基于共词分析的国内生物信息学热点领域研究

利用共词分析和可视化方法对生物信息学的关键词进行聚类分析,探讨该研究领域的学科分类和热点内容.以中国知网、中华医学会数据库中期刊论文为统计来源,对1998～2013年间的5 707篇生物信息学相关文献进行计量分析,提取出40个高频关键词.利用ROST软件得到关键词共词矩阵,在此基础上利用SPSS进行因子分析、聚类分析和多维尺度分析.结合因子分析和聚类分析将生物信息学领域主要研究内容分为7类,结合多维尺度分析对研究热点及变化趋势进行了初步探讨.研究结果较为客观地反映了当前生物信息学领域的学科分类和研究热点,为科研人员进行生物信息学研究提供一些思路.     

国际生物信息学研究的可视化分析

利用当前主流的信息可视化分析软件Cite Space对2005~2014年间SCI收录的生物信息学的5种高影响力外文期刊所刊载论文的题录数据进行统计和可视化分析,绘制该领域的关键词共现、膨胀词共现、经典文献共现、高被引文献共现和关键节点文献共现的网络可视化图谱,试图揭示生物信息学领域的研究热点、研究前沿以及知识基础,以期帮助研究人员了解该领域在国际范围内的研究态势。     

生物多样性信息资源.Ⅱ.环境类型数据

环境类型数据是研究生物多样性分布格局、多样性形成与维持机制、物种保育等很多重要生态学问题的基础。近年来,随着环境监测网络在全球范围内的不断扩张与新监测手段的不断涌现,区域和全球尺度上的不同类型的环境数据呈爆炸式增长。然而,这些海量的数据零散地分布在互联网的各个角落,给生物多样性研究人员了解数据信息、高效选择和利用数据等带来了挑战。面对环境数据来源广、分布零散的现状,本文从气候、地形地貌土壤与生境异质性、土地覆盖、水文和其他等5个方面对环境数据进行整理,并且选取其中一些使用频率较高的数据集,从它们的数据来源、数据结构、数据获取方式、数据精度以及数据使用情况等方面举例介绍。本文共介绍了45个不同类型的数据集,既包括WorldClim气候数据、HWSD(Harmonized World Soil Database)土壤数据等在生态学中频繁使用的数据集,也包括气候变化速率、EarthEnv生境异质性数据、全球森林覆盖数据、全球光污染数据等最新发布或较少使用的数据集。另外,需要指出的是,这些数据集远不能涵盖目前所能获得并在持续增加的环境类型数据。作者希望本文的不完整总结能够为研究人员高效选择和有效利用这些和其它相似的环境数据提供参考。     

基于文献计量分析的喀斯特植被生态学研究态势

喀斯特植被是喀斯特生态系统结构与功能稳定的重要维持者。国内外学者较早关注喀斯特植被的结构、功能和管理等方面研究并发表了诸多成果,但对该领域的发展历程、研究趋势和热点等却鲜有评论。利用1990—2017年Web of Science(WoS)和CNKI数据库中喀斯特植被生态学研究的相关文献信息,运用文献计量统计和可视化方法对年度发文量、引用频次、作者、国家、机构、期刊、关键词等进行分析,解析了28年间国内外该领域的研究态势并对未来发展提出了建议。结果表明,1990—2017年间WoS和CNKI数据库中分别收录了该领域文献457篇和1256篇,28年间发文量呈现波动增长趋势,且在2006年后步入快速发展期。WoS中的文献涉及全球60个国家,我国的发文量占发文总量的50.33%,遥居全球榜首,其次是美国和斯洛文尼亚等国。此外,发文量前10的作者均来自我国,发文量较多的机构也多来自我国,这充分表明我国学者在喀斯特植被生态学方面的研究非常活跃,是全球该领域前沿动向和发展趋势的引领者。期刊分析结果表明,《Environmental Earth Sciences》和《生态学报》分别是该领域外文和中文文献的主要期刊载体。喀斯特、植被和石漠化等为文献高频度关键词,表明喀斯特石漠化区域的植被恢复是该领域的研究热点和核心内容。为促进喀斯特植被生态学研究的发展,建议国内外学者以及机构间加强合作,建立全球的喀斯特植被监测网络,长期观测并对比分析不同区域或类型喀斯特植被的动态过程和生态功能演变机理。此外,运用大数据、遥感、野外控制实验、数学模型和系统发育等方法构建适用于喀斯特生境的植被格局、过程与动态的生态理论、假说或模型,进一步揭示变化环境下喀斯特植物群落的构建过程、植物多样性的多尺度格局、退化植被的适应性修复等科学问题。     

