Three‐unit semicircles curve: A compact 3D graphical representation of DNA sequences based on classifications of nucleotides

A new three‐dimensional graphical representation of DNA sequences, three‐unit semicircles (TUS)‐curve, which maps a given sequence into a dot sequences embedded in three‐unit semicircles, is proposed based on three biclassifications of nucleotides. TUS‐curve has the merit of compactness and could avoid the degeneracy and loss of information. The geometrical center of the curve, which indicates the distribution of base frequencies of the corresponding DNA sequence, is extracted and applied to analyze the similarity of various species. Phylogenetic tree of 11 species based on their first exons of β‐globin genes showed that the TUS‐curve is a powerful tool to get valuable biological information. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

On the normalized Laplacian of Möbius phenylene chain and its applications

Let denote a molecular graph of linear [n] phenylene with n hexagons and n squares, and let the Möbius phenylene chain be the graph obtained from the by identifying the opposite lateral edges in reversed way. Utilizing the decomposition theorem of the normalized Laplacian characteristic polynomial, we study the normalized Laplacian spectrum of , which consists of the eigenvalues of two symmetric matrices ℒ _R and ℒ _Q of order 3n. By investigating the relationship between the roots and coefficients of the characteristic polynomials of the two matrices above, we obtain an explicit closed-form formula of the multiplicative degree-Kirchhoff index as well as the number of spanning trees of . Furthermore, we determine the limited value for the quotient of the multiplicative degree-Kirchhoff index and the Gutman index of .     

Maximizing the mean subtree order

This article focuses on properties and structures of trees with maximum mean subtree order in a given family; such trees are called optimal in the family. Our main goal is to describe the structure of optimal trees in and , the families of all trees and caterpillars, respectively, of order . We begin by establishing a powerful tool called the Gluing Lemma, which is used to prove several of our main results. In particular, we show that if is an optimal tree in or for , then every leaf of is adjacent to a vertex of degree at least . We also use the Gluing Lemma to answer an open question of Jamison and to provide a conceptually simple proof of Jamison's result that the path has minimum mean subtree order among all trees of order . We prove that if is optimal in , then the number of leaves in is and that if is optimal in , then the number of leaves in is . Along the way, we describe the asymptotic structure of optimal trees in several narrower families of trees.     

A Tree-valued Markov Process Associated with an Admissible Family of Branching Mechanisms

Let E?R be an interval. By studying an admissible family of branching mechanisms{ψt,t ∈E} introduced in Li [Ann. Probab., 42, 41-79(2014)], we construct a decreasing Levy-CRT-valued process {Tt, t ∈ E} by pruning Lévy trees accordingly such that for each t ∈E, Tt is a ψt-Lévy tree. We also obtain an analogous process {Tt*,t ∈E} by pruning a critical Levy tree conditioned to be infinite. Under a regular condition on the admissible family of branching mechanisms, we show that the law of {Tt,t ∈E} at the ascension time A := inf{t ∈E;Tt is finite} can be represented by{Tt*,t∈E}.The results generalize those studied in Abraham and Delmas [Ann. Probab., 40, 1167-1211(2012)].     

