Fast algorithm for constructing neighbor-joining phylogenetic trees

To improve the performance of Saitou and Nei＇s algorithm （SN） and Studier and Keppler＇s improved algorithm （SK） for constructing neighbor-joining phylogenetic trees and reduce the time complexity of the computation, a fast algorithm is proposed. The proposed algorithm includes three techniques. First, a linear array A[N] is introduced to store the sum of every row of the distance matrix （the same as SK）, which can eliminate many repeated computations. Secondly, the value of A [i] is computed only once at the beginning of the algorithm, and is updated by three elements in the iteration. Thirdly, a very compact formula for the sum of all the branch lengths of operational taxonomic units （OTUs） i and j is designed, and the correctness of the formula is proved. The experimental results show that the proposed algorithm is from tens to hundreds times faster than SN and roughly two times faster than SK when N increases, constructing a tree with 2 000 OTUs in 3 min on a current desktop computer. To earn the time with the cost of the space and reduce the computations in the innermost loop are the basic solutions for algorithms with many loops.

Parkland trees on smallholder farms ameliorate soil physical-chemical properties in the semi-arid area of Tigray,Ethiopia

Proposed agroforestry options should begin with the species that farmers are most familiar with,which would be the native multipurpose trees that have evolved under smallholder farms and socioeconomic conditions.The African birch(Anogeissus leiocarpa(DC.)Guill.&Perr.)and pink jacaranda(Stereospermum kunthianum Cham.)trees are the dominant species in the agroforestry parkland system in the drylands of Tigray,Ethiopia.Smallholder farmers highly value these trees for their multifunctional uses including timber,firewood,charcoal,medicine,etc.These trees also could improve soil fertility.However,the amount of soil physical and chemical properties enhanced by the two species must be determined to maintain the sustainable conservation of the species in the parklands and to scale up to similar agroecological systems.Hence,we selected twelve isolated trees,six from each species that had similar dendrometric characteristics and were growing in similar environmental conditions.We divided the canopy cover of each tree into three radial distances:mid-canopy,canopy edge,and canopy gap(control).At each distance,we took soil samples from three different depths.We collected 216 soil samples(half disturbed and the other half undisturbed)from each canopy position and soil depth.Bulk density(BD),soil moisture content(SMC),soil organic carbon(SOC),total nitrogen(TN),available phosphorus(AP),available potassium(AK),p H,electrical conductivity(EC),and cation exchange capacity(CEC)were analysed.Results revealed that soil physical and chemical properties significantly improved except for soil texture and EC under both species,CEC under A.leiocarpus,and soil p H under S.kunthianum,all the studied soils were improved under both species canopy as compared with canopy gap.SMC,TN,AP,and AK under canopy of these trees were respectively 24.1%,11.1%,55.0%,and 9.3% higher than those soils under control.The two parkland agroforestry species significantly enhanced soil fertility near the canopy of topsoil through improving soil physical and chemical properties.These two species were recommended in the drylands with similar agro-ecological systems.

Tree mycorrhizal associations determine how biodiversity,large trees,and environmental factors drive aboveground carbon stock in temperate forests

Biodiversity,large trees,and environmental conditions such as climate and soil have important effects on forest carbon stocks.However,recent studies in temperate forests suggest that the relative importance of these factors depends on tree mycorrhizal associations,whereby large-tree effects may be driven by ectomycorrhizal(EM)trees,diversity effects may be driven by arbuscular mycorrhizal(AM)trees,and environment effects may depend on differential climate and soil preferences of AM and EM trees.To test this hypothesis,we used forest-inventory data consisting of over 80,000 trees from 631 temperate-forest plots(30 m×30 m)across Northeast China to examine how biodiversity(species diversity and ecological uniqueness),large trees(top 1%of tree diameters),and environmental factors(climate and soil nutrients)differently regulate aboveground carbon stocks of AM trees,EM trees,and AM and EM trees combined(i.e.total aboveground carbon stock).We found that large trees had a positive effect on both AM and EM tree carbon stocks.However,biodiversity and environmental factors had opposite effects on AM vs.EM tree carbon stocks.Specifically,the two components of biodiversity had positive effects on AM tree carbon stocks,but negative effects on EM tree carbon stocks.Environmental heterogeneity(mean annual temperature and soil nutrients)also exhibited contrasting effects on AM and EM tree carbon stocks.Consequently,for the total carbon stock,the positive large-tree effect far surpasses the diversity and environment effect.This is mainly because when integrating AM and EM tree carbon stock into total carbon stock,the opposite diversity-effect(also environment-effect)on AM vs.EM tree carbon stock counteracts each other while the consistent positive large-tree effect on AM and EM tree carbon stock is amplified.In summary,this study emphasized a mycorrhizal viewpoint to better understand the determinants of overarching aboveground carbon profile across regional forests.