中国粮食安全问题研究进展——基于CSSCI文献计量的综述

运用文献计量分析方法，基于CSSCI来源期刊1998—2019年的“粮食安全”相关文献，对我国粮食安全问题研究动态进行梳理分析。粮食安全研究领域发文量多年来变化不明显，粮食生产、粮食产量、国家粮食安全、粮食政策是比较重要的关键词，多集中于粮食安全的概念内涵与评价体系，供给和需求、政策和国际环境等因素对粮食安全的影响。研究动态上还表现出今后可能在粮食安全的概念内涵以及评价指标、可持续发展与粮食安全、提高粮食综合生产力、政府粮食安全政策与战略研究等方面继续探索。     

哺乳动物的蛰眠: 类型、物种分布与模式

哺乳动物的蛰眠(包括冬眠、夏眠和日蛰眠等)是最具吸引力的生命现象之一,是动物应对寒冷、食物
短缺、干旱等不良环境条件的适应策略之一。冬眠生理学(生态学) 研究具有重要的理论和实际意义。国际学
术界在该领域发展比较迅速,国内发展相对缓慢。本文从哺乳动物蛰眠的季节和持续时间、蛰眠期间所利用能
量的来源和贮存方式、启动蛰眠的信号来源等方面综述了哺乳动物蛰眠的类型;介绍了蛰眠的哺乳动物物种的
系统学分布;并对温带或北极动物的冬眠和冬眠阵及其各阶段的体温和代谢率变化特征、日温剧烈波动环境下
的冬眠特征以及日眠和日眠阵等方面进行了概括介绍,以期能促进国内相关领域的发展。     

社会-生态系统恢复力研究进展——基于CiteSpace的文献计量分析

社会-生态系统恢复力为深化人类与自然的复杂相互作用过程与机理研究提供了新的视角,并成为推动跨学科整合与全球可持续发展的重要工具。运用CiteSpace文献计量方法,以社会-生态系统恢复力研究文献为对象,通过对关键词、作者、研究机构与引证文献等要素的分析,得出了国外社会-生态系统恢复力研究的总体特征,并从概念内涵、评估量化、体制转换与适应性管理4个方面系统总结了该领域主要研究内容及其进展动态,结合我国研究现状对未来研究提出展望。研究发现:社会-生态系统恢复力相关文章数量呈快速上升趋势,主要集中在生态环境与地理学领域;斯德哥尔摩大学的Folke是该领域的代表性学者;社会-生态系统恢复力研究呈现多元分散特征,理论分析、实证方法与实践层面的适应性管理是该领域主要的研究热点;尺度问题、社会-生态系统整合、恢复力量化评估以及体制转换与恢复力变化关系是该领域未来研究需要进一步强化与深化的内容。     

水产经济鱼类基因组大数据平台的构建与应用

水产经济鱼类是人类重要的蛋白质来源,对其基因组的研究在分子育种、分析水生生物进化等方面起到重要作用。目前,国内缺少分析水产经济鱼类基因测序数据的综合性数据平台。本文搜集并整理了20余种水产经济鱼类的基因组测序数据,并开发了水产经济鱼类基因组大数据平台。该平台包括数据存储、数据下载、数据分析,以及数据可视化展示等模块。通过该平台,用户可以快速检索鱼类基因的功能、表达水平、基因保守性以及共线性等。本研究开发的鱼类大数据平台将促进水产领域对鱼类基因组的分析。该大数据平台可通过IP 47.96.156.188访问。     

