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。     

Reference bias in reports of drug trials.

Articles published before 1985 describing double blind trials of two or more non-steroidal anti-inflammatory drugs in rheumatoid arthritis were examined to see whether there was any bias in the references they cited. Althogether 244 articles meeting the criteria were found through a Medline search and through examining the reference lists of the articles retrieved. The drugs compared in the studies were classified as new or as control drugs and the outcome of the trial as positive or not positive. The reference lists of all papers with references to other trials on the new drug were then examined for reference bias. Positive bias was judged to have occurred if the reference list contained a higher proportion of references with a positive outcome for that drug than among all the articles assumed to have been available to the authors (those published more than two years earlier than the index article). Altogether 133 of the 244 articles were excluded for various reasons--for example, 44 because of multiple publication and 19 because they had no references. Among the 111 articles analysed bias was not possible in the references of 35 (because all the references gave the same outcome); 10 had a neutral selection of references, 22 a negative selection, and 44 a positive selection--a significant positive bias. This bias was not caused by better scientific standing of the cited articles over the uncited ones. Thus retrieving literature by scanning reference lists may produce a biased sample of articles, and reference bias may also render the conclusions of an article less reliable.     

Characteristics of papers that affect citations in the Journal of Fish Biology

Identifying the factors that influence the citation of articles helps authors improve the impact and reach of their research. Analysis of publications in the Journal of Fish Biology between 2008 and 2021 revealed that variables such as the number of keywords, abstract length, number of authors, and page length were associated with higher impact papers. These trends applied to both review and regular papers. These findings suggest that papers that are more informative, have higher numbers of authors, and have more keywords are more likely to be cited. Adoption of some simple “best-practice” behaviors can improve the likelihood that a paper is cited.     

Flying over water: how “On bird species diversity” influenced aquatic ecology

Habitat complexity has long been known to influence animal community structure by increasing the number of available habitats. Fifty years have passed since MacArthur brothers published the seminal paper “On bird species diversity”, which revolutionized studies of habitat structure. This paper first evidenced and quantified the relationship between species diversity (birds) and habitat structural complexity (the number of stratified layers of landscape vegetation). In this article, we aim to pay homage to R. H. MacArthur’s contribution and to briefly analyze the citation history and influence of “On bird species diversity”, focusing primarily on aquatic studies. We searched for all papers that cited “On bird species diversity” on Thomson Reuters (ISI—Web of Knowledge) and analyzed them for temporal citation trends. In addition, considering only aquatic papers, we explored whether and how habitat complexity was measured, as well as the ecological organization level, attributes of organisms, taxonomic groups and study design (observational or experimental). “On bird species diversity” citations increased over time, but this paper was less cited by limnologists compared to terrestrial and marine scientists. The majority of investigations in aquatic ecosystems quantified habitat complexity, but few used mathematical modeling. The high number of citations, which continues to increase, shows the great influence of “On bird species diversity” on ecological studies and typifies it as a classic in the ecological literature. However, the low citation frequency found in papers devoted to freshwater ecosystems indicates that limnologists in general neglect this original contribution in studies of habitat complexity.     

The influence of “Homage to Santa Rosalia” on aquatic ecology: a scientometric approach

In 1959, G.E. Hutchinson provided a general explanation for the diversity of species in his paper “Homage to Santa Rosalia or why are there so many kinds of animals?” To assess the contribution of the ideas Hutchinson introduced in “The Homage” to aquatic ecology research, we performed a bibliometric evaluation of all the articles that cited this paper between 1960 and 2009. The articles were retrieved using the database from Thomson Reuters (ISI Web of Knowledge) in March 2009. For each paper, we first identified the studied environment (terrestrial, marine or freshwater) and whether the study was theoretical or empirical. For marine and freshwater studies, we recorded the journal where the article was published, the year of publication, the number of citations, the taxonomic group (e.g. fish, phytoplankton, zooplankton, macroinvertebrates or macrophytes), the habitat (e.g. wetlands, lakes, rivers, streams or ocean) and the main ideas addressed. A total of 1345 articles cited “The Homage”, and the number of citations increased significantly with time. Most of the articles that cited “The Homage” described research carried out in a terrestrial environment or were theoretical, and a lesser number of citations came from freshwater and marine papers, which used mainly fish and invertebrates as model organisms. In the aquatic sciences, most of the papers discussed the influences of competition and energy (productivity) on diversity. Our results indicate that “The Homage” can still be considered a “citation classic” and a breakthrough contribution, and that it is still having a great impact on different fields of ecology, including limnology and marine ecology.     

论文引用率影响因素——中外生态学期刊比较

本文选择8种有代表性中外生态学期刊,对其一定发表周期内的论文引用率进行分析,探讨生态学论文引用率的影响因素及中外生态学期刊的差异.结果表明：4种英文期刊的年均被引次数均远大于4种中文期刊;英文期刊1位作者的论文数量百分比相对较高;所有期刊的合著论文比例均较高,体现了合作性在现代生态学研究中的重要性;论文作者数量与引用率之间有一定的正相关关系,但不显著;英文期刊论文的长度显著高于中文论文;随着论文长度的增加,年均被引次数增多.对中外期刊论文的引用率变化动态进行分析表明,英文期刊中总被引次数高的论文其增长速率也较快,表明其持续影响力强于中文生态学论文.我们希望这些结果会对生态学者以及相关期刊工作者有所裨益.     

