mutations (C↔T; A↔G) were more frequent than transversion. The database is freely accessible and follows a ‘three-tier architecture,’ organizing marker information in MySQL tables. It has a user-friendly interface, written in JavaScript, PHP, and HTML code. Users can employ flexible search parameters, including marker location in the chromosome, transferability, polymorphism, and functional annotation, among others. These distinctive features distinguish the Musa Marker Database (MMdb) from existing marker databases by offering a novel approach that is tailored to the precise needs of the Musa research community. Despite being an in silico method, searching for markers based on various attributes holds promise for Musa research. These markers serve various purposes, including germplasm characterization, gene discovery, population structure analysis, and QTL mapping.

The theory of water transport in trees, according to which the main driving force of water movement is the suction created by the evaporation of water by the meniscus (the curved surface of the capillary liquid column) on the evaporating elements, supported from below by root pressure, is flawed. The capillary effect in nature is around one meter. In the case of open-air gaps, the leaf cannot suck in the water against gravity because, in this case, the plant would not be sucking in water, but air through the open-air gap. If not, how do trees transport water? When evaporation occurs, there is no suction towards the canopy, but pressure is due to a reduction in the cross-section of the water pipe caused by heat loss through evaporation. At night, when evaporation stops, a thermal equilibration process is triggered, which restores the original cross-section of the pipe. This generates suction and draws water from the soil. As the hydrostatic pressure in the pipe is high for tall trees, the pipe is cut off. To prove my theory, I have given several examples. Water transport is not based on physical mechanical laws alone. There may be complex physiological, biochemical, and biophysical processes behind the operation of the pipe system.

Spodoptera frugiperda (J.E. Smith) is a global agricultural pest that poses a threat to crop production, characterized by its refractory polyphagous nature that makes it difficult to control and may lead to damage to woody plants. However, research on its adaptability to woody plants remains limited. This study compares the feeding adaptations (survival rate, pupation time, pupation rate, weight, length, and feeding volume), protective enzyme activities, and feeding preferences of S. frugiperda on leaves of six economically significant tree species (Areca catechu, Aquilaria sinensis, Cocos nucifera, Camellia oleifera, Dalbergia odorifera and Hevea brasiliensis) and maize as a control treatment. The results indicate that A. sinensis as the most vulnerable trees in high risk, H. brasiliensis and C. nucifera presented varying degrees of susceptibility, A. catechu, C. oleifera, and D. odorifera were unsuitability for S. frugiperda. In conclusion, this report extensively explores the feeding effects of S. frugiperda on six economically important tree species, and provides insights into the feeding preferences on these plants, thereby informing the potential threat posed by S. frugiperda to economically vital trees.

A key step in the study of tree pathology is the identification of appropriate method for inoculating pathogens of diseases in branch and trunk. Pathogens of diseases in branch and trunk are commonly inoculated through punching, burning, and toothpick inoculation. However, there is a lack of comparative analysis of the inoculation outcomes of these three methods. In this work, Six‐year‐old P. alba var. pyramidalis were inoculated with V. sordida, using punching, burning, and toothpick techniques, respectively, to investigate the differences in the effectiveness of these inoculation methods. Results reveal that the incidence rate was 93.55% in the toothpick inoculation group, significantly higher than 80.65% in the burning inoculation group (p = 0.007), while punching inoculation exhibited significant pathological responses in the early stages, with spontaneous healing in the later stage. Addi-tionally, toothpick inoculation was more efficient in inducing Valsa canker when inoculating the pathogen at the bottom of the tree, with lower intra‐ and inter‐row spacing (stand density) providing better outcomes than higher intra‐ and inter‐row spacing. The results of this study demonstrate that toothpick inoculation is an optimal option for studying the artificial inoculation of V. sordida in six‐year‐old P. alba var. pyramidalis, providing technical support for research on poplar diseases and offering a theoretical basis for the inoculation of other diseases in branch and trunk.

Precise individual tree or sample-based inventories derived from 3D point cloud data of mobile laser scanning can improve our comprehensive understanding of the structure, function, resilience, biodiversity, and ecosystem services of urban forests. This study assessed the performance of a hand-held laser scanning system for the extraction of tree position, diameter at breast height (DBH) and tree height (H) in an urban area. A total of 2083 trees of 13 species from 34 plots were analyzed. The results showed that the registration of tree positions using ground control points (GCPs) demonstrated high accuracy, with errors consistently below 0.4 m, except for a few instances. The extraction accuracy of DBH for all trees and individual species remained consistently high, with a total root mean square error (RMSE) of 2.06 cm (6.89%) and a bias of 0.62 cm (2.07%). Notably, broad-leaved trees outperformed coniferous trees, with RMSE and bias values of 1.86 cm (6%) and 0.76 cm (2.46%) compared to 2.54 cm (9.46%) and 0.23 cm (0.84%). Tree height extraction accuracy varied significantly among different species, with R2 values ranging from 0.65 to 0.92. Generally, both DBH and height were underestimated. Linear mixed effects models (LME) were applied to evaluate factors affecting the performance of HLS with the plot as a random factor. LME analysis revealed that plant type and terrain significantly influenced the accuracy of DBH and H derived from HLS data. Other fixed factors of plot area, tree density and trajectory length didn’t have significance. With a large sample size, we concluded that the HLS demonstrated sufficient accuracy in extracting individual tree parameters in urban forests.

Simple Summary: The distribution of typical bacterial redox enzymes such as pyruvate-ferredoxin oxidoreductase (PFOR) in protozoa remains interestingly puzzling. Previous studies have demonstrated diverse cellular localizations of PFOR in some amitochondriate anaerobic protozoa. PFOR is of particular pharmacological importance because it catalyzes the reductive bio-activation of nitro-based prodrugs to cytotoxic radical metabolites. Metronidazole was developed primarily as an antiprotozoal agent against infections caused by Trichomonas vaginalis. However, its antimicrobial spectrum was subsequently expanded to cover anaerobic bacterial infections. It has been shown that mutations in the genes encoding PFOR result in inherent resistance of PFOR-possessing anaerobic protozoa and bacteria to nitro-based prodrugs. Deciphering the evolutionary history of PFOR is crucial in deepening our understanding of the evolution of anaerobic pathogens and unfold new approaches for drug discovery and targeting in pathogen chemotherapy. Abstract: The present frontrunners in the chemotherapy of infections caused by protozoa are nitro-based prodrugs that are selectively activated by PFOR-mediated redox reactions. This study seeks to analyze the distribution of PFOR in selected protozoa and bacteria by applying comparative bioinformatics approaches to test the hypothesis that PFOR was most likely acquired through horizontal gene transfer (HGT) from bacteria. Furthermore, to identify other genes that were putatively acquired using proteome-wide and gene expression analyses. A plausible explanation for the patchy occurrence of PFOR in protozoa is based on the hypothesis that bacteria are potential sources of genes that enhance optimal adaptation of protozoa in hostile environments. The exclusively expressed proteins obtained from Entamoeba histolytica and the putative gene donor, Desulfovibrio vulgaris, showed an over-expression of eleven genes involved in intermediary metabolism. If these results can be reproduced in other PFOR-possessing protozoa, it would provide a more validated evidence to support the horizontal transfer of pfor from bacteria.

Timely and accurate information on tree species is crucial for the sustainable management of natural resources, forest inventory, biodiversity detection, and carbon stock calculation. The advancement of remote sensing technology and artificial intelligence has facilitated the acquisition and analysis of remote sensing data, resulting in more precise and effective classification of tree species. Multimodal remote sensing data and deep learning seem to be the current tree species classification research mainstream, whether or not. The current review on the remote sensing data and deep learning tree species classification methods perspectives to analyze the unimodal and multimodal remote sensing data and classification methods in this realm is missing. To bridge the gap, we search for major trends in the remote sensing data and tree species classification methods, provide a detailed overview of classic deep learning-based methods for tree species classification, and discuss the limitations.

This review deals with the developmental origins of extraocular, jaw and laryngeal muscles, the expression, regulation and functional significance of myosin heavy chains (MyHCs) they express and changes in MyHC expression during phylogeny. Myogenic progenitors from mesoderm in the prechordal plate and branchial arches specify craniofacial muscle allotypes with different repertoires for MyHC expression. To cope with very complex eye movements, extraocular muscles express 11 MyHCs, ranging from the superfast extraocular MyHC to the slowest, non-muscle MyHC IIB. They have distinct global and orbital layers, singly- and multiply-innervated fibres, longitudinal MyHC variations, and palisade endings that mediate axon reflexes. Jaw-closing muscles express the high-force masticatory MyHC, cardiac or limb MyHCs depending on the appropriateness for the acquisition and mastication of their food. Laryngeal muscles express extraocular and limb muscle MyHCs but shift towards slower MyHCs in large animals. During postnatal development, MyHC expression of craniofacial muscles is subject to neural and hormonal modulation. The primary and secondary myotubes of developing EOMs are postulated to induce, via different retrogradely transported neurotrophins, the rich diversity of neural impulse patterns that regulate the specific MyHCs they express. Thyroid hormone shifts 2A MyHC towards 2B in jaw, laryngeal muscles and possibly extraocular muscles.

This review deals with the adaptive mechanisms that plants can implement to cope with the challenge of salt stress. Plants tolerant to NaCl implement a series of adaptations to acclimate to salinity, including morphological, physiological and biochemical changes. These changes include increases in the root/canopy ratio and in the chlorophyll content in addition to changes in the leaf anatomy that ultimately lead to preventing leaf ion toxicity, thus maintaining the water status in order to limit water loss and protect the photosynthesis process. Furthermore, we deal with the effect of salt stress on photosynthesis and chlorophyll fluorescence and some of the mechanisms thought to protect the photosynthetic machinery, including the xanthophyll cycle, photorespiration pathway and water-water cycle. Finally, we also provide an updated discussion on salt-induced oxidative stress at the subcellular level and its effect on the antioxidant machinery in both salt-tolerant and salt-sensitive plants. The aim is to extend our understanding of how salinity may affect the physiological characteristics of plants.

Long-term, multi-decade research on planted tree survival in urban settings is sparse. One understudied urban environment is highway rights-of-way (ROW), lands adjacent to high-speed, unsignalized roadways. We conducted a re-inventory of tree planting cohort in northern Illinois, U.S. on a 48 km-long highway near Chicago which were 10-, 21-, and 30-years old to evaluate long-term patterns of survival and diversity. Using each randomly selected planting site along the highway as a unit of observation and analysis, we compared the number of trees documented in record drawing to the number of trees currently alive to determine percent survival. We evaluated 224 planting sites which originally contained 2,944 trees and collected data about the planting site location. For the oldest cohort, 26% of trees were still alive in 2018 (median survival by species = 16%, Q1 = 0%, Q3 = 48%), while 31% of the 21-year-old cohort (med. = 6%, Q1 = 0%, Q3 = 47%) and 86% of the 10-year-old cohort were still alive (med. = 85%, Q1 = 74%, Q3 = 96%). The survival of the 21- and 30-year-old cohort matches urban tree survival estimates by other researchers, while the 10-year-old survival is higher than expected. The only planting location characteristic that significantly affected survival was traffic islands (areas between the highway and entrance/exit ramps). Species with low drought tolerance were less likely to be alive for the 10-year-old cohort. Waterlogging tolerant species were more likely to be alive in the 10-year-old cohort. Since some species in the 21- and 30-year-old cohorts had very low survival, the tree species richness and diversity s in study areas declined between the initial record drawings and reinventory. This study demonstrates the challenges of maintaining long-term survival and diversity in the highway ROW and emphasizes the importance of species selection.

In plants and animals, endogenous biological molecules, termed damage-associated molecular patterns (DAMPs) or alarmins, are released by damaged, stressed or dying cells following abiotic stress such as radiation and drought stress. In turn, a cascade of downstream signaling events is initiated leading to the up-regulation of defense-related genes. In the present study, in an effort to investigate the conservation status of the molecular mechanisms implicated in the danger signaling, thorough in silico phylogenetic and structural analyses of the effector biomolecules were performed in taxonomically diverse plant species. On the basis of our results, the defense mechanisms appear to be largely conserved within the plant kingdom. Of note is our finding that the sequence and/or function of several components of these mechanisms were found to be conserved in animals, as well.

Tree biomass and diversity relationship in mixed forest impacts on forest ecosystem services provisions. Tree biomass yield is driven by several aspects such as species identity, site condition, stand density, tree age as well as tree diversity expressed as species mingling and structural diversity. By comparing diverse degrees of tree mixture in natural forests we can insight on the ecosystem services provision level and dynamic. Two monitoring sites in the Castilian Northern Plateau (Spain) have been analyzed to disentangle the relationships between biodiversity levels and tree biomass yield. Two permanent one ha squared plots were established at Llano de San Marugan and Valdepoza. In each plot all individual trees were measured (diameter and height), georeferenced and its species identity defined. Tree species in the two sites were Pinus sylvestris, Pinus nigra, Pinus pinea, Quercus pyrenaica, Quercus ilex, Quercus faginea and Juniperus thurifera. From these datasets ten diversity indices that fall in three categories (species richness indices, species compositional/mingling indices and vertical structural indices) were used as predictor variables to fit several candidate models. By merging the trees by site (without considering the species identity) selected models include individual tree basal area as explanatory variable combining by addition or interaction with diversity indices. When species are analyzed independently structural diversity impacts on biomass yield in combination (additive or multiplicative) with tree size is negative Pinus nigra and positive for the other species.

The severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) viral genome is an RNA virus consisting of approximately 30,000 bases. As part of testing efforts, whole genome sequencing of human isolates has resulted in over 1,600 complete genomes publicly available from GenBank. We have performed a comparative phylogenetic analysis of the sequences, in order to detect common mutations within the population. Analysis of variants occurring within the assembled genomes yields 417 variants occurring in at least 1% of the completed genomes, including 229 within the 5’ untranslated region (UTR), 152 within the 3’UTR, 2 within intergenic regions and 34 within coding sequences.

Phytoplasma diseases pose a substantial threat to diverse crops of agricultural importance. Management measures are usually implemented only after the disease has already occurred. Early detection of such phytopathogens, prior to disease outbreak, has rarely been attempted but would be highly beneficial for phytosanitary risk assessment, disease prevention and mitigation. In this study we present the implementation of a recently proposed proactive disease management protocol (DAMA: Document, Assess, Monitor, Act) for a group of vector-borne phytopathogens. We used insect samples collected during a recent biomonitoring program in southern Germany to screen for the presence of phytoplasmas. Insects were collected with Malaise traps in different agricultural settings. DNA was extracted from these mass trap samples and subjected to PCR-based phytoplasma detection and COI sequence metabarcoding. In about 1% of the analyzed samples, phytoplasma DNA was detected. Phytoplasma group identification was performed by 16S rRNA gene sequence analysis and the detected phytoplasmas could be assigned to the 16SrI subgroups B and L. Insect species in the sample were identified by DNA metabarcoding. By using established databases, checklists, and archives, we documented historical associations and records of phytoplasmas and its hosts in the study region. For the assessment in the DAMA protocol, phylogenetic triage was performed in order to determine the risk for tri-trophic interactions (plant-insect-phytoplasma) and associated disease outbreaks in the study region. A phylogenetic heat map constitutes the basis for risk assessment and was used here to identify a minimum number of seven leafhopper species suggested to be monitored by stakeholders in this region. A proactive stance in monitoring changing patterns of association between hosts and pathogens can be a cornerstone in capabilities to prevent future phytoplasma disease outbreaks. To our knowledge, this is the first time that the DAMA protocol has been applied in the field of phytopathology and vector-borne plant diseases.

Bacillus anthracis, the causative agent of anthrax, has two virulence plasmids: pXO1 and pXO2. Plasmid pXO2 carries the genes of an antiphagocytic capsule synthesis. Plasmid pXO1 carries the genes pagA, lef, and cya encoding anthrax toxins, as well as atxA, which encodes the main regulator of pathogenicity factor expression. In the present paper, we evaluated the polymorphism of the pagA, lef, cya, and atxA genes for 85 B. anthracis strains belonging to different evolutionary lineages and canSNP groups and three B. cereus strains possessing pXO1-like plasmids. We found 19 genotypes (GT) strongly correlated with the main evolutionary lineages; they were mainly correlated with the canSNP group within these lines. In some cases, one GT combined the strains of several canSNP groups, and some canSNP groups were divided into several GTs. The most interesting of such cases were 1) the formation of a separate GT by strains of the A.Br.008/009 group isolated in the former USSR; 2) the presence of a unique GT in some American strains of the A.Br.Aust94 group; 3) the division of the A.Br.001/002 group into two subgroups, one of which may be a transitional link to the group A.Br.Ames; 4) the fact that European isolates of the B.Br.CNEVA group and Arctic strains of the B.Br.001/002 group have a common GT.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as the current coronavirus pandemic is an infectious disease that initially confirmed in China in late December 2019. In this study, we analyzed 131 complete sequences of SARS-CoV-2 from Asia. Our results show that there are fifteen major mutations in Asia which most of them are co-evolved. There were five groups based on co-mutations which three of them resulted in clade G including (241C>T, 3037C>T, 14408C>T, and 23403A>G), (28881G>A, 28882G>A, 28883G>C and 23403A>G) and (25563G>T and 23403A>G). Co-mutations in (8782C>T and 28144T>C) and (1397G>A, 28688T>C, 29742G>T and 11083G>T) were clustered in clade S and a new clade outside of GISAID classification, respectively. Sequences with a mutation in 26144G>T had low variability without any co-mutation which formed clade V. In this study, we showed that Most of the circulated viruses in Asia collected in five co-mutation groups which may affect the transmissibility and vaccine designing strategies.

Urban tree classification is pivotal in urban planning and management, facilitating informed decision-making processes. In this study, we introduce a novel data presentation method termed Pseudo Tree Crown, designed to enhance the accuracy and efficiency of urban tree classification. Leveraging the latest advancements in artificial intelligence (AI), we employ a state-of-the-art classification scheme, PyTorch, to maximize the accuracy of tree classification. Our results demonstrate a robust classification accuracy of over 95% from high spatial resolution imagery from Unmanned Aerial Vehicle (UAV), underscoring our proposed approach’s effectiveness. Moreover, the adaptability of our method renders it applicable to various study areas, highlighting its versatility and potential for widespread implementation in urban planning and management initiatives.

Malaxidinae is one of the confusing groups with classification in Orchidaceae. Previous phylogenetic analysis reveals that the relationships among the taxa in Malaxidinae have not yet been reliably established using a few plastome regions or nuclear ribosomal internal transcribed spacer (nrITS). In the present study, the complete plastomes of Oberonia integerrima and Crepidium purpureum were assembled using high-throughput sequencing. Combined with publicly available complete plastome data, this resulted in a data set of 19 plastomes, including 17 species of Malaxidinae. The plastome feature and phylogenetic relationship were compared and analyzed. The results showed that: (1) The plastomes of Malaxidinae species possessed the quadripartite structure of typical angiosperms, with sizes ranging from 142,996 bp to 158,787 bp and encoding from 125 to 133 genes. The ndh genes were lost or pseudogenized with varying degrees in six species. An unusal inversion was detected in the Large Single-Copy region (LSC) of Oberonioides microtatantha. (2) A total of 8 regions, including ycf1, matK, rps16, rpl32, ccsA-ndhD, clpP-psbB, trn-FGAA-ndhJ, and trnSGCU-trnGUCC, were identified as mutational hotspots. (3) Based on complete plastomes, 68 protein-coding genes and 51 intergenic regions, respectively, the phylogenetic analyses resolved genera-level relationships in this subtribe with strong support. The Liparis was supported as polyphyletic.

Growth and yield of boreal tree species are discussed. A growth model is applied, along with verified yield models of sawlogs and veneer logs. Using the normal forest-principle, thinning schedules and rotation ages maximizing the estate-level capital return rate are clarified. Regeneration expenses are amortized at the end of any rotation. Consequently, capitalizations are greater and rotations longer than in recent studies. The capital return rate is a weak function of initial stem count but differs by tree species. The initial stem count strongly contributes to biomass stored in trees. The most promising way of increasing the capital return rate is the reduction of regeneration expenses. Thinnings are triggered by stand volumes of at least 200 m3/ha. The average commercial trunk volume of trees removed in thinnings always exceeds 200 liters. Risk aversion theory proposes short rotations and low stem count in seedling planting unless carbon storage compensation exists.

Clock Network Design (CDN) is a critical step while designing any Integrated-Circuits (ICs). It holds vital importance in the performance of entire circuit. Due to continuous scaling, 3D ICs stacked with TSV are gaining importance, with an objective to continue with the Moore's law. Through-Silicon-Via (TSV) provides the vertical interconnection between two die, which allows the electrical signal to flow through it. 3D ICs has many advantages over conventional 2D planar ICs like reduced power, area, cost, wire-length etc. The proposed work is mainly focused on power reduction and obstacle avoidance for 3D ICs. Various techniques have already been introduced for minimizing clock power within specified clock constraints of the 3D CND network. Proposed 3D Clock Tree Synthesis (CTS) is a combination of various algorithms with an objective to meet reduction in power as well as avoidance of obstacle or blockages while routing the clock signal from one sink to other sink. These blockages like RAM, ROM, PLL etc. are fixed during the placement process. The work is carried out mainly in three steps- first is Generation of 3D Clock tree avoiding the blockages, then Buffering and Embedding and finally validating the results by SPICE simulation. The experimental result shows that our CTS approach results in significant 9% reduction in power as compare to the existing work.

The great Greek philosopher Aristotle (384–322 BCE) is almost unanimously acclaimed as the founder of zoology. There is a consensus that he was interested in attributes of animals, but whether or not he tried to develop a zoological taxonomy remains controversial. Fürst von Lieven and Humar compiled a data matrix and showed, through a parsimony analysis published in 2008, that these data produced a hierarchy that matched several taxa recognized by Aristotle. However, their analysis leaves some questions unanswered because random data can sometimes yield fairly resolved trees. In this study, we update the scores of many cells and add four new characters to the data matrix (147 taxa scored for 161 characters) and quote passages from Aristotle’s Historia animalium to justify these changes. We confirm the presence of a phylogenetic signal in these data through a test using skewness in length distribution of a million random trees, which shows that many of the characters discussed by Aristotle were systematically relevant. Our parsimony analyses on the updated matrix recover far more trees than reported by Fürst von Lieven and Humar, but their consensus includes many taxa that Aristotle recognized and apparently named for the first time, such as selachē (selachians) and dithyra (Bivalvia). This study suggests that even though taxonomy was clearly not Aristotle’s chief interest in Historia animalium, it was probably among his secondary interests. These results may pave the way for further taxonomic studies in Aristotle’s zoological writings in general. Despite being almost peripheral to Aristotle’s writings, his taxonomic contributions are clearly major achievements.

Globin-like superfamily constitutes a superfamily of both extracellular and intracellular proteins that are found in 3 kingdoms of life. Globins are respiratory proteins that usually bind an oxygen molecule .Earlier, phylogenetic study of globin like superfamily was based on morphological character, however, molecular basis of their functional diversity is not completely understood. The present study focuses on the phylogenetic analysis of globin at molecular level. Firstly, proteins of SCOP families of globin like superfamily were retrieved from NCBI and then similar proteins are retrieved from PSI BLAST results and then pfam was used to predict the domains and two domains: Globin and Phycobilisome were analysed. Other analysis predicted the localization in cytoplasm of most of the proteins. The nucleotide sequences of same species for protein analysis were retrieved from NCBI, and phylogenetic analysis of aligned fasta files of proteins and nucleotides by using MEGA at molecular level was performed and analysis shows the difference on taxonomic tree and phylogenetic tree.

Multi-level direct networks fueled by the evolving technology of active optical cables and increasing pin-bandwidth achieve reduced diameters and cost, with high-radix switches. These networks, like Dragonfly, are becoming the preferred aspirants for extreme high-performance parallel machines such as exa-scale computing. In this paper, we introduce a Hyper Z-Tree topology, which deploys the Z-Tree, a variant of fat-tree, as a computing node of a Generalized Hypercube (GHC) configuration. The resulting configuration provides higher bisection bandwidth, lower latency for some applications and higher throughput. Furthermore, the levels of the fat tree offer several path diversities across the GHC dimensions, hence conceding a more fault tolerant architecture. To profit from these path diversities, we propose two adaptive routing algorithms, which are extensions to the routing algorithm suggested in HyperX topology. These two algorithms exhibit better latencies and throughput than the HyperX.

Balsam fir trees are a specialty agricultural species that are largely used as Christmas trees. Soil or tissue sampling is seldom performed to assess balsam fir nutrition needs, which can contribute to over or under fertilization and subsequent environmental challenges. Remote sensing to determine the normalized difference vegetation index (NDVI) has had strong relationships with nutrition in other plants. This research aimed to determine whether there is a relationship between NDVI and nutrition in balsam fir. A random sample of 45 trees was selected in autumn of 2021 and then another 70 trees selected in spring of 2022. Soil and needle tissue samples were analyzed for N, P, K, Ca, Mg, S, Fe, Zn, Mn, B, and Cu. An uncrewed aerial vehicle equipped with a multispectral camera was flown over the orchard to determine the NDVI for each tree. Nutrition and NDVI were analyzed for correlations through all sampled trees. Separate correlation analyses were repeated for mature trees (greater than 5 years old) and young trees (less than 5 years old). Soil nutrients N, P, K had a significant relationship with NDVI in autumn sampling. Only N was correlated consistently in both autumn and spring, with R2 of 37% and 33% respectively. Relationships were much stronger when only mature trees were considered, increasing to 60% and 51% respectively. NDVI was found to offer predictive power for tissue N that can be useful to producers to help optimize fertilizer input. However, further work is needed to refine these relationships.

Apomictic plants (reproducing via asexual seeds), unlike sexual individuals, avoid meiosis and egg cell fertilization. Consequently, apomixis is very important for fixing maternal genotypes in the next plant generations. Despite the progress in the study of apomixis, molecular and genetic regulation of the latter remains poorly understood. So far APOLLO (Aspartate Glutamate Aspartate Aspartate histidine exonuclease) is one of the very few described genes associated with apomixis in Boechera species. The centromere-specific histone H3 variant encoded by CENH3 gene is essential for cell division. Mutations in CENH3 disrupt chromosome segregation during mitosis and meiosis since the attachment of spindle microtubules to a mutated form of the CENH3 histone fails. This paper presents in silico characteristic of APOLLO and CENH3 genes, which may affect apomixis. Also, we characterize the structure of CENH3, study expression levels of APOLLO and CENH3 in gynoecium/siliques of the natural diploid apomictic and sexual Boechera species at the stages of before and after fertilization. While CENH3 was a single copy gene in all Boechera species, the APOLLO gene have several polymorphic alleles associated with sexual and apomictic reproduction in the Boechera genera. Expression of the APOLLO apo-allele during meiosis was upregulated in gynoecium of apomict B. divaricarpa downregulating after meiosis until 4th day after pollination (DAP). On the 5th DAP, expression in apomictic siliques increased again. In sexual B. stricta gynoecium and siliques APOLLO apo-allele did not express. Expression of the APOLLO sex-allele during and after meiosis in gynoecium of sexual plants was several times higher than that in apomictic gynoecium. However, after pollination the sex-allele was downregulated in sexual siliques to the level of apomicts and increased sharply on the 5th DAP, while in apomictic siliques it almost did not express. At the meiotic stage, the expression level of CENH3 in the gynoecium of apomicts was two times lower than that of the sexual Boechera, decreasing in both species after meiosis and keep remaining very low in siliques of both species for several days after artificial pollination until the 4th DAP, when the expression level raised in sexual B. stricta siliques exceeding 5 times the level in apomictic B. divaricarpa siliques. We also discuss polymorphism and phylogeny of the APOLLO and CENH3 genes.

