Prokaryotic branch of the Tree of Life： A composition vector approach

The Composition Vector Tree (CVTree) is a parameter-free and alignment-free method to infer pro-karyotic phylogeny from their complete genomes. It is distinct from the traditional 16S rRNA analysis in both the input data and the methodology. The prokaryotic phylogenetic trees constructed by using the CVTree method agree well with the Bergey’s taxonomy in all major groupings and fine branching patterns. Thus, combined use of the CVTree approach and the 16S rRNA analysis may provide an objective and reliable reconstruction of the prokaryotic branch of the Tree of Life.

How Parenting Affects Children＇s Futures：Empirical Study in Japan

In this study, we conducted a survey on Japanese adults about the way they were raised in their childhood and analyzed the influence of parenting method on children＇s futures. Using the major factor method, we conducted principal factor analysis of the responses fi＇om a 20-question survey of Japanese adults to assess the parent-child relationship during childhood. Four factors （＂interest＂, ＂trust＂, ＂norm＂, and ＂independence＂） are derived. We added ＂time spent together＂ with parent（s） and parent＇s ＂strict discipline＂ to the indices and classified the parenting methods into five types： （1） supportive, （2） tiger, （3） indulgent, （4） uninvolved, and （5） abusive. Then we compared the average earnings, sense of well-being, and educational career of the respondents classified according to the parenting type. Among the five types, the ＂supportive＂ type showed the highest achievement in all the three items, and the ＂abusive＂ type the lowest in all the items.

水洞沟的新年代测定及相关问题讨论

水洞沟是中国北方的一处独具特色的旧石器时代晚期遗址 ,在阐释区域性技术传统的成因、远古文化的发展和变异 ,以及晚更新世人类在东北亚的迁徙、扩散和交流具有重要的地位。本文报道在水洞沟 2号地点发现的新材料和新的研究成果 :野外考察发现系列的火塘遗迹并采集到石制品、骨器等文化遗物 ;系统的AMS14 C测年将水洞沟遗址的年代确定在距今 2 90 0 0— 2 4 0 0 0前 ;新的研究为探讨水洞沟工业的渊源和细石器技术的起源提供了珍贵的信息。

基于营卫倾移的证解释模型的构建

借鉴现代复杂性科学的模型化方法和中医理论建构的原始思路,以“证”为研究对象,分别选择营卫作为两个基本变量,以营卫强度(I)和通滞度(R)两个状态矢量作为坐标系的主正交轴,并以时间(t)和空间(s)作为辅助正交轴来建立证诠释模型。这个模型有助于中医证候的理解和规范化,并且为中医理论借鉴和吸收现代医学的相关知识开辟了一条新的可行道路。但目前该模型还存在过度笼统以及进一步的数据萃取的难题,因而模型的优化和发展会是一个长期的过程。

Computational History:Challenges and Opportunities of Formal Approaches

We propose a program for a computational analysis,based on large scale datasets,of deep conceptual and formal structures,representing the mechanisms of historical transformations in different domains ranging from biological to social,cultural,and knowledge systems.We conceptualize such systems as consisting of complex multi-layer networks.Structural properties of such networks may explain the spreading of innovations.Temporal relations between the dynamics of interacting networks may help to identify causalities.Complex systems may show path and context dependencies.We illustrate our approach by case studies from all those types of systems.

Advantages and Disadvantages of Rotating Spatial Closures for Managing Fisheries

Marine protected areas are becoming an increasingly important tool in fisheries management.Particularly for species with relatively sedentary adults,the basic approach taken is to permanently close areas to fishing,which allows species to recover inside the reserve and export larvae to outside of it that can eventually be harvested.Two key issues posed are ensuring the movement of larvae outside the reserve to support fisheries and the sociological and economic impact of marine reserves.An alternative approach that addresses these issues is rotational zoning systems,which have been implemented for some fisheries.What has been missing is an analysis of the relative impact of marine reserves versus rotational zoning systems on fisheries yields that could be used to provide important principles to guide management.Using a simplified model with clear assumptions,we show that rotational zoning systems are inferior in fisheries management targeting low-fecundity species or species with a low proliferation rate,especially when the fraction of the coastline protected is relatively small(approximately less than 20%)and the rotational fraction results in landings far below optimal fisheries yields.These results are tested with hypothetical species,providing quantitative guidelines in cases where decisions must be made with limited data as well as a framework for more detailed analyses in cases where more data are available.