Role of outdoor trees on pedestrian wind and thermal conditions around a pre-education building for sustainable energy management

Finding sustainable energy resources is essential to face the increasing energy demand.Trees are an important part of ancient architecture but are becoming rare in urban areas.Trees can control and tune the pedestrian-level wind velocity and thermal condition.In this study,a numerical investigation is employed to assess the role of trees planted in the windward direction of the building complex on the thermal and pedestrian wind velocity conditions around/inside a pre-education building located in the center of the complex.Compared to the previous studies(which considered only outside buildings),this work considers the effects of trees on microclimate change both inside/outside buildings.Effects of different parameters including the leaf area density and number of trees,number of rows,far-field velocity magnitude,and thermal condition around the main building are assessed.The results show that the flow velocity in the spacing between the first-row buildings is reduced by 30%-40% when the one-row trees with 2 m height are planted 15 m farther than the buildings.Furthermore,two rows of trees are more effective in higher velocities and reduce the maximum velocity by about 50%.The investigation shows that trees also could reduce the temperature by about 1℃around the building.

Enhanced Cooling Efficiency of Urban Trees on Hotter Summer Days in 70 Cities of China

Increasing the urban tree cover percentage(TCP) is widely recognized as an efficient way to mitigate the urban heat island effect. The cooling efficiency of urban trees can be either enhanced or attenuated on hotter days, depending on the physiological response of urban trees to rising ambient temperature. However, the response of urban trees' cooling efficiency to rising urban temperature remains poorly quantified for China's cities. In this study, we quantify the response of urban trees' cooling efficiency to rising urban temperature at noontime [~1330 LT(local time), LT=UTC+8] in 17summers(June, July, and August) from 2003–19 in 70 economically developed cities of China based on satellite observations. The results show that urban trees have stronger cooling efficiency with increasing temperature, suggesting additional cooling benefits provided by urban trees on hotter days. The enhanced cooling efficiency values of urban trees range from 0.002 to 0.055℃ %-1 per 1℃ increase in temperature across the selected cities, with larger values for the lowTCP-level cities. The response is also regulated by background temperature and precipitation, as the additional cooling benefit tends to be larger in warmer and wetter cities at the same TCP level. The positive response of urban trees' cooling efficiency to rising urban temperature is explained mainly by the stronger evapotranspiration of urban trees on hotter days.These results have important implications for alleviating urban heat risk by utilizing urban trees, particularly considering that extreme hot days are becoming more frequent in cities under global warming.

Exploring Trees Diversity and Ecological Value of Mountain Forests in the Blue Nile Region of Sudan

We carried out this research at Abu-Gaddaf Natural Forest Reserve (ANFR) which is located east of Blue Nile River, in Blue Nile State, Sudan. It aims at exploring tree composition assessing their diversity indices, and ecological importance values. For survey of types and estimation of density of tree species in the forest, we randomly distributed 97 circular sample plots (0.1 hectare (ha)). In each sample plot we identified all trees to the species level, recorded their frequencies and computed species diversity and importance value indices (IVI). A total of 13 tree species, which belong to 12 genera and nine families, were identified in the tree layer of the forest. Mean tree density in ANFR was 116 trees/ha, composed mainly of Boswellia papyrifera (Del.) Hochst. (48), followed by Combretum hartmannianu (19) and Lannea fruticosa (18). Fabaceae was the most common family followed by Combretaceae and Malvaceae. B. papyrifera Delile Hochst was the most abundant while Acacia seyal was the least abundant species. Species richness (R = 1.71), evenness (E = 0.69), dominance (0.24) indices and Simpson’s Index of Diversity (D' = 0.76) suggest a moderate diversity, moderate numbers of individuals in each species and a moderate community stability. The research provides empirical results on diversity and ecological importance value of species, signifies the urging need to safeguard threatened species and to prioritize them for conservation, as well as the need to promote management of abundant species to provide multiple forest ecosystem services.