基于CiteSpace和VOSviewer可视化分析国内近30年肠道菌群在中医药领域的研究热点与趋势CSCD

目的 分析近30年来肠道菌群在中医药领域的研究热点与趋势。方法 检索中国知网数据库中肠道菌群在中医药研究领域的中文学术文献,运用VOSviewer软件对文献的作者、来源机构及关键词进行网络共线分析;运用CiteSpace软件进行文献的年发表数量统计、关键词聚类分析及关键词突现分析。结果 最终纳入符合标准的文献1 519篇,论文发表数量从2014年开始呈现逐年上升的趋势;文献作者之间形成了以谭周进、杨景云、贾连群、段金廒等为代表的多个稳定核心作者团体;关联机构共408家,核心机构之间关联性较差;关键词之间形成14个聚类标签,包含溃疡性结肠炎、肠道菌群、代谢、针刺、肠道微生态、中医药等主要聚类模块;突现关键词生成25个,近2年突现关键词为脑―肠轴、免疫功能及艾滋病。结论 通过可视化图谱直观展示了肠道菌群在中医药领域30年的研究概况,近10年来学者们对该领域的研究逐渐深入,发展趋势较好。脑―肠轴、免疫功能及艾滋病的研究成为该领域的主要新兴热点,同时,目前研究尚存在各机构或各团体之间跨领域合作较少、研究深度不足等问题。     

数据挖掘在生物信息学中的应用——文献计量学视角

基因组和蛋白质结构与功能方面已积累了海量数据。如何从海量数据中获取有效信息成为生物信息学迫切要解决的问题。本文以相关主题词检索文献,分析了该领域历年文章数量、发文最多的机构和作者、被引用频次居前论文、期刊载文量,并对关键词和被引用频次居前论文的作者进行共现分析。我们发现,生物信息学中运用数据挖掘方法的文献逐年增多,该领域30.1%的文献发表在十个期刊上,分类、聚类、特征选择和支持向量机等数据挖掘方法使用较多。本研究描绘了生物信息学与数据挖掘这一交叉领域的研究概况,为后续数据挖掘方法与生物信息学研究相结合提供帮助。     

基于公众参与地理信息系统的广州大学城环境安全感评价研究

现有基于地点的校园环境安全研究主要以客观的案件数据为研究对象,未能揭示学生安全感与特定地点环境因素的内在联系。利用Maptionnaire问卷平台,以广州大学城为例,通过公众参与地理信息系统分析学生对校园交通、事故和人身财产方面的环境安全感评价及其空间分布。研究发现学生整体安全感评价较低,评价低的地点集中在高校周边公园绿地、城中村、体育场馆,评价高的地点主要位于高校用地范围内。结合对评价低的地点进行实地调研,基于环境设计预防犯罪（crime prevention through environmental design,简称CPTED）理论分析影响学生安全感的环境因素,针对相关问题提出对应的提升学生安全感的环境设计优化建议。     

The long hard road to the doability of interdisciplinary research projects: the case of biosocial criminology

This paper combines Bourdieu’s Field Theory with the concept of “doability” to investigate an interdisciplinary scientific project, namely biosocial criminology. Biosocial criminologists seek to incorporate genetic and neuroscientific findings in criminology. Drawing on literature analysis and semi-structured interviews, I show how the doability of this interdisciplinary research project, which is mainly determined by considerations surrounding data and technologies, is a function of biosocial researchers’ position within the scientific field. This is made apparent at two different levels. First, the availability of genetic data, which is attributable to behavior geneticists’ “generosity” and inter-field exchanges, largely explains why biosocial criminologists mostly focused on genetic factors of crime and neglected neuroscience, a more costly area of endeavor. Second, the problem of doability prevents biosocial criminologists from performing any kind of genetic research. Because behavior geneticists’ generosity has its limits too, biosocial criminologists cannot resort to the most advanced methodological designs.     