原核生物系统发生学与分类学的一致性:组份矢量树与原核生物分类系统的详尽比较

截至2006年12月31日,NCBI共有432个原核生物的全基因组可供下载.基于这些数据,我们用组份矢量方法构建了原核生物的进化树.最新的《伯杰系统细菌学手册》的在线大纲体现了细菌学家的分类系统.我们对两者从各个分类单元、各个分支进行了详尽的比较.组份矢量方法所得到的亲缘树和伯杰分类系统在整体结构和绝大多数的细微分支上都相当一致.同时,两者的多数不同之处也已经在一定程度上为生物学家所知,从而为原核生物分类系统的修正提供了一定的启示.本文重点阐述两者之间分岐之处的生物学含义,而不再对居主导地位的相同之处做详细叙述.

植物-微生物互惠共生:演化机制与生态功能

植物-微生物互惠共生是一种特殊的合作形式,在整个生命和陆地生态系统的演化历史中起着至关重要的作用。在全球环境变化背景下,植物和微生物间的互惠共生对生态系统功能的维持具有重要意义。尽管合作/互惠共生如此重要,在生物学中却存在着对它的历史偏见与忽视。特别地,尽管互惠共生的理论与建模发展已有较长的历史,但不同学科分支间仍存在着多种不同的观点。本综述从两个看似对立的视角概述植物-微生物互惠共生的概念框架,即微生物学家关心的微观机制和生态系统生态学家关注的宏观影响。宏观模型通常从一组过于简单的假设出发,便于理论分析。但微观机制是开展定量预测的基础,因此新一代基于过程的宏观模型需嵌入微观机制,这对预测全球变化下的生态系统响应至关重要。此外,希望本文也可以吸引更多学者关注合作/互惠的重要作用,并将这一概念应用于解决其他生态学和社会学问题。

Whole-genome based Archaea phylogeny and taxonomy: A composition vector approach

The newly proposed alignment-free and parameter-free composition vector (CVtree) method has been successfully applied to infer phylogenetic relationship of viruses, chloroplasts, bacteria, and fungi from their whole-genome data. In this study we pay special attention to the phylogenetic positions of 56 Archaea genomes among which 7 species have not been listed either in Bergey’s Manual of Systematic Bacteriology or in Taxonomic Outline of Bacteria and Archaea (TOBA). By inspecting the stable monophyletic branchings in CVTrees reconstructed from a total of 861 genomes (56 Archaea plus 797 Bacteria, using 8 Eukarya as outgroups) definite taxonomic assignments were proposed for these not-fully-classified species. Further development of Archaea taxonomy may verify the predicted phylogenetic results of the CVTree approach.

Prokaryote phylogeny meets taxonomy: An exhaustive comparison of composition vector trees with systematic bacteriology

We perform an exhaustive, taxon by taxon, comparison of the branchings in the composition vector trees (CVTrees) inferred from 432 prokaryotic genomes available on 31 December 2006, with the bacte-riologists' taxonomy-primarily the latest online Outline of the Bergey's Manual of Systematic Bacteri-ology. The CVTree phylogeny agrees very well with the Bergey's taxonomy in majority of fine branchings and overall structures. At the same time most of the differences between the trees and the Manual have been known to biologists to some extent and may hint at taxonomic revisions. Instead of demonstrating the overwhelming agreement this paper puts emphasis on the biological implications of the differences.

