基于图论的景观图表达、分析及应用

景观结构和空间格局一直是景观生态学的核心问题,图论的应用为景观格局的分析提供了一种研究框架,基于图论的景观图逐渐被应用于生物多样性保护的连通性建模和景观规划的决策支持研究,景观图的表达、分析和应用已成为保护生物学和景观生态学研究的热点。本文首先介绍了景观图的图论基础,在Scopus数据库的基础上,检索了1993—2019年在标题、摘要和关键词中出现 “landscape graph”、“connectivity”和“network”词汇的257篇已发表的期刊论文。从年发文量、来源期刊、研究区域、研究机构、景观类型等方面分析了该领域的研究进展和发展趋势。分析发现,2017年之前,发表的期刊论文数量整体呈上升趋势,2017年之后年发文量逐年下降;主要研究力量集中在美国、西班牙、法国、加拿大和中国,发文量占到86.8%。大部分研究成果发表在“Landscape Ecology”、“Landscape and Urban Planning”和“Biological Conservation”期刊上。在研究内容上,景观图表达主要包括点的定义、边的度量和景观的模拟3方面,景观图分析研究包括分析指数、景观图划分两方面。我们重点关注了景观图在生物多样性保护、景观(生态网络)规划和管理、景观影响评价等科学与实践中的应用。基于图论的景观图通过帮助理解景观连通性变化、动物行为和栖息地保护,影响着保护科学和规划实践者。图论对保护科学和规划的影响来自于丰富的理论基础和成熟的研究方法,基于图论的景观图为景观结构和格局的生态学理解提供了跳板,并将继续成为全球研究人员和实践者的重要工具。     

Evaluating research and impact: a bibliometric analysis of research by the NIH/NIAID HIV/AIDS clinical trials networks

Evaluative bibliometrics uses advanced techniques to assess the impact of scholarly work in the context of other scientific work and usually compares the relative scientific contributions of research groups or institutions. Using publications from the National Institute of Allergy and Infectious Diseases (NIAID) HIV/AIDS extramural clinical trials networks, we assessed the presence, performance, and impact of papers published in 2006-2008. Through this approach, we sought to expand traditional bibliometric analyses beyond citation counts to include normative comparisons across journals and fields, visualization of co-authorship across the networks, and assess the inclusion of publications in reviews and syntheses. Specifically, we examined the research output of the networks in terms of the a) presence of papers in the scientific journal hierarchy ranked on the basis of journal influence measures, b) performance of publications on traditional bibliometric measures, and c) impact of publications in comparisons with similar publications worldwide, adjusted for journals and fields. We also examined collaboration and interdisciplinarity across the initiative, through network analysis and modeling of co-authorship patterns. Finally, we explored the uptake of network produced publications in research reviews and syntheses. Overall, the results suggest the networks are producing highly recognized work, engaging in extensive interdisciplinary collaborations, and having an impact across several areas of HIV-related science. The strengths and limitations of the approach for evaluation and monitoring research initiatives are discussed.     