Enhancing PDF Malware Detection through Logistic Model Trees

Malware is an ever-present and dynamic threat to networks and computer systems in cybersecurity,and because of its complexity and evasiveness,it is challenging to identify using traditional signature-based detection approaches.The study article discusses the growing danger to cybersecurity that malware hidden in PDF files poses,highlighting the shortcomings of conventional detection techniques and the difficulties presented by adversarial methodologies.The article presents a new method that improves PDF virus detection by using document analysis and a Logistic Model Tree.Using a dataset from the Canadian Institute for Cybersecurity,a comparative analysis is carried out with well-known machine learning models,such as Credal Decision Tree,Naïve Bayes,Average One Dependency Estimator,Locally Weighted Learning,and Stochastic Gradient Descent.Beyond traditional structural and JavaScript-centric PDF analysis,the research makes a substantial contribution to the area by boosting precision and resilience in malware detection.The use of Logistic Model Tree,a thorough feature selection approach,and increased focus on PDF file attributes all contribute to the efficiency of PDF virus detection.The paper emphasizes Logistic Model Tree’s critical role in tackling increasing cybersecurity threats and proposes a viable answer to practical issues in the sector.The results reveal that the Logistic Model Tree is superior,with improved accuracy of 97.46%when compared to benchmark models,demonstrating its usefulness in addressing the ever-changing threat landscape.

Seedling potential of trees species along the elevational gradient in temperate hill forest of central Nepal

Regeneration status of tree species along elevation gradient in temperate hill forest was not understood greatly.Present research examined the tree diversity and its regeneration patterns along an elevation gradient in temperate hill forest,central Nepal.Data were collected from 300 sample plots within vertical elevation bands of 10,ranging from 1365 to 2450 m asl.A random sampling method was used for data collection in three seasons,winter,pre-monsoon and post monsoon seasons.Diameter at breast height(DBH)was used to broadly categorize the plant individual into trees,saplings and seedlings.The tree species richness ranged from 12 to 25 with density of 350 to 1200 individuals per hectare.Species richness of tree and sapling showed statistically significant unimodal pattern,which peaked at mid-elevation.Elevation showed a strong and positive linear correlation with the seedling density(Deviance=0.99,p<0.001)and a significant hump-shaped relationship with sapling density(Deviance=0.95,p<0.001).Similarly,elevations showed a statistically significant negative hump-shaped relationship with all trees,saplings and seedling stages(Deviances=0.89,0.87 and 0.57).The highest values of the Shannon-Wiener index and the lowest value of the Simpson index were found at mid-elevation for all growth forms.Nearly 92%of tree species were found at regenerating stage;49%in a good renewal regeneration status,32%in fair renewal regeneration,and 11%at a poor regenerating condition.Nevertheless,4%of tree species were reported as non-regenerating stages and 4%were newly introduced species.Hence,the regeneration status of the study area was considered fairly well since sapling(78.5%)>seedling(10.6%)≤mature(10.9%).Among tested environmental variables,elevation and annual mean rainfall were the most influential factors in the regeneration of tree species.

Efficiency of Bio-Fertilizing as One of the Natural Alternatives to Improve the Growth of Khaya senegalensis and Swietenia mahagoni Trees and for Sustainability