Patterns and ecological determinants of woody plant height in eastern Eurasia and its relation to primary productivity

Aims Plant height is a key functional trait related to aboveground bio-mass,leaf photosynthesis and plant fitness.However,large-scale geographical patterns in community-average plant height(cAPH)of woody species and drivers of these patterns across different life forms remain hotly debated.Moreover,whether cAPH could be used as a predictor of ecosystem primary productivity is unknown.Methods We compiled mature height and distributions of 11422 woody spe-cies in eastern Eurasia,and estimated geographic patterns in cAPH for different taxonomic groups and life forms.then we evaluated the effects of environmental(including current climate and historical climate change since the Last Glacial Maximum(LGM))and evolutionary factors on cAPH.Lastly,we compared the predictive power of cAPH on primary productivity with that of LiDAR-derived canopy-height data from a global survey.Important Findings Geographic patterns of cAPH and their drivers differed among taxonomic groups and life forms.the strongest predictor for cAPH of all woody species combined,angiosperms,all dicots and deciduous dicots was actual evapotranspiration,while temperature was the strongest pre-dictor for cAPH of monocots and tree,shrub and evergreen dicots,and water availability for gymnosperms.Historical climate change since the LGM had only weak effects on cAPH.No phylogenetic signal was detected in family-wise average height,which was also unrelated to the tested environmental factors.Finally,we found a strong correlation between cAPH and ecosystem primary productivity.Primary productivity showed a weaker relationship with cAPH of the tallest species within a grid cell and no relationship with LiDAR-derived canopy height reported in the global survey.Our findings suggest that current climate rather than historical climate change and evolutionary history determine the geographical patterns in cAPH.However,the relative effects of climatic factors representing environmental energy and water availability on spatial variations of cAPH vary among plant life forms.Moreover,our results also suggest that cAPH can be used as a good predictor of ecosystem primary productivity.

Fragrep: An Efficient Search Tool for Fragmented Patterns in Genomic Sequences

Many classes of non-coding RNAs （ncRNAs; including Y RNAs, vault RNAs, RNase P RNAs, and MRP RNAs, as well as a novel class recently discovered in Dictyostelium discoideum） can be characterized by a pattern of short but well-conserved sequence elements that are separated by poorly conserved regions of sometimes highly variable lengths. Local alignment algorithms such as BLAST are therefore ill-suited for the discovery of new homologs of such ncRNAs in genomic sequences. The Fragrep tool instead implements an efficient algorithm for detecting the pattern fragments that occur in a given order. For each pattern fragment, the mismatch tolerance and bounds on the length of the intervening sequences can be specified separately. Furthermore, matches can be ranked by a statistically well-motivated scoring scheme.

Social Computing Unhinged

Social computing is ubiquitous and intensifying in the 21st Century.Originally used to reference computational augmentation of social interaction through collaborative filtering,social media,wikis,and crowdsourcing,here I propose to expand the concept to cover the complete dynamic interface between social interaction and computation,including computationally enhanced sociality and social science,socially enhanced computing and computer science,and their increasingly complex combination for mutual enhancement.This recommends that we reimagine Computational Social Science as Social Computing,not merely using computational tools to make sense of the contemporary explosion of social data,but also recognizing societies as emergent computers of more or less collective intelligence,innovation and flourishing.It further proposes we imagine a socially inspired computer science that takes these insights into account as we build machines not merely to substitute for human cognition,but radically complement it.This leads to a vision of social computing as an extreme form of human computer interaction,whereby machines and persons recursively combine to augment one another in generating collective intelligence,enhanced knowledge,and other social goods unattainable without each other.Using the example of science and technology,I illustrate how progress in each of these areas unleash advances in the others and the beneficial relationship between the technology and science of social computing,which reveals limits of sociality and computation,and stimulates our imagination about how they can reach past those limits together.

Social Scale and Collective Computation:Does Information Processing Limit Rate of Growth in Scale?

Collective computation is the process by which groups store and share information to arrive at decisions for collective behavior.How societies engage in effective collective computation depends partly on their scale.Social arrangements and technologies that work for small-and mid-scale societies are inadequate for dealing effectively with the much larger communication loads that societies face during the growth in scale that is a hallmark of the Holocene.An important bottleneck for growth may be the development of systems for persistent recording of information(writing),and perhaps also the abstraction of money for generalizing exchange mechanisms.Building on Shin et al.,we identify a Scale Threshold to be crossed before societies can develop such systems,and an Information Threshold which,once crossed,allows more or less unlimited growth in scale.We introduce several additional articles in this special issue that elaborate or evaluate this Thresholds Model for particular types of societies or times and places in the world.