Piroplasmosis, caused by Babesia spp. and Theileria spp., poses significant constraints for livestock production and upgradation in Bangladesh. Besides examining blood smears, few molecular reports are available from some selected areas in the country. Therefore, the actual scenario of piroplasmosis in Bangladesh is deficient. This study aimed to screen the piroplasms in different livestock species by molecular tools. A total of 276 blood samples were collected from cattle, gayals (Bos frontalis) and goats in five geographies of Bangladesh. Thereafter, screening was conducted through a polymerase chain reaction, and species were confirmed by sequencing. The prevalence of Babesia bigemina, B. bovis, B. naoakii, B. ovis, Theileria annulata and T. orientalis was 49.28%, 0.72%, 1.09%, 32.26%, 6.52% and 46.01%, respectively. The highest prevalence (79/109; 72.48%) of co-infections was observed with B. bigemina and T. orientalis. The phylogenetic analyses revealed that the sequences of B. bigemina, B. bovis, B. naoakii, B. ovis and T. annulata were included in one clade in the respective phylogram. In contrast, the sequences of T. orientalis were separated into two clades, corresponding to Type 5 and 7. To the best of our knowledge, this is the first molecular report on piroplasms in gayals and goats in Bangladesh.

Family Phyllanthaceae is one of the largest segregates of the eudicot order Malpighiales and its species are herb, shrub, and tree, which are mostly distributed in tropical regions. Certain taxonomic discrepancies exist at genus and family level. Here, we report chloroplast genomes of three Phyllanthaceae species—Phyllanthus emblica, Flueggea virosa, and Leptopus cordifolius— and compare them with six others previously reported Phyllanthaceae chloroplast genomes. The species of Phyllanthaceae displayed quadripartite structure, comprising inverted repeat regions (IRa and IRb) that separate large single copy (LSC) and small single copy (SSC) regions. The length of complete chloroplast genome ranged from 154,707 bp to 161,093 bp; LSC from 83,627 bp to 89,932 bp; IRs from 23,921 bp to 27,128 bp; and SSC from 17,424 bp to 19,441 bp. Chloroplast genomes contained 111 to 112 unique genes, including 77 to 78 protein-coding, 30 transfer RNA (tRNA), and 4 ribosomal RNA (rRNA) that showed similarities in arrangement. The number of protein-coding genes varied due to deletion/pseudogenization of rps16 genes in Baccaurea ramiflora and Leptopus cordifolius. High variability was seen in number of oligonucleotide repeats while analysis of guanine-cytosine (GC) content, codon usage, amino acid frequency, simple sequence repeats analysis, synonymous and non-synonymous substitutions, and transition and transversion substitutions showed similarities in all Phyllanthaceae species. We detected a higher number of transition substitutions in the coding sequences than non-coding sequences. Moreover, the high number of transition substitutions was determined among the distantly related species in comparison to closely related species. Phylogenetic analysis shows the polyphyletic nature of the genus Phyllanthus which requires further verification. We also determined suitable polymorphic coding genes, including rpl22, ycf1, matK, ndhF, and rps15 which may be helpful for the reconstruction of the high-resolution phylogenetic tree of the family Phyllanthaceae using a large number of species in the future. Overall, the current study provides insight into chloroplast genome evolution in Phyllanthaceae.

Agroforestry systems with multipurpose tree species, for the double production of timber and fruit, along with the intercropping with herbaceous crops, can be fundamental land use systems for multiple ecosystems services. Research was conducted in Italy, for one growing season, in 18 years old agroforestry experimental plots with common walnut (Juglans regia L.) trees, according to the previous agroforestry management (AFM) since tree planting. The aim is i) estimating trees growth and herbaceous yield in relation to increasing tree size, especially referring to the trees basal area (G); ii) evaluating the role of nut production as additional product to timber and food crops. Observations were run on tree growth and leaf phenology, total light transmittance (TTL) below tree canopy and hay yield with and without walnut intercropping. Nut yield was estimated from available literature and associated to G. At the end of the study year, representing two third of trees rotation, their height varied between 10 and 11 m, with much larger variation for tree diameter between 17 and 22 cm, according to the previous AFM, including tree mulching with plastic film. Hay yield varied between 4.5 and 3 Mg ha year-1 outside and under tree canopy, respectively. Negative regression were determined for G and TTL, and G and hay yield, with an annual reduction of 5% per G unit. Simulations were run on hay and nut yield, using G as main input parameter. The work points out the following key findings: i) the usefulness of plastic mulching, at tree planting, to increase the long-term timber productivity of the trees intercropped with herbaceous crops; ii) the negative linear relationship between hay productivity and walnut trees G; iii) G influences, in positive way, more markedly nut than hay yield. Suggestions are given on the optimum tree planting spacing and AFM for balancing timber, nut and hay yields.

The bacterial wilt pathogen, first known as Bacillus solanacearum, has undergone numerous taxonomic changes since its first description in 1896. The history and significance of this pathogen is covered in this review with an emphasis on the advances in technology that were used to support each reclassification that finally led to the current separation of Ralstonia solanacearum into three genomic species. Frequent name changes occurred as methodology transitioned from phenotypic, biochemical, and molecular studies, to genomics and functional genomics. The diversity, wide host range and geographical distribution of R. solanacearum has resulted in its inclusion in a “species complex” as genomic analyses of elucidated phylogenetic relationships among strains. Current advances in phylogenetics and functional genomics now open new avenues for research into the epidemiology and control of the devastating bacterial wilt disease.

Littoraria melanostoma (Gray, 1839) is a most common species of gastropods in mangroves. They quickly respond during the early stage of mangrove restoration and usually form a dominant community within a certain period. We characterized the complete mitochondrial genome of the species. The whole mitogenome of L. melanostoma was 16,149 bp in length and its nucleotide composition showed high AT-content of 64.16%. It had 37 genes, including 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes, one control region between tRNA-Phe and COX3. The A/T compositions in the control region is 74.7%, respectively, and are much higher than the overall A/T composition of the mitochondrial genomes. The amino acid composition and codon usage of the mitochondrial genomes of from eight superfamilies of Littorinimorpha were analyzed, and the results showed that CUU (Leu), GCU (Ala), AUU (Ile), UCU (Ser), UUA (Leu), GUU (Gly) and UUU (Phe) are the commonly used codons in this order. The results of phylogenetic analysis were roughly consistent with morphological classification, which showed that L. melanostoma is closely related to L. sinensis, a rock-dwelling species that is widespread in the coastal intertidal zone of China. These results may provide a basis to understand the phylogeny and evolution of the Littorinimorpha.

During the last two decades, ecological speciation has been a major research theme in evolutionary biology. Ecological speciation occurs when reproductive isolation between populations evolves as a result of niche differentiation. Phytophagous insects represent model systems for the study of this evolutionary process. The host-plants on which these insects feed and often spend parts of their life cycle constitute ideal agents of divergent selection for these organisms. Adaptation to feeding on different host-plant species can potentially lead to ecological specialization of populations and subsequent speciation. This process is thought to have given birth to the astonishing diversity of phytophagous insects and is often put forward in macroevolutionary scenarios of insect diversification. Consequently, numerous phylogenetic studies on phytophagous insects have aimed at testing whether speciation driven by host-plant adaptation is the main pathway for the diversification of the groups under investigation. The increasing availability of comprehensive and well-resolved phylogenies and the recent developments in phylogenetic comparative methods are offering an unprecedented opportunity to test hypotheses on insect diversification at a macroevolutionary scale, in a robust phylogenetic framework. Our purpose here is to review the contribution of phylogenetic analyses to investigate the importance of plant-mediated speciation in the diversification of phytophagous insects and to present suggestions for future developments in this field.

The proton exchange membrane fuel cell (PEMFC) is a critical and essential component of zero-emission electro-hydrogen generators. An accurate prediction of its performance is important for optimal operation management and preventive maintenance of these generators. However, the prediction is not simple because the PEMFCs have complex electrochemical reactions with multiple nonlinear relations between operating variables as inputs and voltage as output. In this paper, we propose an efficient prediction approach based on XGBRegressor and Tree-structured Parzen Estimator. In addition, to better select relevant features, Kernel Principal Component Analysis and Mutual Information are jointly used. The proposed approach allows consideration of the dynamic operating conditions of the PEMFC. To test and validate the robustness of the proposed approach, a real data-set of ten PEMFCs was considered. Furthermore, a comparison study with traditional machine learning models, such as artificial neural networks and support vector machine regression, was investigated. The obtained results confirm that our model outperforms the considered traditionel machine learning models.

Tapping panel dryness (TPD) syndrome is a complex disease of Rubber tree (Hevea brasiliensis L.) which causes cessation of latex drainage upon tapping of rubber tree. Rubber tree virus (RTV1) was identified as a novel pathogen associated with rubber tree and a potential causal agent of TPD. RTV1 is a monopartite RNA virus that is linear, non-enveloped and has a single-stranded (ss) positive RNA genome of approximately 6081 nucleotides and is composed of two major open reading frames (ORFs), ORF1 (polyprotein), and ORF2 (movement protein. This study aimed to investigate the possibility of rubber genome encoded tree microRNAs (miRNAs) as novel therapeutic targets against RTV1 using in silico algorithms. Mature rubber tree miRNAs are retrieved from the miRBase database and are used for hybridization of RTV1 using five different five different computational algorithms including miRanda, RNA22, RNAhybrid and psRNATarget. A total of eleven common rubber tree miRNAs were identified based on consensus genomic positions. The consensus of four algorithms predicted the hybridization sites of hbr-miR396a and hbr-miR398 at common locus positions 6676, 1840 respectively. To validate the prediction, secondary structures of the consensual rubber tree miRNAs and free energy of duplex binding were calculated using the RNAfold and RNAcofold algorithms respectively. We created a plot between rubber tree miRNAs and RTV1 ORFs by using Circos algorithm. In this study, we predicted eleven consensual rubber tree miRNAs. Among these miRNAs, hbr-miR398 was identified as the most effectual miRNA that may target the ORF1 gene of the RTV1 genome. The predicted data will be important in the development of rubber trees resistant to RTV1.

Big Data classification has recently received a great deal of attention due to the main properties of Big Data, which are volume, variety, and velocity. The furthest-pair-based binary search tree (FPBST) shows a great potential for Big Data classification. This work attempts to improve the performance the FPBST in terms of computation time, space consumed and accuracy. The major enhancement of the FPBST includes converting the resultant BST to a decision tree, in order to remove the need for the slow K-nearest neighbors (KNN), and to obtain a smaller tree, which is useful for memory usage, speeding both training and testing phases and increasing the classification accuracy. The proposed decision trees are based on calculating the probabilities of each class at each node using various methods; these probabilities are then used by the testing phase to classify an unseen example. The experimental results on some (small, intermediate and big) machine learning datasets show the efficiency of the proposed methods, in terms of space, speed and accuracy compared to the FPBST, which shows great potential for further enhancements of the proposed methods to be used in practice.

Elongate loach (Leptobotia elongata) is an endemic fish in China. Previous studies have provided some insights into the mitochondrial genome composition, and the phylogenetic relationships of L. elongata inferred using protein-coding genes (PCGs). However, the detailed information about is limited. Therefore, in this study, we sequenced the complete mitochondrial genome of L. elongata and analyzed its structural characteristics. The PCGs and mitochondrial genome were used for selective stress analysis and genomic comparative analysis respectively. The complete mitochondrial genome of the L. elongata, together with those of 36 Cyprinidae species, was used to infer the phylogenetic relationships of the Cobitidae family through maximum likelihood (ML) reconstruction. The results showed that the genome sequence has a full length of 16,591 bp, which includes 13 PCGs, 22 transfer RNA genes (tRNA), two ribosomal RNA genes (rRNA), and two non-coding regions (CR D-loop and light chain sub-chain replication origin OL). Overall, L. elongata shared the same gene arrangement and composition of the mitochondrial genes with other teleost fishes. The Ka/Ks ratios of all mitochondrial PCGs were less than 1, indicating that all the PCGs were evolving under purifying selection. Genome comparison analyses showed a significant sequence homology of species of Leptobotia. A significant identity between L. elongata and the other 5 Leptobotia species was observed in the visualization result, except for L. mantschurica, which lacked the tRNA-Arg gene and had a shorter tRNA-Asp gene. The phylogenetic tree revealed that the Cobitidae species examined here can be grouped into two clades, with L. elongata forming a sister relationship with L. microphthalma. This study could provide additional inferences for a better understanding of the phylogenetic relationships among Cobititdae species.