不懈探索, 努力引领中国生物多样性科学发展——《生物多样性》创刊三十周年回顾

为更好地推动我国生物多样性科学的发展, 提升期刊服务能力, 并庆祝创刊30周年, 我们梳理了《生物多样性》2013-2022年的主要进展。(1)近10年中, 期刊的特色进一步凸显。围绕学科前沿、国家重大行动计划、履约等领域共策划出版56个专辑/专题, 新设立编者按、生物编目、数据论文、保护与治理对策、生物文化多样性等特色栏目, 通过发表数据论文、生物编目等文章推动数据共享, 以及通过鼓励学术争鸣、探索中文期刊的国际传播等举措使期刊的特色进一步凸显。(2)期刊载文量快速增加, 报道的内容不断拓展。研究方向由前20年的61个增加为目前的78个, 90%左右的文章聚焦于生物多样性保护、环境科学/生态学等领域; 植物学、动物学、微生物学的稿件分别占41.79%、47.48%和4.61%。基于关键词的文献计量分析表明, 近10年刊登的文章关键词聚类为遗传多样性、群落结构、红外相机、红色名录、生物多样性公约、国家公园、植物多样性、分类学和地理分布等9个子领域。培养了大批生物多样性人才, 10年中共有4,665位作者署名(作者记录数6,295), 发表文章最多的前20位作者主要来自中国科学院相关研究所、中国环境科学研究院、北京大学等机构, 其中60%为编委。(3)刊登的论文被广泛引用和下载。根据中国知网数据(排除了学位论文和会议论文, 2022年10月18日), 近10年刊登的文章有1,211篇累计被引用13,507次, 平均每篇被引11次以上; 网上下载量从2012年的6.64万次增加到2021年的23.85万次。有5篇文章入选中国科协优秀科技论文或中国百篇最具影响国内学术论文; 以国家公园、红外相机、红色名录、多功能性、生物入侵为关键词的文章是受关注的热点。《生物多样性》的影响因子和总被引频次在生物学领域一直排名前列; 是《科技期刊世界影响力指数(WJCI)报告》中全球保护生物学领域唯一的中国期刊, 2019年和2020年分别位列23/48和25/49位。最后我们探讨了今后如何继续引领中国生物多样性研究和保护、建设一流科技期刊面临的挑战和对策以及如何进一步提升科学传播能力。     

Network Structure and Travel Time Perception

The purpose of this research is to test the systematic variation in the perception of travel time among travelers and relate the variation to the underlying street network structure. Travel survey data from the Twin Cities metropolitan area (which includes the cities of Minneapolis and St. Paul) is used for the analysis. Travelers are classified into two groups based on the ratio of perceived and estimated commute travel time. The measures of network structure are estimated using the street network along the identified commute route. T-test comparisons are conducted to identify statistically significant differences in estimated network measures between the two traveler groups. The combined effect of these estimated network measures on travel time is then analyzed using regression models. The results from the t-test and regression analyses confirm the influence of the underlying network structure on the perception of travel time.     

The grand challenges of migration ecology that radar aeroecology can help answer

Many migratory species have experienced substantial declines that resulted from rapid and massive expansions of human structures and activities, habitat alterations and climate change. Migrants are also recognized as an integral component of biodiversity and provide a multitude of services and disservices that are relevant to human agriculture, economy and health. The plethora of recently published studies reflects the need for better fundamental knowledge on migrations and for better management of their ecological and human‐relevant effects. Yet, where are we in providing answers to fundamental questions and societal challenges? Engaging a broad network of researchers worldwide, we used a horizon‐scan approach to identify the most important challenges which need to be overcome in order to gain a fuller understanding of migration ecology, and which could be addressed using radar aeroecological and macroecological approaches. The top challenges include both long‐standing and novel topics, ranging from fundamental information on migration routes and phenology, orientation and navigation strategies, and the multitude of effects migrants may have on resident communities, to societal challenges, such as protecting or preventing migrant services and disservices, and the conservation of migrants in the face of environmental changes. We outline these challenges, identify the urgency of addressing them and the primary stakeholders – researchers, policy makers and practitioners, or funders of research.     

放线菌代谢产物的研究进展：基于Web of Science (WOS)和中国知网(CNKI)

【背景】放线菌是一类极其重要的微生物,代谢产物丰富,在医药、生物技术、农业和酶工业等领域均有广泛应用。【目的】客观分析放线菌代谢产物的研究进展,为该领域相关工作人员提供有效情报,推动该领域高质量发展。【方法】对Web of Science (WOS)和中国知网(China National Knowledge Infrastructure, CNKI)数据库中放线菌代谢产物的发文数量、发文国家、发文机构、发文期刊、发文出版社、发文作者、被引文章和研究方向进行统计分析,利用H指数对相关影响力进行综合评价,其研究热点、发展趋势通过Cite Space和VOSviewer软件进行可视化分析。【结果】WOS结果显示,放线菌代谢产物研究领域全球影响力最大的国家是美国,影响力最大的机构是美国加利福利亚大学,影响力最大的期刊是美国Applied and Environmental Microbiology,影响力最大的出版社是Elsevier,影响力最大的作者是来自英国约翰英纳斯研究中心微生物学部的Mervyn J Bibb教授。全球放线菌代谢产物领域的主要研究方向是微生物学,研究热点是生物合成。研...     