A field experiment was carried out at Ismailia Research Station, Ismailia Governorate from 2020-2022 to improve the growth of Khaya senegalensis and Swietenia mahagoni by using a combination of mineral fertilizer (NPK) and biological fertilizer (Azotobacter chroococcum, Bacillus megatherium, and Bacillus circulant) as recommended dose under new sandy soils conditions. Split plot designed with four treatments (Control, (50% Mineral fertilizer (M.) + 50% Biological fertilizer (Bio.)), 100% M. and 100% Bio.) of each species. Vegetative growth, leaf area, tree biomass, stored carbon, basal area, tree volume, and in the soil both of microbial account and mineral content were determined. The experimental results showed no significant differences between studied species among the most studied parameters except for Khaya senegalensis which gave the highest significant difference in root biomass and below-stored carbon than Swietenia mahagoni. Evidently, the highest significant growth parameters were 100% mineral fertilizer followed by (50% M. + 50% Bio.) as compared with control. No significant difference between 100% M. and (50% M. + 50% Bio.) of shoot dry biomass (15.19 and 12.02 kg, respectively) and above-stored carbon (0.28 and 0.22 Mt, respectively). Microbial account and mineral content in soil were improved after cultivation of tree species compared to before planting and control, especially with 50% mineral fertilizer and 50% bio-fertilizer treatment. In conclusion, a treatment containing 50% mineral fertilizer and 50% bio-fertilizer has led to the ideal Khaya senegalensis and Swietenia mahagoni growth in sandy soil for cheaper and sustainable.

Long-term changes in radial growth of seven tree species in the mixed broadleaf-Korean pine forest in Northeast China:Are deciduous trees favored by climate change?

The role of the temperate mixed broadleaf-Korean pine forest(BKF)in global biogeochemical cycles will depend on how the tree species community responds to climate;however,species-specific responses and vulner-abilities of common trees in BKF to extreme climates are poorly understood.Here we used dendrochronological meth-ods to assess radial growth of seven main tree species(Pinus koraiensis,Picea jezoensis,Abies nephrolepis,Fraxinus mandshurica,Phellodendron amurense,Quercus mongolica,and Ulmus davidiana)in an old-growth BKF in response to climate changes in the Xiaoxing’an Mountains and to improve predictions of changes in the tree species compo-sition.Temperature in most months and winter precipita-tion significantly negatively affected growth of P.jezoensis and A.nephrolepis,but positively impacted growth of P.koraiensis and the broadleaf species,especially F.mandshu-rica and U.davidiana.Precipitation and relative humidity in June significantly positively impacted the growth of most tree species.The positive effect of the temperature during the previous non-growing season(PNG)on growth of F.mandshurica and Q.mongolica strengthened significantly with rapid warming around 1981,while the impact of PNG temperature on the growth of P.jezoensis and A.nephrolepis changed from significantly negative to weakly negative or positive at this time.The negative response of radial growth of P.jezoensis and A.nephrolepis to precipitation during the growing season gradually weakened,and the negative response to PNG precipitation was enhanced.Among the studied species,P.koraiensis was the most resistant to drought,and U.davidiana recovered the best after extreme drought.Ulmus davidiana,P.jezoensis and A.nephrolepis were more resistant to extreme cold than the other species.Climate warming generally exacerbated the opposite growth patterns of conifer(decline)and broadleaf(increase)spe-cies.Deciduous broadleaf tree species in the old-growth BKF probably will gradually become dominant as warming continues.Species-specific growth-climate relationships should be considered in future models of biogeochemical cycles and in forestry management practices.

Enhanced asphalt dynamic modulus prediction: A detailed analysis of artificial hummingbird algorithm-optimised boosted trees

This study introduces and evaluates a novel artificial hummingbird algorithm-optimised boosted tree(AHAboosted)model for predicting the dynamic modulus(E*)of hot mix asphalt concrete.Using a substantial dataset from NCHRP Report-547,the model was trained and rigorously tested.Performance metrics,specifically RMSE,MAE,and R2,were employed to assess the model's predictive accuracy,robustness,and generalisability.When benchmarked against well-established models like support vector machines(SVM)and gaussian process regression(GPR),the AHA-boosted model demonstrated enhanced performance.It achieved R2 values of 0.997 in training and 0.974 in testing,using the traditional Witczak NCHRP 1-40D model inputs.Incorporating features such as test temperature,frequency,and asphalt content led to a 1.23%increase in the test R2,signifying an improvement in the model's accuracy.The study also explored feature importance and sensitivity through SHAP and permutation importance plots,highlighting binder complex modulus|G*|as a key predictor.Although the AHA-boosted model shows promise,a slight decrease in R2 from training to testing indicates a need for further validation.Overall,this study confirms the AHA-boosted model as a highly accurate and robust tool for predicting the dynamic modulus of hot mix asphalt concrete,making it a valuable asset for pavement engineering.