The chloroplast genome is conservative and stable, which can be employed to resolve genotypes. Currently, published nuclear sequences and molecular markers failed to differentiate the species from taxa robustly, including Machilus leptophylla, Hanceola exserta, Rubus bambusarum, and Rubus henryi. In this study, the four chloroplast genomes were characterized, and then their simple sequence repeats (SSRs) and phylogenetic positions were analyzed. The results demonstrated the four chloroplast genomes consisted of 152.624 kb, 153.296kb, 156.309 kb, and 158.953 kb in length, involving 124, 130, 129, and 131 genes, respectively. Moreover, the chloroplast genomes contained typical four regions. Six classes of SSR were identified from the four chloroplast genomes, in which mononucleotide was the class with the most members. The types of the repeats were various within individual classes of SSR. Phylogenetic trees indicated that M. leptophylla was clustered with M. yunnanensis, and H. exserta was confirmed under family Ocimeae. Additionally, R. bambusarum and R. henryi were clustered together, whereas they did not belong to the same species due to the differing SSR features. This research would provide evidence for resolving the species and contributed new genetic information for further study.

Helicases are proteins that use the energy of ATP to unwind nucleic acids and to remodel protein-nucleic acid complexes. They are involved in almost every aspect of the DNA and RNA metabolisms and participate in numerous repair mechanisms that maintain cellular integrity. Helicases are classified into 6 superfamilies (SF1-6). The archaeal Lhr-type proteins are SF2 helicases that are mostly uncharacterized. They have been proposed to be a DNA helicase that acts in DNA recombination and repair processes in Sulfolobales and Methanothermobacter. In parallel, a protein annotated as an Lhr2 protein was also found in the network of proteins involved in RNA metabolism in Thermococcales. To this respect, we performed in-depth phylogenomic analyses to report the classification and taxonomic distribution of Lhr-type proteins in Archaea, and to better understand their relationship with bacterial Lhr. Furthermore, with the goal of envisioning the role(s) of aLhr2 in archaeal cells, we deciphered the enzymatic activities of aLhr2 from Thermococcus barophilus (Tbar). We showed that Tbar-aLhr2 is a DNA/RNA helicase acting on DNA:RNA and RNA:RNA duplexes and proposed that aLhr2 helicases are involved in processes dependent of DNA and RNA transactions.

Aim: Despite the endemic nature of contagious ecthyma in Nigeria, there is limited report on the molecular characterization of the isolates responsible for disease outbreaks. The aim of this study was to molecularly characterize ORFV isolated from clinical infections in goats in Sokoto metropolis. Materials and Methods: Seronegative embryonated chicken eggs were used to isolate ORFV via the chorio allantoic membrane (CAM) route according to the established protocol. Viral DNA was extracted from infected CAM and the full coding region of B2L gene was amplified by PCR and subsequently sequenced by Sanger’s method. The nucleotide sequence results were blasted for identification and phylogenetically analyzed using MEGA and Bioedit softwares. Results and Discussion: The results showed that B2L gene sequences of the ORFV UDUS/01/19/More strain showed slight variability (96- 98.7%) with the reference sequences. Our isolate clustered within the same clade with Korean strain signifying a close genetic relationship. Unique amino acid substitutions were noted in our isolate when compared with other references. This is arguably the first genetic characterisation of B2L gene of ORFV circulating in Nigeria. Conclusion: Our study has provided in sight into the genetic diversity of ORFV in the study area. This is crucial for the design of effective vaccines against the disease which are currently lacking in the country.

Documenting prehistoric and historical hemp retting for fiber extraction is important in the study of human uses of this iconic plant and its cultural implications. In paleoecology, hemp retting is usually inferred from indirect proxies, notably anomalously high percentages of Cannabis pollen in lake sediments, but some recent studies have also used specific molecular biomarkers (cannabinol, Cannabis DNA) as a more straightforward evidence. Here we provide direct evidence of hemp retting by identifying phylogenetic signatures (16S rRNA genes) from pectinolytic bacteria actually responsible for the fermentation process that separates the fiber from the stalk, namely Bacillus, Clostridium, Escherichia, Massilia, Methylobacterium, Pseusomonas, Rhizobium and Rhodobacter. These analyses have been performed in the sediments from an Iberian lake previously considered as an important hemp retting site during the last five centuries, on the basis of Cannabis pollen abundances. The good match between biomarker and pollen evidence, in the context of the recent historical development of hemp industry in Spain, can be useful to interpret paleoecological records from other similar lakes in the way toward a more regional view on the introduction, spreading, uses and associated cultural connotations of Cannabis in the Iberian Peninsula within European and Mediterranean contexts.

The age-related mortality and morbidity risk of COVID-19 has been considered speculative without enough scientific evidence. This study aimed to collect more evidence on the association between patient age and risk of severe disease state and/or mortality from SARS-CoV-2 infection. Genomic dataset along with metadata (3608 samples) retrieved from GISAID from different geographical regions were grouped into 10 age groups (0-10, 11-20, 21-30, 31-40, 41-50, 51-60, 61-70, 71-80, 81-90, 91-100 years) as well as high-risk or low-risk according to patient clinical status. Genomic sequences were aligned and analyzed using MAFFT and FASTTREE to build a phylogenetic tree in order to identify age-risk associations based on phylogenetic clustering. Case fatality rates (CFR), as well as the Odds ratio (OR) for high-risk outcomes, were calculated for different age groups. Results revealed that individuals aged between 25-50 years have the best immune response to the infection. On the other hand, disease fatality was higher in patients aging above 50 years. We created an application to calculate the OR of being at high risk given a certain age threshold from GISAID datasets. OR values increased between ages 1-10 years (1.271) and 11-20 years (1.313) but reduced at age range 21-30 years (1.290) and increased again for 61-70 years (2.465). CFR calculated for each of the age groups had peak values at 90-100 years (26.8%) and the lowest at 0-10 years (0%). The CFR for ages above 50 years was about twice greater (11.6%-26.8%) than that for ages below (0-6.6%). The phylogenetic analysis revealed that the majority of samples obtained from India showed low-risk among different age groups and were defined as clade GH. Another cluster from Singapore visualization showed unfavorable patient outcome across several age groups and were classified under clade O. To conclude, this study analyses showed a variety of age-risk associations. As scientists from different countries upload more genomes to globally shared databases, more evidence will reinforce mortality risk associations in COVID-19 patients.

Pruning is one of the most important tree fruit production activities, which is highly dependent on human labor. Skilled labor is in short supply, and the increasing cost of labor is becoming a big issue for the tree fruit industry. Growers are motivated to seek mechanical or robotic solutions for reducing the amount of hand labor required for pruning. This paper reviews the research and development of sensing and automated systems for branch pruning for tree fruit production. Horticultural advancements, pruning strategies, 3D structure reconstruction of tree branches, as well as practice mechanisms or robotics are some of the developments that need to be addressed for an effective tree branch pruning system. Our study summarizes the potential opportunities for automatic pruning with machine-friendly modern tree architectures, previous studies on sensor development, and efforts to develop and deploy mechanical/robotic systems for automated branch pruning. We also describe two examples of qualified pruning strategies that could potentially simplify the automated pruning decision and pruning end-effector design. Finally, the limitations of current pruning technologies and other challenges for automated branch pruning are described, and possible solutions are discussed.

Bulbophyllum is one of the largest genera and presents some of the most intricate taxonomic problems in the family Orchidaceae, including species of ornamental and medical importance. The lack of knowledge regarding the characterization of Bulbophyllum chloroplast (cp) genomes has imposed current limitations on our study. Here, we reported the complete cp genomes of seven Bulbophyllum species, including B. ambrosia, B. crassipes, B. farreri, B. hamatum, B. shanicum, B. triste and B. violaceolabellum, and compared with related taxa to provide a better understanding of their genomic information on taxonomy and phylogeny. A total of 28 Bulbophyllum cp genomes exhibit typical quadripartite structures with lengths ranging from 145,092 bp to 165,812 bp and GC content of 36.60% to 38.04%. Each genome contained 125–132 genes, encompassing 74–86 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The genome arrangements, gene contents and length were similar with differences observed in ndh gene composition. A total of 18–49 long repeats and 38–80 simple sequence repeats (SSRs) were detected and the single-nucleotide (A/T) was dominant in Bulbophyllum cp genomes, with an obvious A/T preference. An analysis of relative synonymous codon usage (RSCU) revealed Leucine (Leu) was the most frequently used codon, while cysteine (Cys) was the least used. Six highly variable regions including ndhF-trnLUAG, trnTUGU-trnLUAA, trnFGAA-ndhJ, rps15-trnNGUU, rbcL-accD and psbI-trnSGCU were identified based on the ranking of the Pi values, had the potential to serve as DNA markers for species identification and phylogeny of the genus Bulbophyllum. Phylogenetic analysis based on the complete cp genome sequences and 68 protein-coding genes strongly supported 28 Bulbophyllum species can be divided into four branches and sects. Brachyantha, Cirrhopetalum, Leopardinae defined by morphology were non-monophyly. Our results enriched the genetic resources of Bulbophyllum species, providing valuable information to illustrate the complicated taxonomy, phylogeny and evolution process of the genus.

Objective: To identify and characterise genomic and phylogenetically isolated SARS-CoV-2 viral isolates in patients from Lambayeque, Peru. Methods: nasopharyngeal swabs were taken from patients from the Almanzor Aguinaga Asenjo Hospital, Chiclayo, Lambayeque, Peru, which have been considered mild, moderate and severe cases of COVID-19. Patients had to have tested positive for COVID-19, using a positive RT-PCR for SARS-CoV-2. Subsequently, the SARS-CoV-2 complete viral genome sequencing was carried out using Illumina MiSeq®. The sequences obtained from the sequence were analysed in Nextclade V1.10.0 to assign the corresponding clades, identify mutations in the SARS-CoV-2 genes and perform quality control of the sequences obtained. All sequences were aligned using MAFFT v7.471. The SARS-CoV-2 isolate Wuhan NC 045512.2 was used as a reference sequence to analyse mutations at the amino acid level. The construction of the phylogenetic tree model was achieved with IQ-TREE v1.6.12. Results: it was determined that during the period December 2020 and January 2021, the lineages s C.14, C.33, B.1.1.485, B.1.1, B.1.1.1, B.1.111 circulated, lineage C.14 the most predominant with 76.7% (n=23/30), these lineages were classified in clade 20D mainly and also within clade 20B and 20A. On the contrary, the variants found in the second batch of samples of the period September – October 2021 were Delta Variant (72.7%), Gamma (13.6%), Mu (4.6%), Lambda (9.1%), distributed between clades 20J, 21G, 21H, 21J and 21I. Conclusions: This study reveals updated information on the viral genomics of SARS-CoV-2 in the Lambayeque region, Peru, which is crucial to understanding the origins and dispersion of the virus and provides information on viral pathogenicity, transmission and epidemiology.

Avipoxvirus (APV), a linear dsDNA virus belonging to the subfamily Chordopoxvirinae of the family Poxviridae, infects more than 278 species of domestic and wild birds. It is responsible for causing the avian pox disease, which is characterized by its cutaneous and diphtheric forms. With a high transmission capacity, it can cause high economic losses and damage to the ecosys-tem. Several diagnostic methods are available and vaccination of birds can be an effective pre-ventive measure. To update the molecular characterization and phylogenetic analysis of viruses isolated in Portugal between 2017 and 2023, ten APV-positive samples were analyzed. A P4b gene fragment was amplified by PCR and the nucleotide sequence of the amplicons was deter-mined by Sanger sequencing. The sequences obtained were aligned using ClustalW, and a max-imum likelihood phylogenetic tree was constructed. With this study, it was possible to verify that the analyzed sequences are distributed in subclades A1, A2, B1, and B3. Since some of them are quite similar to others from different countries and obtained in different years, it is possible to conclude that there have been several viral introductions in Portugal. Finally, it was possible to successfully update the data on avipoxviruses in Portugal.

Vernonia amygdalina is an important nutritional and medicinal plant that is used to treat various diseases such as malaria and diabetes in Nigeria. In this study, we sequenced, assembled, and annotated the complete nucleotide sequence of the chloroplast genome of a V. amygdalina species isolated in Awka, Nigeria. The chloroplast genome is 153 149 bp in length and has a conserved structure that includes the LSC (84261 bp) region, the SSC (13152 bp) region, and the IR (27868 bp) regions. A total of 131 genes were identified, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Comparative analysis of the genome revealed species variations in the LSC region associated with the geographical location of the V. amygdalina plant. Phylogenetic analysis of the chloroplast genomes using FastTree showed that V. amygdalina clustered closest to the chloroplast of the Crepidiastrum genus. This study identifies the characteristics of the V. amygdalina chloroplast genome, which will improve our understanding of intraspecies diversity and the identification of potential molecular markers to determine geographical origin.

The Ponto-Caspian region is the main donor of invasive amphipods to freshwater ecosystems, with at least 13 species successfully established in European inland waters. Dikerogammarus spp. and Pontogammarus robustoides are among the most successful, due to their strong invasive impact on local biota. However, genomic knowledge on these invaders is scarce, while phylogeography and population genetics have been based on short fragments of mitochondrial markers or nuclear mi-crosatellites. In this study, we provide: (i) reconstruction of four mitogenomes for four invasive gammarids; (ii) comparison between the structure of the newly obtained mitogenomes and to those from literature; (iii) SNP calling rates for individual D. villosus and D. haemobaphes from different invasion sites across Europe; and (iv) the first time-calibrated full mitogenome reconstruction of several Ponto-Caspian taxa. We have sequenced, assembled and annotated four mitogenomes, each from D. villosus, D. hae-mobaphes, D. bispinosus and Pontogammarus robustoides. We found that, in comparison to other gammarids, the mitogenomes of Ponto-Caspian species show a translocation between the tRNA-E and tRNA-R positions. Phylogenetic reconstruction using the mitogenomes identified that Ponto-Caspian gammarids form a well-supported group that originated in the Miocene. Our study supports paraphyly in the family Gammaridae. These mitogenomes serve as vital genetic resources for the development of new markers for PCR-based identification methods and demographic studies.