Saline Systems highlights for 2005

On the 4^th of July, 2005, the Saline Systems editorial group launched the new online open access journal, Saline Systems, with BioMed Central as the publisher. The scope of the journal includes both basic and applied research on halophilic organisms and saline environments, from gene systems to ecosystems. The stated goal of the journal is to meet publication needs for researchers working in coastal and inland saline environments and provide an interdisciplinary and readily accessible forum for scientists worldwide. The inaugural volume of the journal contains a significant number of high quality original research papers and reviews on a wide range of relevant topics. At the end of the launch period, from January 1, 2006 onwards, the journal will be introducing article-processing charges to cover the cost of publication. Charges will be partly or completely waived for authors from BioMed Central institutional subscribers and in cases of financial hardship.     

The Golden Anniversary of the Society of Protozoologists (1947-1997)1

ABSTRACT The history of the Society of Protozoologists is traced from its birth, half a century ago, to the present time. Emphasis is placed on events of the formative years, since data from the scattered records and memories of those times need to be assembled in one place before they are entirely forgotten or “misremembered.” As is true in the establishment of any new association, the people involved are responsible for its later success. Thus tribute is especially paid to the original founding fathers and the early charter members who worked so hard and so unselfishly to assure the permanence—and long—lasting usefulness-of their Society in a specialized branch of biology. An obvious value of a new scientific organization lies in its production of a scholarly journal. In the present case, such a publication was launched early, and it rapidly became known worldwide as a protozoological research outlet of the highest quality. The aims and goals of the founders seem to have been well met over the past 50 years, but the international Society of Protozoologists faces new challenges and obligations in the years ahead.     

Comparative analysis of Acinetobacters: three genomes for three lifestyles

Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i) whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss); ii) strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii) several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors) were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS). Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil.     

Understanding the Evolution of Industrial Symbiosis Research

This study analyzes the evolution of the research field of industrial symbiosis (IS). We elucidate its embedding in industrial ecology (IE), trace the development of research themes, and reveal the evolution of the research network through analysis of the core literature and journals that appeared from 1997 to 2012 by citation analysis, cocitation analysis, and network analysis. In the first period (1997–2005), IS research held a minority share in the IE literature. The research revolved around the concept of IS, the assessment of eco‐industrial park projects, and the establishment of waste treatment and recycling networks. In the second period (2006–2012), diverse research approaches and theories enriched the field, which has led to a maturation in theory building. Our findings clearly illustrate that IS evolved from practice‐oriented research toward coherent theory building through a systematic underpinning and linking of diverse topics. As scientific attention shifted from exploring a phenomenon to elucidating underlying mechanisms, IS knowledge found worldwide practical implementation. The coauthorship network shows that the academic communities of IS are distributed worldwide and that international collaboration is widespread. Through bibliometric and network analysis of IS, we have created a systemic, quantitative image of the evolution of the IS research field and community, which gives IS researchers an underpinned overview of the IS research and may help them to identify new directions and synergy in worldwide research.     

Stromal cell derived factor-2 (Sdf2): A novel protein expressed in mouse

The stromal derived factor (SDFs) family comprises a group of molecules generated by stromal cells. SDF1 and SDF4 are chemokines; SDF2 and SDF5 are not yet functionally and structurally defined. In human and mouse, Sdf2 has a paralogous gene, Sdf2l1, whose protein sequences are 78% similar and 68% identical. Human SDF2L1 is an endoplasmic reticulum-stress inducible-gene. In Arabidopsis thaliana, SDF2-like (39% and 37% amino acid sequence identity with Mus musculus Sdf2 and Sdf2l1) has also been implicated in activating the UPR in ER-stress. Here we have cloned, expressed and purified recombinant Sdf2 and raised an anti-Sdf2 antibody. We demonstrated that the protein is expressed in several tissues and is localized in the endoplasmic reticulum. We suggest that Sdf2, initially predicted as a secretory protein because it lacks the canonical ER retention signals in its C-terminal, could be ER-resident through accessory binding proteins or other amino acid sequence motifs, as suggested for the homolog protein SDF2-like. Furthermore, the crystal structure of SDF2-like from Arabidopsis thaliana is a typical β-trefoil containing three MIR motifs; all hydrophobic residues considered important for maintaining the bottom layer of the β-trefoil barrel seem to be conserved in the Sdf2 family. Multiple alignment using 43 sequences for SDF2 and 38 for SDF2L1 paralogous families also revealed a very similar residue conservation profile. Comparing the amino acid sequence and predicted 3D structure with other Sdf2-like proteins we suggest a role of mouse Sdf2 in the Unfolded Protein Response and ER-stress, similar to that of Sdf2l1 from human and mouse and SDF2-like from Arabidopsis thaliana. Chronic ER stress has been associated with many human diseases including cancer and diabetes. Identification of new factors associated with the ER stress pathway can help to identify and define key targets of this response.     