A Review of the Statistical and Quantitative Methods Used to Study Alcohol-Attributable Crime

Modelling the relationship between alcohol consumption and crime generates new knowledge for crime prevention strategies. Advances in data, particularly data with spatial and temporal attributes, have led to a growing suite of applied methods for modelling. In support of alcohol and crime researchers we synthesized and critiqued existing methods of spatially and quantitatively modelling the effects of alcohol exposure on crime to aid method selection, and identify new opportunities for analysis strategies. We searched the alcohol-crime literature from 1950 to January 2014. Analyses that statistically evaluated or mapped the association between alcohol and crime were included. For modelling purposes, crime data were most often derived from generalized police reports, aggregated to large spatial units such as census tracts or postal codes, and standardized by residential population data. Sixty-eight of the 90 selected studies included geospatial data of which 48 used cross-sectional datasets. Regression was the prominent modelling choice (n = 78) though dependent on data many variations existed. There are opportunities to improve information for alcohol-attributable crime prevention by using alternative population data to standardize crime rates, sourcing crime information from non-traditional platforms (social media), increasing the number of panel studies, and conducting analysis at the local level (neighbourhood, block, or point). Due to the spatio-temporal advances in crime data, we expect a continued uptake of flexible Bayesian hierarchical modelling, a greater inclusion of spatial-temporal point pattern analysis, and shift toward prospective (forecast) modelling over small areas (e.g., blocks).     

Putting the "landscape" in landscape genetics

Landscape genetics has emerged as a new research area that integrates population genetics, landscape ecology and spatial statistics. Researchers in this field can combine the high resolution of genetic markers with spatial data and a variety of statistical methods to evaluate the role that landscape variables play in shaping genetic diversity and population structure. While interest in this research area is growing rapidly, our ability to fully utilize landscape data, test explicit hypotheses and truly integrate these diverse disciplines has lagged behind. Part of the current challenge in the development of the field of landscape genetics is bridging the communication and knowledge gap between these highly specific and technical disciplines. The goal of this review is to help bridge this gap by exposing geneticists to terminology, sampling methods and analysis techniques widely used in landscape ecology and spatial statistics but rarely addressed in the genetics literature. We offer a definition for the term "landscape genetics", provide an overview of the landscape genetics literature, give guidelines for appropriate sampling design and useful analysis techniques, and discuss future directions in the field. We hope, this review will stimulate increased dialog and enhance interdisciplinary collaborations advancing this exciting new field.     

珊瑚礁生态系统模型研究现状及热点分析

以Web of Science数据库中的Web of Science ~(TM)核心合集和中国期刊全文数据库为数据源,对2018年10月前国内外发表的珊瑚礁生态系统模型研究相关文献进行计量分析,评估该领域的研究现状及热点。研究表明:国外珊瑚礁生态系统模型研究起始于1974年,相关文献的发文量整体呈大幅度增长趋势;国内研究于1997年起步,发文量增长较缓慢,近三年显著增加。高频关键词统计分析可以看出,国外对于珊瑚礁中生活的各种生物及其生态分布研究较为广泛,生态系统的生物群落多样性是该领域的研究热点,关于珊瑚礁生态系统风险、威胁、胁迫和修复的模型研究近几年有所起色,在今后一段时间内将是该领域的主要研究趋势。国内相关研究局限于珊瑚礁地质环境与波浪传播等方面,应在扩大研究范围的同时,将重点放在珊瑚礁生态系统退化诊断与修复的探究上。     

The Complexity of Crime Network Data: A Case Study of Its Consequences for Crime Control and the Study of Networks