我国林木良种繁育基地建设发展形势及可持续发展策略

1964年,福建省洋口国有林场杉木 (Cunninghamia lanceolata) 种子园、广东省台山红岭湿地松(Pinus eliottii)种子园、黑龙江省林口县青山林场兴安落叶松(Larix gmelinii)、日本落叶松(L. olgensis)、樟子松(P. sylvestris var. mongolica)种子园的建立,标志着规模化树木改良和林木良种繁育基地建设在我国的开始。经过半个多世纪的发展,我国已建立:国家林木种质资源库99个;国家重点林木良种基地294个,生产林木种子1.7亿kg,苗木2 800多亿株;审定认定林木良种3 224个, 造林树种良种使用率提高到65%。其中,浙江省杉木无性系种子园第1代、1.5代、第2代的6年生子代测定结果表明材积遗传增益分别为16.97%、22.58%、26.42%;而种源种子园和双无性系种子园遗传增益更高,分别达到32.82%和37.93%。福建省第3代杉木无性系种子园材积遗传增益达76%。进入21世纪,我国对林木良种繁育基地建设的树种结构进行了调整。由于我国树种资源非常丰富(乔木树种就有2 000多种,其中不少树种具有特殊用途和特异性功能),我国良种繁育基地经营和树种改良方向更加多元化。除开展一般工业用材树种如松属(Pinus)、杉木属 (Cunninghamia)、落叶松属(Larix)等树种选育外,同时开展遗传改良的树种还包括:特殊用材树种如降香黄檀(Dalbergia odorifera)、楠木(Phoebe bournei)、水曲柳(Fraxinus mandahurica)等;抗逆性生态树种如梭梭(Haloxylon ammodensron)、沙棘(Hippophae rhamnoide)、胡杨(Populus euphratica)等; 园林景观树种如亚美马褂木(又称杂交马褂木或杂交鹅掌楸)(Liriodendron sino-americanum)、玉兰(Magnolia denudata)、金钱松(Pseudolarix amabilis)等; 油料香料树种如油茶(Camellia oleifera)、油桐 ( Vernicia fordii)、八角(Illicium verum )等;干果树种如山核桃(Carya cathayensis)、香榧(Torreya grandis)、枣子(Ziziphus jujuba)等;药用树种如杜仲(Eucommia ulmoides)、厚朴(Magnolia officinalis)、山茱萸(Cornus officinalis)等。笔者认为,我国林木良种繁育基地建设是实现我国林业现代化的一项基础性工程,是林木种子工程建设的重点内容,今后我国林木良种繁育基地建设可持续发展策略性措施包括下列6项内容:①稳定长期经济补贴投资机制,确保良种繁育基地长期正常运转;②加强行政管理监督,制定和修订技术标准、法规;③加强科学技术支撑力度,健全“三结合”协作机制;④制定长期良种基地规划和育种计划,确保基地建设长期持续前行;⑤成立良种基地管理指导委员会,建立科学决策机制;⑥定期举办良种基地与林木育种研讨班,商讨关键科学技术和经营管理重大问题。     

Embedding hypertrees into steiner triple systems

In this paper, we are interested in the following question: given an arbitrary Steiner triple system on vertices and any 3‐uniform hypertree on vertices, is it necessary that contains as a subgraph provided ? We show the answer is positive for a class of hypertrees and conjecture that the answer is always positive.     

Logging damage and injured tree mortality in tropical forest management

Using insights from the forest ecology literature, we analyze the effect of injured trees on stand composition and carbon stored in above‐ground biomass and the implications for forest management decisions. Results from a Faustmann model with data for a tropical forest on Kalimantan show that up to 50% of the basal area of the stand before harvest can consist of injured trees. Considering injured trees leads to an increase in the amount of carbon in above‐ground biomass of up to 165%. These effects are larger under reduced impact logging than under conventional logging. The effects on land expectation value and cutting cycle are relatively small. The results suggest that considering injured trees in models for tropical forest management is important for the correct assessment of the potential of financial programs to store carbon and conserve forest ecosystem services in managed tropical forests, such as reducing emissions from deforestation and forest degradation and payment for ecosystem services. Recommendations for Resource Managers

• Considering the role of injured trees is important for managing tropical forests
• These trees can cover up to 50% of basal area and contain more than 50% of the carbon stored in above‐ground biomass
• Reduced impact logging leads to a larger basal area of injured trees and more carbon stored in injured trees than conventional logging
• Injured trees play an important role when assessing the potential for carbon storage in the context of payment for forest ecosystem services.

     

Hierarchical Model-Based Clustering for Large Datasets

In recent years, hierarchical model-based clustering has provided promising results in a variety of applications. However, its use with large datasets has been hindered by a time and memory complexity that are at least quadratic in the number of observations. To overcome this difficulty, this article proposes to start the hierarchical agglomeration from an efficient classification of the data in many classes rather than from the usual set of singleton clusters. This initial partition is derived from a subgraph of the minimum spanning tree associated with the data. To this end, we develop graphical tools that assess the presence of clusters in the data and uncover observations difficult to classify. We use this approach to analyze two large, real datasets: a multiband MRI image of the human brain and data on global precipitation climatology. We use the real datasets to discuss ways of integrating the spatial information in the clustering analysis. We focus on two-stage methods, in which a second stage of processing using established methods is applied to the output from the algorithm presented in this article, viewed as a first stage.