A Light and Simplified Branch Bending Method for Young Pear Trees

Aiming at high cost and low efficiency of conventional branch bending method in the modern intensive planting and labor-saving cultivation mode of young pear trees,this paper provides a new branch bending method with wide source of raw materials,cheap price and simple operation,which is also suitable for the management of low-age branches in the process of high grafting and upgrading of traditional big trees.

Insights from i-Tree Eco-efficiency Assessment Management of Urban Trees in Oxford,UK

In the era of stock development following the acceleration of urbanization,the revitalization of urban green space has assumed an increasingly significant role.Consequently,the management of urban trees has emerged as a critical focus of urban governance,contributing to the enhancement of livability in human settlements.This study offers a comprehensive analysis of the urban tree management system in Oxford,UK,identifying that its primary objective is to optimize and maintain a harmonious balance between human activities and the natural environment through the implementation of high-quality planting practices.The system emphasizes enhanced management practices and establishes a robust framework for the development of targeted policies and management regulations,utilizing i-Tree eco-efficiency assessment and real-time feedback mechanisms.China’s urban tree management is in its nascent stages,and there is an urgent need for the development of urban green space.By adopting the refined management assessment methodologies employed for urban trees in Oxford,UK,it is possible to enhance the ecological value of urban trees,which represent a significant green resource within cities,and contribute to the creation of more livable urban spaces.

Advances in Molecular Regulatory Mechanisms of Fruit Trees under Low Temperature Stress

The most recent research findings on the tolerance of fruit trees to cold stress are reviewed from a molecular perspective,including the perception and transduction of low temperature calcium signaling,CBF-dependent molecular regulatory mechanisms,non-CBF-dependent molecular regulatory mechanisms,and so forth.The objective is to provide a reference basis for further improving the cold resistance of fruit trees and cultivating new varieties of hardy plants.

基于Decision Trees的配电网中性点不接地系统选线

针对配电网中性点不接地系统,使用录波数据解决单相接地选线不准的难题,提出了基于Decision Trees算法进行单相接地选线的方法.使用PSCAD仿真10kV配电网单相接地故障得到录波数据,转换成通用格式,提取稳态数据并进行预处理,通过对比多个机器学习分类算法,选择基于Decision Trees算法进行单相接地选线.选择的Decision Trees算法训练准确度高达99.99%,且模型小,训练速度快.将训练后的模型导出,使用实际的故障录波数据进行验证,选线准确度高达95%以上.结果表明该方法易于实现,准确度高,适合在实际中应用.

适于GlobalAllomeTree国际数据平台的标准化中国主要树种树高-胸径方程研建

GlobalAllomeTree作为共享异速方程的国际网络平台,逐渐受到全球高度关注。当前,为促进该项国际合作,针对当前该平台缺乏中国主要树种生长异速方程的现状,系统性更新标准化中国主要树种树高-胸径方程。由于树冠和下部灌木及草丛遮挡,树高相对于胸径测量具有一定的难度,因此需要使用数学工具进行计算。选取了36个树种为材料构建树高-胸径关系方程,以全国主要树种的二元材积模型、各地区一元材积表为基础材料,以取样径阶为1 cm间隔所生成1692组树高-胸径数据作为建立方程样本,1238组外业调查数据为验证样本。建模结果表明:36个主要树种的1692组树高-胸径数据建立的全国通用性树高-胸径方程拟合相关系数(R2)为0.801,方程拟合结果较好,说明可以通过测定胸径,带入树高(H,m)-胸径(D,cm)方程(H=aDb)预估树高;对36个主要树种的树高-胸径方程进行拟合,决定系数R2值均大于0.916,平均误差(ME)、平均绝对误差(MAE)和均方根误差(RMSE)相对较小,方程整体精度较高,可广泛推广;将外业采集的1238组树高-胸径数据,根据36个主要树种树高-胸径方程拟合公式及参数估计值a、b进行方程精度验证,方程预测的平均相对误差为16.86%,在误差允许范围内,并且模型形式规范,可为GlobalAllomeTree平台用户提供科学参考。