The field of social network analysis has received increasing attention during the past decades and has been used to tackle a variety of research questions, from prevention of sexually transmitted diseases to humanitarian relief operations. In particular, social network analyses are becoming an important component in studies of criminal networks and in criminal intelligence analysis. At the same time, intelligence analyses and assessments have become a vital component of modern approaches in policing, with policy implications for crime prevention, especially in the fight against organized crime. In this study, we have a unique opportunity to examine one specific Swedish street gang with three different datasets. These datasets are the most common information sources in studies of criminal networks: intelligence, surveillance and co-offending data. We use the data sources to build networks, and compare them by computing distance, centrality, and clustering measures. This study shows the complexity factor by which different data sources about the same object of study have a fundamental impact on the results. The same individuals have different importance ranking depending on the dataset and measure. Consequently, the data source plays a vital role in grasping the complexity of the phenomenon under study. Researchers, policy makers, and practitioners should therefore pay greater attention to the biases affecting the sources of the analysis, and be cautious when drawing conclusions based on intelligence assessments and limited network data. This study contributes to strengthening social network analysis as a reliable tool for understanding and analyzing criminality and criminal networks.     

Perspectives in innate and acquired cardioprotection: cardioprotection acquired through exercise.

Emerging evidence indicates that exercise training can provide significant protection against myocardial ischemia-reperfusion injury. In this brief review, we provide a synthesis of current literature in the field and summarize the findings to date. Our intent is to identify the unique elements of cardioprotection acquired by exercise, and to illustrate what distinguishes this physiological acquisition of cardioprotection from all other known types of acquired cardioprotection. Finally, we point to future directions for research in this exciting area.     

Design and analysis of experiments with high throughput biological assay data

The design and analysis of experiments using gene expression microarrays is a topic of considerable current research, and work is beginning to appear on the analysis of proteomics and metabolomics data by mass spectrometry and NMR spectroscopy. The literature in this area is evolving rapidly, and commercial software for analysis of array or proteomics data is rarely up to date, and is essentially nonexistent for metabolomics data. In this paper, I review some of the issues that should concern any biologists planning to use such high-throughput biological assay data in an experimental investigation. Technical details are kept to a minimum, and may be found in the referenced literature, as well as in the many excellent papers which space limitations prevent my describing. There are usually a number of viable options for design and analysis of such experiments, but unfortunately, there are even more non-viable ones that have been used even in the published literature. This is an area in which up-to-date knowledge of the literature is indispensable for efficient and effective design and analysis of these experiments. In general, we concentrate on relatively simple analyses, often focusing on identifying differentially expressed genes and the comparable issues in mass spectrometry and NMR spectroscopy (consistent differences in peak heights or areas for example). Complex multivariate and pattern recognition methods also need much attention, but the issues we describe in this paper must be dealt with first. The literature on analysis of proteomics and metabolomics data is as yet sparse, so the main focus of this paper will be on methods devised for analysis of gene expression data that generalize to proteomics and metabolomics, with some specific comments near the end on analysis of metabolomics data by mass spectrometry and NMR spectroscopy.     

Harmonic Dissonance: Reflections on Dwelling in the Field

Focusing on the idea of dwelling in the field, this paper explores the moral grammar of living with others in field settings, including the texture of membership in one's own family and host families. Through a comparative analysis of two ethnographic research contexts – one on transnational Christian non-governmental organizations in the US and Zimbabwe in 1996 –97, and the other on orphans and philanthropy in India in 2004–05 – I interrogate what it means to inhabit the field. In the world of multi-sited ethnography all research sites are not created equal; both in terms of the kinds of data one can collect and the types of observations one can make. How ethnographers are situated in a web of affliations affects their experience in the field, what they observe, and their research practice. I propose renewed attention to how anthropologists live in the field, including how relationships are interpreted in the field by ethnographers and their informants.