The Semantic-Enhanced Tree-LSTM (SeT-LSTM) network, a novel advancement in the realm of linguistic modeling, marks a significant step forward from traditional Tree-based Long Short Term Memory (LSTM) networks. By intricately weaving in the nuances of typed grammatical dependencies, SeT-LSTMs offer a more nuanced understanding of language semantics. Traditional models often overlook the semantic shift caused by variations in word or phrase roles, a gap this paper aims to fill by focusing on the types of grammatical connections, or typed dependencies, within sentences. Our proposed architecture, dubbed the Semantic Relationship-Guided LSTM (SRG-LSTM), leverages a control mechanism to model the interplay between sequence elements. Additionally, we present a novel Tree-LSTM variant, the Semantic Dependency Tree-LSTM (SDT-LSTM), which integrates dependency parse structures with dependency types for more robust sentence embedding. The SDT-LSTM demonstrates superior performance in Semantic Relatedness Scoring and Sentiment Analysis compared to its predecessors. Qualitatively, it shows resilience to changes in sentence voice and heightened sensitivity to nominal alterations, aligning well with human intuition. This research underlines the pivotal role of grammatical relationships in sentence understanding and paves the way for further exploration in this domain.

The aim of the work was to carry out an ergonomic assessment of the workload when working with a chainsaw during motor-manual tree processing. Wearable technology was used, namely Garmin, Biostrap and Whoop devices, which are generally available. The dependence of the heart rate (HR) on physical workload was examined to calculate Heart Rate Index. The case study was done with one worker, three variations of chainsaw devices cutting the poplar wood. It was proved that the use of a heavier work tool, MS 500i /90 cm 9,3 kg, significantly contributes both to the creation of a non-physiological working position and to an increase in the energy required to perform work, which was represented by an increase in heart rate. With a lighter work tool and a shorter cutting blade, both a decrease in heart rate and a reduction in the working time were performed in a non-physiological position. The results can be used in common practice for workers´ self-assessment to increase safety and health protection at work or work productivity not only in motor-manual processing in forestry related professions.

Identifying the total number of fruits on trees has long been of interest in agricultural crop estimation work. Yield prediction of fruits in practical environment is one of the hard and significant tasks to obtain better results in crop management system to achieve more productivity with regard to moderate cost. Utilized color vision in machine vision system to identify citrus fruits, and estimated yield information of the citrus grove in-real time. Fruit recognition algorithms based on color features to estimate the number of fruit. In the current research work, some low complexity and efficient image analysis approach was proposed to count yield fruits image in the natural scene. Semi automatic segmentation and yield calculation of fruit based on shape analysis is presented. Color and shape analysis was utilized to segment the images of different fruits like apple, pomegranate obtained under different lighting conditions. First the input sectional tree image was converted from RGB colour space into the colour space transform (i.e., YUV, YIQ, or YCbCr). The resultant image was then applied to the algorithm for fruit segmentation. After it is applied Morphological Operations which is enhanced image then execute Blob counting method which identify the object and count the number of it. Accuracy of this algorithm used in this thesis is 82.21% for images that have been scanned.

Chaphamaparvovirus (ChPV) is an ancient virus that has been detected in a variety of hosts. In this study, based on the phylogenetic analysis and the adaptability of ChPV to multiple hosts, we evaluated the potential of feline (FeChPV) and canine ChPV (CaChPV) for cross-species transmis-sion. Phylogenetic analysis showed that FeChPV and CaChPV were closely related. Notably, two strains of ChPVs isolated from domestic cats and 2 from dogs clustered together with CaChPVs and FeChPVs, respectively, suggesting the stringent boundaries between canine and feline ChPV may be broken. Further analysis revealed that CaChPV and FeChPV were more adapted to dogs than to cats, strongly suggesting the possibility of unidirectional or bidirectional transmission be-tween dogs and cats. Mutation analysis identified several shared mutations in cross-species-transmissible strains that were not located within immune epitopes. Furthermore, the VP struc-tures of FeChPV and CaChPV exhibited a high degree of similarity across both cross-species-transmissible and non-cross-species-transmissible strains. However, definitive experimental evi-dence is lacking, and its capacity for cross-species transmission should be approached with cau-tion and elucidated in further studies.

Rett syndrome (RTT), a neurodevelopmental disorder, is mainly caused by mutations in methyl CpG-binding protein 2 (MECP2), which alter the functions of domains to either bind to methylated DNA or interact with a transcriptional co-repressor complex. It has been established that alterations in cyclin-dependent kinase-like 5 (CDKL5) or forkhead box protein G1 (FOXG1) correspond to distinct neurodevelopmental disorders, given that a series of studies have indicated that RTT is also caused by alterations in either one of these genes. We tried to elucidate RTT through evolution and structure assessment of MeCP2, CDKL5, and FOXG1, by focusing on their binding partners and disordered structures. Here, we provide insight into the similarities of the FOXG1 and MECP2 binding partners evolution and function. On the other hand, we suggest that CDKL5 could be a potential candidate for a classical RTT treatment, particularly based on its disordered structure that spans after the catalytic domain to the C-terminus, which shows abundant linear motifs that can bind to molecules with divergent structures of similar affinity. Additionally, we provide insight into the relationship between disordered structure and disease.

In tobacco plants, symbiont endophytic fungi are widely distributed in all tissues where they play important roles. It is therefore important to determine the species distribution and characteristics of endophytic fungi in tobacco. Here, two parasitic fungi Leptosphaerulina chartarum and Curvularia trifolii were isolated and identified from normal tobacco tissue. We sequenced the mitogenomes of these two species and analysed their features, gene content, and evolutionary histories. The L. chartarum and C. trifolii mitochondrial genomes were 68,926 bp and 59,100 bp long circular molecules with average GC contents of 28.60% and 29.31%, respectively. The L. chartarum mitogenome contained 36 protein coding genes, 26 tRNA genes, and 2 rRNA genes (rrnL and rrnS), which were located on both strands. The C. trifolii mitogenome contained 26 protein coding genes, 29 tRNA genes, and 2 rRNA genes (rrnL and rrnS). The L. chartarum 26 tRNAs ranged from 70 bp to 84 bp in length, whereas the 29 tRNAs in C. trifolii ranged from 71 bp to 85 bp. L. chartarum and C. trifolii mtDNAs had an identical mitochondrial gene order and orientation and were phylogenetically identified as sisters. These data therefore provide an understanding of the gene content and evolutionary history of species within Pleosporales.

During the last decades West Nile Virus (WNV) outbreaks have continuously occurred in the Mediterranean area. In August 2020 a new WNV outbreak affected 71 people with meningoencephalitis in Andalusia and 6 more cases in Extremadura (south-west of Spain), causing a total of eight deaths. The whole genomes of four viral isolates were obtained and phylogenetically analyzed in the context of recent outbreaks. The Andalusian viral samples belonged to the lineage 1 and were relatively similar to previous outbreaks occurred in the Mediterranean region. Here we present a detailed analysis of the outbreak, including an extensive phylogenetic study.

Tropical forests provide habitats for diverse flora and fauna. In addition, they are essential in regulating the climate while at the same time millions of people depend on them for their livelihoods. As seen by rising political commitment and worldwide promises to reduce rates of deforestation and boost restoration of degraded forest ecosystems, forests are becoming more widely acknowledged for their role as a nature-based solution to many sustainable development concerns. Understanding tropical forest dynamics and their conservation have so become more important. This study analyzed, the forest stand structure, tree species composition, abundance and diversity and the regeneration status of Londiani Forest. Londiani Forest is divided into three blocks, namely Kedowa, Chebewor and Londiani and from each of these blocks belt transects 25 m wide and 1 km long were established 100 m from the edge of the forest to reduce edge effects. At every 200 m along the transect, 25 m × 25 m quadrats were set up in which, an inventory of all tree species was done. For tree species that could not be identified in the field, the local name was provided by para-taxonomists who participated in the data collection and the species name was later identified with the help of a taxonomist or a manual of woody tree species of Londiani Forest. The diameter at breast height (DBH) was measured at 1.3 m from the ground using a diameter tape. Tree height was measured using a Suunto angular clinometer. A nested quadrat 5 m x 5 m quadrat within the 25 m x 25 m quadrat was used to sample saplings while a 1 m x 1 m quadrat was used for sampling seedlings. Regeneration status was assessed using the number of seedlings and saplings. Stumps of trees cut were counted including identifying tree species from which the tree stump was derived. Data from the quadrats were entered into Microsoft Excel. Total stem density, species density, basal area, species basal area, relative density and species diversity were determined. A total of 1,308 individual trees belonging to 34 different species from 24 families were recorded. Kedowa had the highest (27) species richness followed by Chebewor (19) then Londiani (14). There was a statistically significant difference in species richness among the three forest blocks (p<0.05). There were no statistically significant differences in the mean DBH (F=0.560; p=0.729) and height class distribution (F= 0.821, p=.558) among the three forest blocks. There was a statistically significant difference in stem density (F=12.22; p=0.005) and woody species diversity (F=0.32; p=0.001) within the three forests blocks. There was no statistically significant difference in the basal area distribution within the three forest blocks p>0.005. The similarity index ranged from 0.34 to 0.47. In all the forest blocks, there was evidence of seedlings and saplings indicating that there was regeneration. Results clearly show that while the Londiani Forest shows variation in characteristics, there is clear evidence that it is regenerating.

Badminton tactics refer to the techniques and strategies employed by players to win a match. Analyzing these tactics can help players improve their performance and outsmart their opponents. To study the tactics of top players, we use a gaming tree to analyze matches between two of the most powerful badminton players in history: Lin and Lee. By employing the Nash Equilibrium, we can discover the most beneficial strategies for both players, which reflect their most powerful techniques. Additionally, with the help of this gaming tree, we can precisely predict how players will implement their tactics. Empirical experimental results demonstrate that our proposed method not only evaluates and identifies each player's weaknesses and strengths but also has powerful capabilities to predict their tactics.

In our article in Genome Biology Ecology six years ago, one complete plastid genome of Belian was assembled for comparative analyses of the plastomes in Lauraceae. However, Ariati et al. (2023) concluded that our sequenced Belian individual could be located in the clade of Myristicaceae instead of that of Lauraceae. Here, we performed re-analyses of additional two Belian plastomes, along with 42 plastomes from plants spanning ten families of the Magnoliids. The plastomes of the three Belian individuals range from 157,535 to 157,577 bp in length. Comparative genomic analysis revealed 170 mutation sites in their plastomes, which include 111 substitutions, 53 indels, and six microinversions. Phylogeny was reconstructed using maximum likelihood and Bayesian approaches for 44 magnoliids species indicated that our three Belian individuals are nested among the species in the family Lauraceae rather than Myristicaceae.

The provenance of the aminoacyl-tRNA synthetases (aaRS) poses challenging questions because of their role in the emergence and evolution of genetic coding. We investigate evidence about their ancestry from curated structure-based multiple sequence alignments of a structurally invariant “scaffold” shared by all 10 canonical Class I aaRS. Three uncorrelated phylogenetic metrics—residue-by-residue conservation, its variance, and row-by-row cladistic congruence—imply that the Class I scaffold is a mosaic assembled from distinct, successive genetic sources. These data are especially significant in light of: (i) experimental fragmentations of the Class I scaffold into three partitions that retain catalytic activities in proportion to their length; and (ii) evidence that two of these partitions arose from an ancestral Class I aaRS gene encoding a Class II ancestor in frame on the opposite strand. Phylogenetic metrics of different modules vary in accordance with their presumed functionality. A 46-residue Class I “protozyme” roots the Class I molecular tree prior to the adaptive radiation of the Rossmann dinucleotide binding fold that refined substrate discrimination. Such rooting is consistent with near simultaneous emergence of genetic coding and the origin of the proteome, resolving a conundrum posed by previous inferences that Class I aaRS evolved long after the genetic code had been implemented in an RNA world. Further, pinpointing discontinuous enhancements of aaRS fidelity establishes a timeline for the growth of coding from a binary amino acid alphabet.

The phylogenetic relationships among the Peninsular Malaysian orchid genus Coelogyne were studied by morphological characteristics and by sequencing the internal transcribed region (ITS) from the nuclear ribosomal DNA (nrDNA). Coelogyne is a large genus of about 200 species distributed in pantropical areas from the Himalayas, Sri Lanka, India, Southern China and throughout South East Asia to Papua New Guinea. The widely accepted previous classification system was exclusively based on floral morphology. There were very few molecular systematic studies of Coelogyne done in Peninsular Malaysia thus far. In this study, 59 Coelogyne taxa were collected from throughout Peninsular Malaysia and 57 of them were identified to the species level. To study the phylogeny of this genus, morphological characters were utilized together with molecular evidences to generate the systematic hypotheses. Cluster analysis was performed using both the vegetative and floral characters. The results showed that three sections of Peninsular Malaysian Coelogyne, namely Longifoliae, Speciosae and Fuliginosae were sister groups which were more closely related by forming one clade than they were with the other sections. Another clade consisted of four other sections, namely Flaccidae, Coelogynae, Tomentosae and Verrucosae. Molecular phylogenies obtained by using the Neighbour Joining method revealed the close relationship between the sections Tomentosae and Verrucosae, whereas usage of the Maximum Likelihood method demonstrated that three sections namely Longifoliae, Speciosae and Fuliginosae were sister groups since they formed a single clade.