基于自动终止准则改进的kd-tree粒子近邻搜索研究

对于大规模运动模拟问题而言,近邻点的搜索效率将对整体的运算效率产生显著影响。本文基于关联性分析建立kd-tree的最大深度dmax与粒子总数N的自适应关系式,提出了kd-tree自动终止准则,即ATC-kd-tree,同时还考虑了叶子节点大小阈值n_(0)对近邻搜索效率的影响。试验表明,ATC-kd-tree具有更高的近邻搜索效率,相较于不使用自动终止准则的kd-tree搜索效率最高提升46%,且适用性更强,可求解不同N值的近邻搜索问题,解决了粒子总数N发生改变时需要再次率定最大深度dmax的问题。同时,本文还提出了网格搜索法组合坐标下降法的两步参数优化算法GSCD法。通过2维阿米巴虫形状的参数优化试验发现,GSCD法可更为快速地率定ATC-kd-tree的可变参数,其优化效率比网格搜索法最高提升了205%,相较于改进网格搜索法最高提升了90%。研究结果表明,ATC-kd-tree和GSCD法不仅提高了近邻搜索的效率,也为复杂运动中近邻粒子搜索问题提供了一种更为高效的解决方案,能够显著降低计算资源的消耗,进一步提升模拟的精度和效率。

Novel Soft ComputingModel for Predicting Blast-Induced Ground Vibration in Open-Pit Mines Based on the Bagging and Sibling of Extra Trees Models

This study considered and predicted blast-induced ground vibration(PPV)in open-pit mines using bagging and sibling techniques under the rigorous combination of machine learning algorithms.Accordingly,four machine learning algorithms,including support vector regression(SVR),extra trees(ExTree),K-nearest neighbors(KNN),and decision tree regression(DTR),were used as the base models for the purposes of combination and PPV initial prediction.The bagging regressor(BA)was then applied to combine these base models with the efforts of variance reduction,overfitting elimination,and generating more robust predictive models,abbreviated as BA-ExTree,BAKNN,BA-SVR,and BA-DTR.It is emphasized that the ExTree model has not been considered for predicting blastinduced ground vibration before,and the bagging of ExTree is an innovation aiming to improve the accuracy of the inherently ExTree model,as well.In addition,two empirical models(i.e.,USBM and Ambraseys)were also treated and compared with the bagging models to gain a comprehensive assessment.With this aim,we collected 300 blasting events with different parameters at the Sin Quyen copper mine(Vietnam),and the produced PPV values were also measured.They were then compiled as the dataset to develop the PPV predictive models.The results revealed that the bagging models provided better performance than the empirical models,except for the BA-DTR model.Of those,the BA-ExTree is the best model with the highest accuracy(i.e.,88.8%).Whereas,the empirical models only provided the accuracy from 73.6%–76%.The details of comparisons and assessments were also presented in this study.

基于FP-tree的新能源汽车产业国际竞争力影响因素关联挖掘算法

为充分挖掘新能源汽车产业国际竞争力影响因素、探究价值增长点,提出了基于FP-tree的影响因素关联挖掘算法。通过构建国际竞争力各指标影响因素的关联规则,分析任意事务数据集中的关联数据,利用最小支持度参数minsup按照从上到下的方式搜索,确定最长的频繁项目集,采用FP-tree关联频繁项目集,设定分支关联性挖掘标准,实现了新能源汽车产业国际竞争力影响因素的挖掘。测试结果表明,设计算法的最小支持度和数据关联挖掘时间较短,置信度分析具有较高的稳定性。

基于CatBoost用信预测模型的TreeSHAP解释性研究

银行客户申请信用贷款在授信通过后,精准预测客户是否用信及分析影响客户用信的关键因素,对提高银行客户服务能力及盈利能力具有重要意义.目前,机器学习算法鲜有在用信预测方面的应用,且金融用信领域缺乏模型可解释性的研究,为此提出一种基于CatBoost的TreeSHAP解释性用信预测模型.通过CatBoost构建用信预测模型,利用3种超参数优化算法对该模型进行对比优化,与基线模型在4项主要性能指标上进行实验对比,结果表明经TPE算法优化后的模型性能均优于其他模型,然后结合TreeSHAP方法从全局和局部的层面增强模型的可解释性,解释性分析客户用信的影响因素,为银行对客户进行精准化营销提供决策依据.