Integrating Systemic Risk and Risk Analysis Using Copulas

Systemic risk research is gaining traction across diverse disciplinary research communities, but has as yet not been strongly linked to traditional, well-established risk analysis research. This is due in part to the fact that systemic risk research focuses on the connection of elements within a system, while risk analysis research focuses more on individual risk to single elements. We therefore investigate how current systemic risk research can be related to traditional risk analysis approaches from a conceptual as well as an empirical point of view. Based on Sklar's Theorem, which provides a one-to-one relationship between multivariate distributions and copulas, we suggest a reframing of the concept of copulas based on a network perspective. This provides a promising way forward for integrating individual risk(in the form of probability distributions) and systemic risk(in the form of copulasdescribing the dependencies among such distributions)across research domains. Copulas can link continuous node states, characterizing individual risks, with a gradual dependency of the coupling strength between nodes on their states, characterizing systemic risk. When copulas are used for describing such refined coupling between nodes,they can provide a more accurate quantification of a system's network structure. This enables more realistic systemic risk assessments, and is especially useful when extreme events(that occur at low probabilities, but have high impacts) affect a system's nodes. In this way, copulas can be informative in measuring and quantifying changes in systemic risk and therefore be helpful in its management. We discuss the advantages and limitations of copulas for integrative risk analyses from the perspectives of modeling, measurement, and management.

Inaugural Message from Editors-in-Chief

On behalf of the Editorial Board,it is our privilege to present the first issue of the Journal of Social Computing,affectionately shortened JoSoCo.Social computing concerns the intersection of social behavior and computational systems.Historically focused on recreating human social conventions and contexts through software and technology,we propose its expansion to the full interface between social interaction and computation.

A Generalized Discrete Morse-Floer Theory

Forman has developed a version of discrete Morse theory that can be understood in terms of arrow patterns on a(simplicial,polyhedral or cellular)complex without closed orbits,where each cell may either have no arrows,receive a single arrow from one of its facets,or conversely,send a single arrow into a cell of which it is a facet.By following arrows,one can then construct a natural Floer-type boundary operator.Here,we develop such a construction for arrow patterns where each cell may support several outgoing or incoming arrows(but not both),again in the absence of closed orbits.Our main technical achievement is the construction of a boundary operator that squares to 0 and therefore recovers the homology of the underlying complex.

Cities and Methods from Complexity Science

The dynamics of human society is now been studying in the context of the artificial environment created by cities. In this work, the authors describe some of the formal methods used in complexity science to study urban systems. The authors discuss some of the important quantitative approaches on cities paying attention to some of the deepest controversies in present scientific studies.The authors will stress the importance of a transdisciplinary approach when studying this type of cooperative social environments.

Long-range current-induced spin accumulation in chiral crystals

Chiral materials,similarly to human hands,have distinguishable right-handed and left-handed enantiomers which may behave differently in response to external stimuli.Here,we use for the first time an approach based on the density functional theory(DFT)+PAOFLOW calculations to quantitatively estimate the so-called collinear Rashba–Edelstein effect(REE)that generates spin accumulation parallel to charge current and can manifest as chirality-dependent charge-to-spin conversion in chiral crystals.Importantly,we reveal that the spin accumulation induced in the bulk by an electric current is intrinsically protected by the quasi-persistent spin helix arising from the crystal symmetries present in chiral systems with the Weyl spin–orbit coupling.In contrast to conventional REE,spin transport can be preserved over large distances,in agreement with the recent observations for some chiral materials.This allows,for example,the generation of spin currents from spin accumulation,opening novel routes for the design of solid-state spintronics devices.

U7 snRNAs:A Computational Survey

U7 small nuclear RNA （snRNA） sequences have been described only for a handful of animal species in the past. Here we describe a computational search for functional U7 snRNA genes throughout vertebrates including the upstream sequence elements characteristic for snRNAs transcribed by polymerase Ⅱ. Based on the results of this search, we discuss the high variability of U7 snRNAs in both sequence and structure, and report on an attempt to find U7 snRNA sequences in basal deuterostomes and non-drosophilids insect genomes based on a combination of sequence, structure, and promoter features. Due to the extremely short sequence and the high variability in both sequence and structure, no unambiguous candidates were found. These results cast doubt on putative U7 homologs in even more distant organisms that are reported in the most recent release of the Rfam database.