The present paper reviews evidence for ecological evolution of Montiaceae. Montiaceae (Portulacineae) comprise a family of ca. 275 species and ca. 25 subspecific taxa of flowering plants distributed mainly in extreme western America, with additional endemism elsewhere, including other continents and islands. They have diversified repeatedly across steep ecological gradients. Based on narrative analysis, I argue that phylogenetic transitions from annual to perennial life history have been more frequent than suggested by computational phylogenetic reconstructions. I suggest that a reported phylogenetic correlation between the evolution of life history and temperature niche is coincidental and not causal. I demonstrate how statistical phylogenetic comparative analysis (PhCA) missed evidence for marked moisture niche diversification among Montiaceae. I discount PhCA evidence for the relation between Montiaceae genome duplication and ecological diversification. Based on the present analysis of Montiaceae evolution, I criticize the premise of the prevalent statistical approach to PhCA, which tests Darwinian deterministic hypotheses against stochastic evolutionary null models. I discuss theoretical/empirical evidence that evolution is neither stochastic, nor Darwinistically-determined, but idiosyncratic. Idiosyncraticity describes the outcome of a stochastically perturbed nonlinear chaos-like process. The Principle of Evolutionary Idiosyncraticity (PEI) is based on the evolutionary theory of Natural Drift, which maintains that determinism in evolution is a property of the organism and not, as maintained by the theory of Natural Selection, its traits or its milieu. This determinism is characteristic of chaotic functions, which are absolutely determinate, generate self-similarity, but remain absolutely unpredictable. PEI explains precisely observations that evolution proceeds not linearly, but chaotically, producing both quasi-linear fractal-like patterns and non-linear jumps. PEI has ramifications for all areas of macroevolutionary research. In particular, it demonstrates both the fallacy and futility of the statistical PhCA approach that interprets evolutionary causes in terms of evolutionary correlations. However, statistical methods of PhCA can be applied heuristically and fruitfully to reveal idiosyncraticity and discover evolutionary novelty. This, in turn, is demonstrated by the emergence of statistical anomalies in evolutionary analyses of Montiaceae.

We aimed to apply DNA barcoding tool for the molecular identification of horn snails T. telescopium using mitochondrial cytochrome oxidase I gene (mt-COI) and to investigate their evolutionary relationship along with location-specific bio-geographical variations. The molecular data sets of this study indicate that strong probability of T. telescopium species taxonomic confirmation using mt-COI sequences. Results of the phylogenetic analysis suggest that Telescopium sp. was monophyletic with disseminated nodes and the evolution of group II originated from group I. The substantial genetic distance among the mt-COI sequences (0.005 to 0.184) were noticed. Large divergence between the south-west coast of India and Australia region population indicates limited gene flow between the two continents. Our study suggests that the genera Telescopium is globally ubiquitous but genetically showing inter-region differentiation. We conclude that mt-COI gene can be used to identify gastropod T. telescopium species.

Groundwater represents a pivotal asset in conserving natural water reservoirs for potable consumption, irrigation, and diverse industrial uses. Nevertheless, human activities intertwined with industry and agriculture contribute significantly to groundwater contamination, highlighting the critical necessity to appraise water quality for safe drinking and effective irrigation. This research primarily focused on employing the Water Quality Index (WQI) to gauge water's appropriateness for these purposes. However, the generation of an accurate WQI can prove time-intensive owing to potential errors in sub-index calculations. In response to this challenge, an artificial intelligence (AI) forecasting model was devised, aiming to streamline the process while mitigating errors. The study collected 422 data samples from Mirpurkash, a city nestled in the province of Sindh, for a comprehensive exploration of the region's WQI attributes. Furthermore, the study probed into unraveling the interdependencies amidst variables in the physiochemical analysis of water. Diverse machine learning classifiers were employed for WQI prediction, with findings revealing that random forest and gradient boosting eclipsed other algorithms, achieving an accuracy rate of 99%. In close pursuit were SVM and XGBoost, registering accuracy scores of approximately 95% and 93%, respectively, while KNN and Decision Trees garnered accuracy rates of 88% and 87%, respectively. In addition to WQI prediction, the study conducted an uncertainty analysis of the models using the R-factor, providing insights into the reliability and consistency of predictions. This dual approach, combining accurate WQI prediction with uncertainty assessment, contributes to a more comprehensive understanding of water quality in Mirpurkash and enhances the reliability of decision-making processes related to groundwater utilization

We use binary string to represent a natural number and show the composite procedure of odd-number and even-number functions, thus we propose full binary directed tree to represent the set of natural numbers and give another partition the natural number set to three sets: pure odd, pure even and mixed number. For the Collatz conjecture we make use of the parity of a natural number to analyse the sequence of iteration (or composite) of Collatz function and reduced Collatz function analog to the inverse function. We give tabular and binary strings to the algebra expression to state the sequence of Collatz, this is the key topic to proof the conjecture: the discrete powers of 2 can be changed to ultimately continuous powers of 2, finally get to pure even number and to the smallest number 1. The sequence created by the infinite iterations of the Collatz function becomes the ultimately periodic sequence if any natural number is the beginning value, proving the conjecture that has been held for 87 years.

The art of representing source code is pivotal in numerous programming analysis applications. Recent strides in neural networks have marked notable successes in this realm. However, the peculiar structural characteristics inherent in programming languages have not been fully exploited in existing models. While neural models based on abstract syntax trees (ASTs) adeptly manage the tree-like nature of source codes, they fall short in discerning the diverse substructural nuances within programs. This paper introduces the Dynamic Syntax Tree Model (DSTM), an innovative approach that fuses various neural network modules into tree architectures tailored to the specific AST of the input. Distinct from preceding tree-based neural models, DSTM adeptly discerns the semantic variances across different AST substructures. We validate DSTM through rigorous testing in program classification and code clone detection, outperforming contemporary methods and demonstrating the benefits of harnessing intricate source code structures.

The $k$-set tree connectivity, as a natural extension of classical connectivity, is a very important index to evaluate the fault-tolerance of interconnection networks. Let $G=(V, E)$ be a connected graph and a subset $S\subseteq V$, an $S$-tree of graph $G$ is a tree $T=(V',E')$ that contains all the vertices of $S$. Two $S$-trees $T$ and $T'$ are internally disjoint if and only if $E(T)\cap E(T')=\varnothing$ and $V(T)\cap V(T')=S$. The cardinality of maximum internally disjoint $S$-trees is defined as $\kappa_{G}(S)$, and the $k$-set tree connectivity is defined by $\kappa_{k}(G)=\min\{\kappa_{G}(S)|S\subseteq V(G)\ \text{and} \ |S|=k\}$. In this paper, we show that the $k$-set tree connectivity of hierarchical folded hypercube when $k=4$, that is, $\kappa_{4}(HFQ_{n})=n+1$, where $HFQ_{n}$ is hierarchical folded hypercube for $n\geq 7$.

This article delves into the pivotal role that biodiversity of soil microbes plays in bolstering tree health and overall agroecosystem productivity. With the advent of regenerative agricultural practices, there has been a resurgence of interest in understanding the complex interactions between soil microbiota and plant roots, particularly through processes like rhizophagy. Rhizophagy, the digestion of living root cells by soil microorganisms, stands out as a fundamental mechanism in nutrient cycling and overall tree vitality. By examining the impact of enhanced microbial diversity on tree health, we shed light on the practical applications, such as the utilization of the BEAM Inoculant product, which has demonstrated remarkable efficacy in augmenting soil health and, consequently, tree Vigor

Development and redevelopment are important drivers of tree removal and canopy loss in urban landscapes. Local ordinances are often used to curtail tree removal, but punitive regulations alone may not be enough to reduce urban tree canopy loss in land development. In Florida (US), efforts to balance trees and development have so far focused on fees and fines, but with a recent backlash against tree regulations and the fast pace of urban growth, we explored the possible role of incentives in urban tree policies. We interviewed 20 land developers across Florida to understand their perspectives on current barriers and potential incentives for tree preservation and planting. We collected data from developers, whose perspectives on tree preservation are often unknown or overlooked, despite their significant role in tree planting, removal, and retention in and around cities. Our results show that major barriers to tree preservation and planting include requirements to grade sites for stormwater management, site constraints, and monetary costs. Most developers did not know of any existing incentives beyond intrinsic motivations but said that financial incentives would be most appealing to them. Top incentive suggestions include increasing building density, reducing impact fees and tax liability, and changing tree mitigation policies. Another promising finding is that developers are willing to work with regulators to find solutions that benefit both parties. Future research should consider evaluating the level of support and viability of different incentives by gathering feedback from policymakers, land developers, and the public.

As an established and widely available infrastructure, wireless local area networks (WLANs) have emerged as a viable option for indoor localization of both mobile and stationary users. In planning a mobile communications network and radio system design, the critical role of coverage prediction becomes evident, empowering network operators to optimize cellular networks and elevate the overall customer experience. Moreover, WLANs present several challenges that must be fulfilled when it comes to localization based on Wi-Fi signals to get a proper coverage prediction map. This paper presents a study based on application of the extra trees regression (ETR) for indoor localization by using coverage prediction maps. The aim of the proposed method is to accurately estimate a user’s position within a radio environment map (REM) area using collected received signal strength indicator (RSSI) values. The proposed scheme investigates several machine learning (ML) regression algorithms for localization, where the training dataset is obtained from the REM by using the nearest neighbors method. Parameter tuning is conducted to optimize the performance of the ETR scheme by using 10-fold cross-validation. In the numerical results, we first demonstrate the effectiveness of utilizing ML regression techniques for generating coverage maps, which enables accurate estimation of the Wi-Fi signal strength in indoor environments. Then, we showcase the superior performance of the proposed ETR-based method compared to several other ML schemes for indoor localization using the REM. ML algorithms, including decision tree regression and the ETR, are compared to evaluate the system model. Based on error metrics, the proposed ETR-based approach exhibits the best performance among the evaluated techniques. The combination of coverage map generation and localization using regression techniques offers a powerful approach for analyzing the radio frequency (RF) environment in indoor spaces.

As synthetic/artificial life forms become more abundant and sophisticated, an increasing number of bizarre creatures - xenobots, robots, soft A-life entities, genetically engineered organisms, etc. - are invading our society. Therefore, we need to bring order to all this, to establish what is living and what is not. Here, I intend to classify all these non-natural entities and clarify their status with reference to their consideration or not as living beings, leaving the door open to an uncertain future in which perhaps we can see how "the artificial" and "the natural" merge to originate something new. To order all this "new biodiversity" and to also give entry to viruses (which are excluded of the three-domains tree of life), I propose the creation of a new domain, Lithbea (from the name: life-in-the-border entities), in which all these new human-made entities as well as the viruses will be included. Within this domain there would be two kingdoms, Virus and Humade (contraction of human-made), based on their origin, natural or human-made. A brief description of each component of Lithbea is included and the implications for society and biology of this “new biodiversity” is briefly discussed.

The article presents a mathematical model to investigate the operability envelopes for subsea production tress (SPT) installation using drill pipe. The finite differential method was used to solve the established governing equations in which the ocean conditions were considered. Based on the evaluations of the ocean wave, ocean current, water depth, specification of drill pipe and SPT weight that might dominate the mechanical behaviors of the pipe, the operability envelopes with permissible ocean conditions for SPT installation were obtained. The results indicate that changes of depths in deep water and SPT weight have few effects on the operation conditions and it would be better to choose smaller pipe to obtain larger permissible ocean conditions during SPT installation.

The SARS-CoV-2 virus, causative agent of COVID-19, is known for its genetic diversity. Virus variants of concern (VOCs) as well as variants of interest (VOIs) are classified by the World Health Organization (WHO) according to their potential risk to global health. This study seeks to enhance the identification and classification of such variants by developing a novel bioinformatics criterion centered on the virus's spike protein (SP1), a key player in host cell entry, immune response, and a mutational hotspot. To achieve this, we pioneered a unique phylogenetic algorithm which calculates EIIP-entropy as a distance measure based on the distribution of the Electron-Ion Interaction Potential (EIIP) of amino acids in SP1. This method offers a comprehensive, scalable, and rapid approach to analyze large genomic data sets and predict the impact of specific mutations. This innovative approach provides a robust tool for classifying emergent SARS-CoV-2 variants into potential VOCs or VOIs. It could significantly augment surveillance efforts and understanding of variant characteristics, while also offering potential applicability to the analysis and classification of other emerging viral pathogens and enhancing global readiness against emerging and re-emerging viral pathogens.

The fungal family Microthyriaceae is represented by relatively few mycelial cultures and DNA sequences. As a result, the taxonomy and classification of this group of organisms remain poorly understood. Here, based on DNA sequences at four gene fragments (nuLSU rDNA, nuSSU rDNA, TEF1 and RPB2) in our analyses of aquatic hyphomycetes from southern China, we identify and report four new genera (Antidactylaria, Isthmomyces, Keqinzhangia, Pseudocoronospora) and thirteen new species (Antidactylaria minifimbriata, Pseudocoronospora hainanensis, Isthmomyces oxysporus, I. dissimilis, I. macrosporus, I. relanceatus, Keqinzhangia aquatica, Triscelophorus anakonajensis, T. anisopterioides, T. guizhouensis, T. mugecuoensis, T. multibrachiatus, T. neoseptatus; new combinations Isthmomyces asymmetrica, I. basitruncata, I. geniculata, I. lanceata, I. minima, I. rotundata) belonging to Microthyriaceae. Our results provided the first molecular evidence of asexual morph of this family and strengthened the phylogenetic placement of the family in class Dothideomycetes. The addition of these new taxa made Microthyriaceae the largest family comprising freshwater asexual genera in Pleosporomycetidae. In addition, we confirmed the monophyly of the genus Triscelophorus, the paraphyly of the genus Isthmolongispora, and revised 6 new combinations in Isthmolongispora. ITS barcoding of 13 species were also provided to help identify aquatic hyphomycetes in the future. Our results suggest that the asexual genera and sexual genera identified so far within this family have completely different ecological niches.