Structure and Chromosomal Localization of the Human Stromal Cell-Derived Factor 1 (SDF1) Gene

Stromal cell-derived factors 1α and 1β are small cytokines belonging to the intercrine CXC subfamily and originally isolated from a murine bone-marrow stroma cell line by the signal sequence trap method. cDNA and genomic clones of human SDF1α and SDF1β (SDF1A and SDF1B) were isolated and characterized. cDNAs of SDF1α and SDF1β encode proteins of 89 and 93 amino acids, respectively. SDF1α and SDF1β sequences are more than 92% identical to those of the human counterparts. The genomic structure of the SDF1 gene revealed that human SDF1α and SDF1β are encoded by a single gene and arise by alternative splicing. SDF1α and SDF1β are encoded by 3 and 4 exons, respectively. Ubiquitous expression of the SDF1 gene, except in blood cells, was consistent with the presence of the GC-rich sequence in the 5′-flanking region of the SDF1 gene, as is often the case in the "housekeeping" genes. Although genes encoding other members of the intercrine family are localized on chromosome 4q or 17q, the human SDF1 gene was mapped to chromosome 10q by fluorescence in situ hybridization. Strong evolutionary conservation and unique chromosomal localization of the SDF1 gene suggest that SDF1α and SDF1β may have important functions distinct from those of other members of the intercrine family.     

Gene expression databases and data mining

The DNA microarray technology has arguably caught the attention of the worldwide life science community and is now systematically supporting major discoveries in many fields of study. The majority of the initial technical challenges of conducting experiments are being resolved, only to be replaced with new informatics hurdles, including statistical analysis, data visualization, interpretation, and storage. Two systems of databases, one containing expression data and one containing annotation data are quickly becoming essential knowledge repositories of the research community. This present paper surveys several databases, which are considered "pillars" of research and important nodes in the network. This paper focuses on a generalized workflow scheme typical for microarray experiments using two examples related to cancer research. The workflow is used to reference appropriate databases and tools for each step in the process of array experimentation. Additionally, benefits and drawbacks of current array databases are addressed, and suggestions are made for their improvement.     

Enhancing the Functional Content of Eukaryotic Protein Interaction Networks

Protein interaction networks are a promising type of data for studying complex biological systems. However, despite the rich information embedded in these networks, these networks face important data quality challenges of noise and incompleteness that adversely affect the results obtained from their analysis. Here, we apply a robust measure of local network structure called common neighborhood similarity (CNS) to address these challenges. Although several CNS measures have been proposed in the literature, an understanding of their relative efficacies for the analysis of interaction networks has been lacking. We follow the framework of graph transformation to convert the given interaction network into a transformed network corresponding to a variety of CNS measures evaluated. The effectiveness of each measure is then estimated by comparing the quality of protein function predictions obtained from its corresponding transformed network with those from the original network. Using a large set of human and fly protein interactions, and a set of over GO terms for both, we find that several of the transformed networks produce more accurate predictions than those obtained from the original network. In particular, the measure and other continuous CNS measures perform well this task, especially for large networks. Further investigation reveals that the two major factors contributing to this improvement are the abilities of CNS measures to prune out noisy edges and enhance functional coherence in the transformed networks.     