This study addresses the problem of accurately predicting azimuth and elevation angles of signals impinging on an antenna array employing Machine Learning (ML). Using the information obtained at a receiving system when a transmitter’s signal hits it, a Decision Tree (DT) model is trained to estimate azimuth and elevation angles simultaneously. Simulation results demonstrate the robustness of the proposed DT-based method, showcasing its ability to predict the Direction of Arrival (DOA) in diverse conditions beyond the ones present in the training dataset, i.e., the results display the model’s generalization capability. Additionally, the comparative analysis reveals that DT-based DOA estimation outperforms the state-of-the-art MUltiple SIgnal Classification (MUSIC) algorithm, establishing DTs as competitive alternatives for DOA estimation in signal reception systems.

Urban trees are often more sun- and wind-exposed than their forest-grown counterparts. These environmental differences can impact how many species grow – impacting trunk taper, crown spread, branch architecture, and other aspects of tree form. Given these differences, windthrow models derived from traditional forest production data sources may not be appropriate for urban forest management. Additionally, visual abnormalities historically labeled as “defects” in timber production may not have a significant impact on tree failure potential. In this study, we look at urban tree failures associated with Hurricane Irma in Tampa, Florida, USA. We used spatial analysis to determine if patterns of failure existed among our inventoried trees. We also looked at risk assessment data to determine which visual defects were the most common and the most likely to be associated with branch or whole-tree failure. Results indicate that there was no spatial pattern associated with the observed tree failures – trees failed or withstood the storm as individuals. While some defects like decay and dead wood were associated with increased tree failure, other defects like weak branch unions and poor branch architecture were less problematic.

While many practitioners and experts understand the risks associated with low urban tree diversity, they often lack the ability to rectify issues they encounter on their own. The current system of tree production and procurement is complex – shaped by market pressures, nursery and site constraints, local governance, and differing professional objectives among those who grow, specify, and plant trees. To understand this complexity as well as constraints to- and opportunities for increasing urban tree diversity, we conducted a series of focus groups comprised of nursery growers, landscape architects, and urban foresters. Our results highlight a significant list of considerations and constraints to diversity (both shared among green industries and some specific to growers or purchasers). More importantly, in discussing our findings we outline actionable strategies for increasing urban tree diversity.

Distinguishable annual growth rings produce in Pinus roxburghii are an asset to find out the age of individual tree. This paper aimed to determine the age of P. roxburghii through coring samples and test the relationship with forest production. The biomass estimated, girths measured at two different sections and heights measured which allowed to determine the rate of tapering of the stand. The regression analysis was performed to test the relationship between various variables. The mean age of the P. roxburghii stand was found to be 23.97 (~24 years). The result showed the significant (p<0.05) positive correlation coefficient has been seen between age with girth at breast height, biomass, volume and carbon stock. However, no significant (p>0.05) correlation (r = 0.08) was found between age and height of the stand. In contrast, a correlation between diameter at breast height (DBH) was significant (p<0.05) and positive with volume, biomass, but no significant (p>0.05) correlation (r = 0.14) found between DBH and height of the stand. However, height has a significant (p<0.05) positive correlation with biomass. The mean biomass was 375 kg and mean annual increment (MAI) was 15 kg per tree. Rate of tapering of the studied stand predicted to be 3 cm diameter decreased with trunk height running at 100 cm from base to upward of P. roxburghii stand and vice versa. Result suggests that height-age relation is very weak whereas age, DBH, biomass and carbon has a significant correlation signifies that time-based forests' production and potential production estimation can be obtained in a relatively accurate way by utilizing the age of stand. The time-based forest production analysis is pioneer work in Nepal. The study affirms the tree ring count in P. roxburghii would be a credible and accurate method to determine the age of standing trees.

Across Central Asia, agriculture largely depends on irrigation due to arid and semi-arid climatic conditions. Water is abstracted from rivers, which are largely fed by glacier melt. In the course of climate change, glaciers melt down so that a reduced glacier volume and reduced water runoffs are expected being available for irrigation. Tree wind breaks are one option to reduce water consumption in irrigated agriculture and build resilience against climate change. This paper therefore assessed water consumption of major crops (cotton, wheat, corn, rice, potato, and barley) in Kyrgyzstan and adjacent areas in combination with tree wind breaks. Crop water consumption was assessed through the Penman Monteith approach. Tree wind break types investigated were single rows from poplars and multiple rows with undergrowth by elm and poplar, respectively. Tree water consumption was determined through sapflow measurements. Seasonal ETo for field crops was 876 mm to 995 mm without wind breaks and dropped to less than half through multiple row wind breaks with undergrowth (50 m spacing). Tree water consumption was 1125 mm to 1558 mm for poplar and 435 mm for elm. Among the wind break crop systems, elm wind breaks resulted in highest reductions of water consumption, followed by single row poplars, at spacing of 50 m and 100 m, respectively. Yet, elm grows much slower than poplar so that poplars might be more attractive for farmers. Furthermore, single row wind breaks might by much easier to be integrated into the agrarian landscape, as they consume less space.

The genetic diversity of local coffee populations is crucial to breed new varieties better adapted to the increasingly stressful environment due to climate change and the evolving consumer preferences. Unfortunately, local coffee germplasm conservation and genetic assessment have not received much attention. Molecular tools offer substantial benefits in identifying and selecting new cultivars or clones suitable for sustainable commercial utilization. New annotation methods, such as chloroplast barcoding, are necessary to produce accurate and high-quality phylogenetic analyses. This study used DNA barcoding techniques to examine the genetic relationships among fifty-six accessions collected from the southern part of Saudi Arabia. PCR amplification and sequence characterization were used to investigate the effectiveness of four barcoding loci, namely atpB-rbcl, TrnL-TrnF, TrnT-TrnL, and TrnL. The maximum nucleotide sites, nucleotide diversity, and an average number of nucleotide differences were recorded for atpB-rbcl, while TrnT-TrnL had the highest variable polymorphic sites, segregating sites, and haploid diversity. Among the four barcode loci, TrnT-TrnL recorded the highest singleton variable sites, while TrnL recorded the highest parsimony information sites. Furthermore, the phylogenetic analysis clustered the Coffea arabica genotypes into four different groups, with three genotypes (KSA31, KSA38, and KSA46) found to be the most divergent genotypes standing alone in the cluster and remained apart during the analysis. The study demonstrates the presence of considerable diversity among coffee populations in Saudi Arabia. Furthermore, it also shows that DNA barcoding is an effective technique for identifying local coffee genotypes, with potential applications in coffee conservation and breeding efforts.

Cattle spread throughout the American continent during the colonization years, originating creole breeds that adapted to a wide range of climate conditions. Population of creole cattle in Peru is decreasing mainly due to the introduction of more productive breeds in recent years. During the last 15 years, there have been a significant progress on cattle genomics. However, little is known about the genetics of the Peruvian creole cattle (PCC) even though its importance to (i) improve productivity in the Andean region, (ii) agricultural labor, and (iii) cultural traditions. In addition, the origin and phylogenetic relationship of the PCC is still unclear. In order to promote the conservation of the PCC, we sequenced for the first time the mitochondrial genome of a creole bull from the highlands of Arequipa, which also possessed exceptional fighting skills and was employed for agricultural tasks. The total mitochondrial genome sequence is 16,339 bp in length with the base composition of 31.43 % for A, 28.64 % for T, 26.81 % for C, and 13.12 % for G. It contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a control region. Among the 37 genes, 28 were positioned on the H-strand and nine were positioned on the L-strand. The most frequently used codons were CUA (Leucine), AUA (Isoleucine), AUU (Isoleucine), AUC (Isoleucine), y ACA (Threonine). Maximum likelihood reconstruction using complete mitochondrial genome sequences clearly demonstrated that the PCC is strongly related to native African breeds, giving insights into the ancestry of PCC. The annotated mitochondrial genome of PCC would serve as an important genetic data set for further breeding work and conservation strategies.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive sense single stranded RNA genome containing virus which has infected millions of people all over the world particularly China. The virus has been mutating rapidly enough resulting in the emergence of new variants and sub-variants which have reportedly been spread from Wuhan city of China, the epicenter of the virus, to the rest of China and all over the world. The occurrence of mutations in the viral genome especially in the viral spike protein region has resulted in the evolution of multiple variants and sub-variants which gives the virus benefit of host immune evasion and render the modern-day vaccines and therapeutics ineffective. Therefore, there is a continuous need to study the genetic characteristics and evolutionary dynamics of the SARS-CoV-2 variants. Hence, in this study, a total of 833 complete genomes of SARS-CoV-2 variants (including the wild-type or reference sequence) from Taiyuan and Wuhan cities of China were genetically characterized and studies their phylogenetic and evolutionary dynamics using phylogenetics, genetic similarity, and phylogenetic network analysis. Our results show a lot of useful information regarding the evolutionary dynamics of the viral variants, their genetic similarities/dissimilarities, and their phylogenetic relationships. It has been reported in this study that the SARS-CoV-2 variants have nine recombinant events which suggest very important information regarding the viral evolution. In addition, the phylogenetic network analysis shows the number of mutations resulting in emergence and clustering of the viral variants of both cities which reveal significant information regarding the phylodynamics of the virus. This study, to the best of our knowledge, is the first ever genetic comparative study of Taiyuan and Wuhan cities. This study will help better understand the virus, cope with the emergence, and spread of new variants at local level as well as at international level and inform the public health authorities to make better informed decisions in designing new viral vaccines and therapeutics.

Flexible implementations of Monte Carlo Tree Search (MCTS), combined with domain specific knowledge and hybridization with other search algorithms, can be a very powerful for the solution of problems in complex planning. We introduce mctreesearch4j, a standard MCTS implementation written as a standard JVM library following key design principles of object oriented programming. We define key class abstractions allowing the MCTS library to flexibly adapt to any well defined Markov Decision Process or turn-based adversarial game. Furthermore, our library is designed to be modular and extensible, utilizing class inheritance and generic typing to standardize custom algorithm definitions. We demon- strate that the design of the MCTS implementation provides ease of adaptation for unique heuristics and customization across varying Markov Decision Process (MDP) domains. In addition, the implementation is reasonably performant and accurate for standard MDP’s. In addition, via the implementation of mctreesearch4j, the nuances of different types of MCTS algorithms are discussed.

Background: Hurricanes and other wind events are significant disturbances that affect coastal urban forests around the world. Past research has led to the creation of wind resistance ratings for different tree species which can be used in urban forest management efforts to mitigate the effects of these storms. While useful, these ratings have been limited to species common to one global region (Florida, USA).Methods: Drawing on past ratings and data from a global literature review on tropical storm research, we created a machine learning model to broaden both the geographic coverage and the variety of species currently assessed for their resistance to wind.Results: We were able to assign wind resistance ratings to 281 new species based on the available data and our modelling efforts. The model accuracy and agreement with the original ratings when applied to the testing data set was high with 91% accuracy.Conclusions: The resulting list of wind resistance ratings has been adapted into a spreadsheet-based decision aid for managers, allowing them to assess the overall susceptibility of their urban forest to wind events like hurricanes.

Effective development of digital twins of real-world objects requires sophisticated data collection techniques and algorithms for automated modeling of individual objects. In City Information Modeling (CIM) systems, individual buildings can be modeled automatically at the second Level Of Detail or LOD 2. Similarly, automated solutions for 3D modeling of individual trees at different levels of details are required for Tree Information Modeling (TIM) and building Forest Digital Twins (FDT). The existing algorithms support the automated modeling of trees by generating models of the canopy and the lower part of the trunk. Our work in this paper is based on the assumption that, similar to the canopy shape, the structure of tree trunk and branches is also an important consideration. An algorithm for automated modeling of tree trunks is proposed. Aiming to generate 3D models of tree trunks, the suggested approach starts by extracting the trunk point cloud, which is then segmented into single stems. Finally, the individual stems are modeled by dividing them into slices. The geometry of the developed tree models is represented in a matrix format. This solution enables automatic comparisons of tree elements over time, which is necessary for monitoring changes in forest stands and promoting sustainable forest management. Despite the huge variation of trunk geometric forms, the proposed modeling approach can gain an accuracy of better than 4 cm in the constructed tree trunk models.

The minimum dominating tree (MDT) problem consists of finding a minimum weight sub-graph from an undirected graph, such that each vertex not in this sub-graph is adjacent to at least one of the vertices in it, and the sub-graph is connected without any ring structures. This paper presents a Dual Neighborhoods Search (DNS) algorithm for solving the MDT problem, which integrates several distinguishing features, such as two neighborhoods collaboratively working for optimizing the objective function, a fast neighborhood evaluation method to boost the searching effectiveness, and several diversification techniques to help the searching process jump out of the local optimum trap thus obtaining better solutions. DNS improves the previous best-known results for 4 public benchmark instances while providing competitive results for the remaining ones. Several ingredients of DNS are investigated to demonstrate the importance of the proposed ideas and techniques.

Recent developments in the cryopreservation space has increased the trend in germplasm collections established through cryopreserved in vitro material. Cryopreservation of recalcitrant seeds through embryos and embryonic axes, is not uncommon. Tropical and sub-tropical plants are not acclimated to the cold season, therefore have no in-built natural resilience to the cold. Also, larger seeds from trees, such as avocado (Persea americana Mill.), mango (Mangifera indica) and durian (Durio zibethinus L.) are sensitive to desiccation, chilling and freezing stress, making them unsuitable for seed banking or cryopreservation. Alternatively, as seeds do not carry the same genetic make-up as the mother plant, especially in the context of woody rainforest species of which the cross-pollination is dominant; seed conservation does not serve the purpose of germplasm preservation. Other plant material and methods are needed for these plants to be successfully stored in liquid nitrogen (LN). One such method commonly used is shoot-tip cryopreservation which ensures the clonal fidelity of germplasm. There are many problems when using shoot tips of tropical recalcitrant-seeded species. These include: 1) the toxic effects of cryoprotective agents towards structural integrity; 2) optimum developmental stage for success and 3) oxidative stress associated with excision injury leading to necrosis triggering cell death and hindering regeneration for the shoot tips in culture. A pre-requisite for any cryopreservation system is the availability of an established tissue culture regeneration platform. This review will outline conservation strategies for avocado with special emphasis on attempts and improvements made in the cryopreservation space for storing this horticulturally important crop ‘avocado’ at ultra-low temperatures.

Trimeresurus albolabris, also known as the white-lipped pit viper or white-lipped tree viper, is a highly venomous snake distributed across Southeast Asia and the cause of many snakebite cases. In this study, we report the first whole genome assembly of T. albolabris obtained with next-generation sequencing from a specimen collected in Mengzi, Yunnan, China. After genome sequencing and assembly, the genome of this male T. albolabris individual was 1.51 Gb in length and included 38.42% repeat-element content. Using this genome, 21,695 genes were identified, and 99.17% of genes could be annotated using gene functional databases. Our genome assembly and annotation process was validated using a phylogenetic tree, which included six species and focused on single-copy genes of nuclear genomes. This research will contribute to future studies on Trimeresurus biology and the genetic basis of snake venom.

The process of rainfall interception by tree organs is crucial in mitigating the impact of intense rainfall on urban drainage systems, particularly in the context of climate change. this study selected ten commonly found tree species in Shanghai. Main parts of trees, including leaves, branches, and bark, were collected to analyze their ability to intercept rainwater. The optimized Artificial Rainfall Simulation System (ARSS) was applied to simulate the rainfall. The time-changing process of rainwater interception in three organs was measured during a 180-minute rainfall event which under four different rainfall intensities (4, 8, 12, and 16 mm/h, respectively). Process models of rainwater interception in different organs were fitted with adsorption kinetic equations. The rainwater interception process of tree organs complied with the quasi 2nd-order adsorption kinetic equation. The rainwater interception capacity of leaves, branches, and bark of ten urban tree species ranged from 0.05 to 0.34 mm, 0.13 to 0.24 mm, and 0.29 to 1.22 mm, respectively. The rainwater interception capacity of three organs significantly differs (p&lt;0.05). It reveals that bark exhibits the highest rainwater interception ability. Coniferous tree species have a greater ability to intercept rainwater than broad-leaved tree species. There are also differences in the rainwater interception ability of trees in urban and natural areas.

The relative position of the orchard robot to the rows of fruit trees is an important parameter for achieving autonomous navigations. The current methods for estimating the position parameters between rows of orchard robots obtain low parameter accuracy, and to address this problem, this paper proposes a machine vision-based method for detecting the relative position of orchard robots and fruit tree rows. Firstly, the fruit tree trunk is identified based on the improved YOLOv4 model; secondly, the camera coordinates of the tree trunk are calculated from the principle of binocular camera triangulation, and the ground projection coordinates of the tree trunk are obtained through coordinate conversion; finally, the midpoints of the projection coordinates of different sides are combined and the navigation path is obtained by linear fitting with the least squares method, and the position parameters of the orchard robot are obtained through calculation. The experimental results show that the average accuracy and average recall of the improved YOLOv4 model for fruit tree trunk detection are 97.05% and 95.42%, respectively, which are 5.92 and 7.91 percentage points higher than those of the original YOLOv4 model. The average errors of heading angle and lateral deviation estimates obtained based on the method in this paper are 0.57° and 0.02 m. The method can accurately calculate heading angle and lateral deviation values at different positions between rows, and can provide a reference for autonomous visual navigation of orchard robots.

The urban environment induces stress on trees and the impact can be identified by observing the condition of the crown. The aim of this study is to correlate the variables crown density (Cdn), crown transparency (Ctr) and dieback (Cdie) with the following vegetation indices: normalized difference vegetation index (NDVI), enhanced vegetation index (EVI2), blue normalized difference vegetation index (BNDVI), green normalized difference vegetation index (GNDVI), green-red vegetation Index (GRVI) and red-green-blue vegetation index (RGBVI) of the tree crown located in urban green areas, as well as chlorophyll fluorescence (Fv/Fm) as an indirect indicator of tree health condition. A total of 549 trees were evaluated, represented in 24 families, 36 genera and 53 species; the variables had average values of 67.96 % in Cdn, 35.19 % in Ctr and 1 % in Cdie. Correlations were found between Fv/Fm, NDVI and BNDVI. NDVI and BNDVI correlated with variables such as Cdn and Ctr, mainly in species such as Ligustrum lucidum, Jacaranda mimosifolia and Fraxinus uhdei. Therefore, it is possible to evaluate tree health condition of trees in urban green environments through the identification of unfavorable conditions at the crown level by using vegetation indices for some of the species studied.

Tree ordinances can be an effective means of preserving urban forests in the face of development pressures. Despite this, they also have the potential to be divisive among the public - especially when applied to privately-owned land. In this study we surveyed 1,716 Florida urban residents to understand how they value regulation and management of the urban forest. Specifically, we asked about: tree protection ordinances, incentive programs to manage or plant trees, justification for tree removal, and development. Most respondents supported tree protections, even when applied to trees on their own property or when they had the potential to limit development activities. Additionally, there was limited support for removing healthy trees for development. Respondents supported the use of funds for urban forestry efforts – particularly at the local or state level.

The increased availability of high resolution remote sensor data for precision agriculture 1 applications permits users to aquire deeper and more relevant knowledge about crops states that lead 2 inevitably to better decisions. The algorithm libraries being developed and evolved around these 3 applications rely on multi-spectral or hyper-spectral data acquired by using manned or unmanned 4 platforms. The current state of the art makes thorough use of vegetational indicies to guide the 5 operational management of agricultural land plots. One of the most challenging sub-problems is 6 to correctly identify and separate crop from soil. Thresholding techniques based on Normalized 7 Difference Vegetation Index (NDVI) or other such similar metrics have the advantage of being simple, 8 easy to read transformations of the data packed with useful information. Obvious difficulties arise 9 when crop/tree and soil have similar spectral responses as in case of grass filled areas in vineyards. 10 In this case grass and canopy are close in terms of NDVI values and thresholding techniques will 11 generally fail. Radiometric approaches could be integrated or replaced by a geometric approach that 12 is based on terrain data like Digital Surface Models (DSMs). These models are one of the ouputs 13 of orthorectification engines usually present in data acquired by using unmanned platforms. In 14 this paper we present two approaches based on DSM that are able to segment crop/tree from soil 15 while over gradient terrain. The DSM data are processed through a two dimensional data slicing or 16 reduction technique. Each slice is separately processed as a one dimensional time series to derive the 17 terrain and tree structures separately, here interpreted as object probability densities. In particular 18 the first approach is a Cartesian grid rasterization (CARSCAN) of the terrain and the second is its 19 immediate generalisation or radial grid rasterization of the DSM model (FANSCAN). The FANSCAN 20 recovers information from the original image at greater frequencies on the Fourier plane. These 21 approaches enable the identification of crop/tree from soil in case of slopes or hilly terrain without 22 any constraint on the displacement / direction of plant/tree row. The proposed algorithm uses pure 23 DSM information even if it is possible to fuse its output with other classifiers.

Cycas (family Cycadaceae), spread throughout tropical and subtropical regions, is crucial in con-servation biology. Due to the subtle morphological variations between species, a solid spe-cies-level phylogeny for Cycas is lacking. Because of the rapid progress in high-throughput se-quencing technology, it has become feasible to acquire complete chloroplast (cp) genome se-quences, which provide a molecular foundation for phylogenetic research. In the present study, we employed next-generation sequencing technology to assemble and analyze the chloroplast genomes of six Cycas plants, including their genome structure, GC content, and nucleotide di-versity. The Cycas chloroplast genome spans 162,038 to 162,159 bp and contains 131 genes, in-cluding 86 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Through a comparative analysis, we found that the chloroplast genome of Cycas was highly conserved, as indicated by the contraction and expansion of the inverted repeat (IR) re-gions and sequence polymorphisms. In addition, several non-coding sites (psbK-psbI, petN-psbM, trnE-UUC-psbD, ndhC-trnM-CAU, and rpl32-trnP-GGG) showed significant varia-tion. The utilization of phylogenetic analysis relying on protein-coding genes has substantiated the division of Cycas primarily into four groups. The application of these findings will prove valuable in evaluating genetic diversity and the phylogenetic connections among closely related species. Moreover, it will provide essential support for the advancement of wild germplasm re-sources.

Phylogeny construction can help to reveal evolutionary relatedness among molecular sequences. The spike (S) gene of SARS-CoV-2 is the subject of an immune selective pressure which increases the variability in such region. This study aimed to identify mutations in the S gene among SARS-CoV-2 sequences collected in the Middle East and North Africa (MENA), focusing on the D614G mutation, that has a presumed fitness advantage. Another aim was to analyze the S gene sequences phylogenetically. The SARS-CoV-2 S gene sequences collected in the MENA were retrieved from the GISAID public database, together with its metadata. Mutation analysis was conducted in Molecular Evolutionary Genetics Analysis software. Phylogenetic analysis was done using maximum likelihood (ML) and Bayesian methods. A total of 553 MENA sequences were analyzed and the most frequent S gene mutations included: D614G=435, Q677H=8, and V6F=5. A significant increase in the proportion of D614G was noticed from (63.0%) in February 2020, to (98.5%) in June 2020 (p<0.001). Two large phylogenetic clusters were identified via ML analysis, which showed an evidence of inter-country mixing of sequences, which dated back to February 8, 2020 and March 15, 2020 (median estimates). The mean evolutionary rate for SARS-CoV-2 was about 6.5 × 10^-3 substitutions/site/year based on large clusters’ Bayesian analyses. The D614G mutation appeared to be taking over the COVID-19 infections in the MENA. Bayesian analysis suggested that SARS-CoV-2 might have been circulating in MENA earlier than previously reported.

Most pathogens are capable of infecting multiple host species and such cross-species transmission (CST) can have dramatic consequences, as highlighted by recent disease emergence events affecting human, animal and plant health. Understanding the ecological and evolutionary factors that constrain or facilitate the ability of disease agents to infect and establish in a novel host is therefore a timely and important research area. Previous work across different pathogens, including rabies virus (RABV), found that increased evolutionary distance between hosts reduces the frequency of cross-species transmission and of permanent host shifts. However, whether this effect of host relatedness still holds for transmission among recently diverged hosts, and the importance of this effect relative to other predictors, is not well understood. We addressed this question by quantifying the CST frequency of RABV between North American bat species within the genus Myotis, using a multi-decade data set containing 128 nucleoprotein (N) sequences from ten host species. For comparison, we also conducted an equivalent analysis of a RABV dataset from North American bat species comprising nine genera. We found that at the within genus scale, host relatedness failed to explain the frequency of CST events. However, CST frequency increased with overlap in species’ host range. Moreover, we found evidence of CST occurring among a higher proportion of species, and CST more frequently resulting in sustained transmission in the novel host in the Myotis dataset compared to the multi-genus dataset. Our results suggest that among recently diverged species, the ability to infect a novel host is no longer restricted by physiological barriers but instead is limited by physical contact. Our results improve predictions of where future CST events for RABV might occur and clarify the relationship between host divergence and pathogen emergence.

Paratemporal methods based on tree expansion have proven to be effective in efficiently generating trajectories of stochastic systems. However, combinatorial explosion of branching arising from multiple choice points presents a major hurdle that must be overcome to implement such techniques. In this paper we tackle this scalability problem by developing a systems theory-based framework covering both conventional and proposed tree expansion algorithms for speeding up discrete event system stochastic simulations while preserving desired accuracy. An example is discussed to illustrate the tree expansion framework in which a discrete event system specification (DEVS) Markov stochastic model takes the form of a tree isomorphic to a free monoid over the branching alphabet. We derive the computation times for baseline, non-merging, and merging tree expansion algorithms to compute the distribution of output values at any given depth. The results show the remarkable reduction from exponential to polynomial dependence on depth effectuated by node merging. We relate these results to the similarly reduced computation time of binomial coefficients underlying Pascal’s triangle. Finally, we discuss application of tree expansion to estimating temporal distributions in stochastic simulations involving serial and parallel compositions with potential real world use cases.

Key elements of Blue-Green Infrastructure are vegetation and stormwater storage. A combination of a bioretention cell with an underlying trench (BC-T) serving as a tree pit is often used in dense urban environments. An adequate ratio of drained area to bioretention cell area is a crucial design parameter. The ratio is derived from the hydrological balance; however, input data are often difficult to obtain or uncertain. The goal is to study the sensitivity of such data (tree water uptake and water holding capacities of soil filter and trench substrate) in the BC-T design. Sensitivity analysis is performed for the setup of a BC-T used in Prague, Czech Republic. A 10-year rainfall series (1 hour resolution) is used as an input. Data that are subject to the sensitivity analysis are changed for different trench exfiltration rates, and the effect on the size of the drained area is studied. At low trench exfiltration rates (1.8 mm.h-1), both the water holding capacity of the trench substrate and potential tree water uptake have a significant influence (more than a 20% change in the size of the drained area) and cannot be neglected. At good exfiltration rates (more than 18 mm.h-1) or when the trench is equipped with an underdrain, all studied parameters can be neglected. However, it is recommended to reduce the size of the drained area by 10-20%.