The scientific research on rhodolith beds: A review through bibliometric network analysis

Rhodolith beds are benthic biogenic calcareous habitats formed by the aggregation of unattached, non-geniculate coralline algae. They have a worldwide distribution and, due to their 3D structural complexity and functioning, they provide several ecosystem services (i.e., provisioning and regulating). Recently, their importance and vulnerability have been internationally recognized by international policy and scientific research, and more attention has been drawn to their investigation and conservation. In this study, we conducted a systematic review integrated with a bibliometric analysis of the academic literature related to rhodolith beds. The analysis was based on published literature data over the period 1965–2022, and allowed the generation of maps based on network data displaying the relationships among countries, researchers, keywords, and scientific journals. A total of 853 publications were identified, revealing that scientific research on rhodolith beds is still relatively limited if compared to other coastal vegetated habitats (e.g., seagrass beds, kelp forests), although it has increased over time. Results showed that the scientific documents were published by 77 countries, 2255 researchers, and 279 journals. USA led the research production in this field with 159 documents and 4802 citations, and Amado-Filho was the most productive author with 36 documents and 1126 citations. The co-occurrence network map of keywords showed that the main research fields linked to rhodolith beds are geology, paleontology, algal taxonomy, community ecology, conservation, and physiology. The results also highlighted that most focus on the subject is recently shifting from geological and paleontological aspects to molecular taxonomic, conservation, and ecophysiological ones, while studies on the current topics of ecosystem services and carbon sequestration are still very limited.     

Journal of Ethnobiology and Ethnomedicine – achievements and perspectives

Last summer we officially launched the Journal of Ethnobiology and Ethnomedicine, published by BioMedCentral, with the aim of establishing a serious, peer-reviewed, open-access online journal that focuses on the multidisciplinary, interdisciplinary, and transdisciplinary fields of ethnobiology and ethnomedicine, drawing on approaches and methods from both the social and biological sciences. The strong start vindicates the widely held belief that the journal responds to a real need within the research community. The success of the journal has been most gratifying. The steady influx of submissions of high scientific standards illustrates the strong demand for a dynamic, proactive, and open-minded scientific journal in these research areas. Our aim has been to dedicate JEE to the "scientific communities" worldwide, particularly those in the developing countries.     

Proximity data-loggers increase the quantity and quality of social network data

Social network analysis is an ideal quantitative tool for advancing our understanding of complex social behaviour. However, this approach is often limited by the challenges of accurately characterizing social structure and measuring network heterogeneity. Technological advances have facilitated the study of social networks, but to date, all such work has focused on large vertebrates. Here, we provide proof of concept for using proximity data-logging to quantify the frequency of social interactions, construct weighted networks and characterize variation in the social behaviour of a lek-breeding bird, the wire-tailed manakin, Pipra filicauda. Our results highlight how this approach can ameliorate the challenges of social network data collection and analysis by concurrently improving data quality and quantity.     

The International Stem Cell Banking Initiative (ISCBI): raising standards to bank on

The International Stem Cell Banking Initiative (ISCBI) aims to create a global network of stem cell banks to facilitate best practice in stem cell research and clinical cell delivery, primary objectives of national and local governments worldwide and stem cell organizations such the International Stem Cell Forum and the International Society of Stem Cell Research. This paper is a brief overview of ISCBI, its primary activities, potential network participants, and the challenges for harmonizing stem cell banking on a global level.     

人类蛋白质相互作用组

高通量酵母双杂交与免疫亲和纯化技术的快速发展和日臻成熟,使得在蛋白质组水平上大规模地研究蛋白质之间的相互作用成为可能。目前,人类蛋白质互作网络在细胞、组织、器官乃至整个个体水平的研究已经陆续展开。蛋白质互作网络中蛋白质数量也由少数几个向整个蛋白质组扩展。同时,功能、疾病、生态等相关的蛋白质互作网络研究也取得了一定的成果。然而,人类的蛋白质互作网络研究正面临着一些问题和挑战。本文综述了人类蛋白质互作网络的研究方法、研究进展以及面临的挑战,同时指出了人类蛋白质互作网络研究的方向和目标。     

Open challenges for microbial network construction and analysis

Microbial network construction is a popular explorative data analysis technique in microbiome research. Although a large number of microbial network construction tools has been developed to date, there are several issues concerning the construction and interpretation of microbial networks that have received less attention. The purpose of this perspective is to draw attention to these underexplored challenges of microbial network construction and analysis.Subject terms: Microbiome, Microbial ecology