The Effects of Aging on Researchers' Publication and Citation Patterns

The average age at which U.S. researchers receive their first grant from NIH has increased from 34.3 in 1970, to 41.7 in 2004. These data raise the crucial question of the effects of aging on the scientific productivity and impact of researchers. Drawing on a sizeable sample of 6,388 university professors in Quebec who have published at least one paper between 2000 and 2007, our results identify two turning points in the professors'' careers. A first turning point is visible at age 40 years, where researchers start to rely on older literature and where their productivity increases at a slower pace—after having increased sharply since the beginning of their career. A second turning point can be seen around age 50, when researchers are the most productive whereas their average scientific impact is at its lowest. Our results also show that older professors publish fewer first-authored papers and move closer to the end of the list of co-authors. Although average scientific impact per paper decreases linearly until about age 50, the average number of papers in highly cited journals and among highly cited papers rises continuously until retirement. Our results show clearly that productivity and impact are not a simple and declining function of age and that we must take into account the collaborative aspects of scientific research. Science is a collective endeavor and, as our data shows, researchers of all ages play a significant role in its dynamic.     

生物多样性数据论文发表趋势分析

近年来有关科学数据共享的呼声越来越高, 基于同行评审的生物多样性数据论文也受到越来越多的关注, 并出现了一些专门发表数据论文的数据期刊。本文总结了近年来生物多样性数据发表方面的进展, 选择两本代表性数据期刊(Biodiversity Data Journal和Scientific Data), 分析了它们自创刊以来的发文数量、涉及生物类群、文章浏览量和被引次数等指标。结果显示两本数据期刊的发文量都呈稳步增长趋势, 其生物多样性数据论文覆盖了包括动物界、植物界、真菌界在内的众多生物类群, 文章浏览量和被引次数方面也有可喜的表现, 说明数据论文正在被越来越多的研究者所接受。对文章作者国别的分析则显示了不同地区的研究者在发表生物多样性数据论文或数据共享方面的不均衡。建议相关领域的中国研究者和期刊关注生物多样性数据论文和数据共享政策, 更多地践行数据共享。     

Bioluminescence and Chemiluminescence Literature: The 1995 Literature: Part 2

The journal provides comprehensive literature searches which will be published in most issues. The literature appears under the following section: 1. BIOLUMINESCENCE 2. CHEMILUMINESCENCE 3. APPLICATIONS—BIOLUMINESCENCE 4. APPLICATIONS—CHEMILUMINESCENCE 5. CELLULAR LUMINESCENCE 6. INSTRUMENTATION AND LIGHT MEASUREMENT 7. PATIENTS INVOLVING BIOLUMINESCENCE AND CHEMILUMINESCENCE Databases searched include Chemical Abstracts, Biological Abstracts, Index Medicus, and World Patents Index. The lists of papers are divided by sub-sections and papers are given sequential unique numbers commencing at the beginning of the list and continuing at the top of the list in the next and subsequent issues of the Journal. Papers which fall into more than one sub-section are quoted in full in the first relevant sub-sections they are referred to by their unique numbers. These lists have been produced regularly since 1986 and in excess of 4500 references have been cited — some by year and some by specialized topic. The compilers would be pleased to receive any comments from the readership. Contact by email:     

Expanding the clinical relevance of the 5′-nucleotidase cN-II/NT5C2

Purine metabolism is depending on a large amount of enzymes to ensure cellular homeostasis. Among these enzymes, we have been interested in the 5′-nucleotidase cN-II and its role in cancer biology and in response of cancer cells to treatments. This protein has been cited and studied in a large number of papers published during the last decade for its involvement in non-cancerous pathologies such as hereditary spastic paraplegia, schizophrenia, and blood pressure regulation. Here, we review these articles in order to give an overview of the recently discovered clinical relevance of cN-II.     

Information literacy in biology education: an example from an advanced cell biology course

Information literacy skills are critically important for the undergraduate biology student. The ability to find, understand, evaluate, and use information, whether from the scientific literature or from Web resources, is essential for a good understanding of a topic and for the conduct of research. A project in which students receive information literacy instruction and then proceed to select, update, and write about a current research topic in an upper-level cell biology course is described. Students research the chosen topic using paper and electronic resources, generate a list of relevant articles, prepare abstracts based on papers read, and, finally, prepare a "state-of-the-art" paper on the topic. This approach, which extends over most of one semester, has resulted in a number of well-researched and well-written papers that incorporate some of the latest research in cell biology. The steps in this project have also led to students who are prepared to address future projects on new and complex topics. The project is part of an undergraduate course in cell biology, but parts of the assignments can be modified to fit a variety of subject areas and levels.     

Controversy of free radical hypothesis: reactive oxygen species--cause or consequence of tissue injury?

For a decade or two, the hypothesis of causality of various disorders by reactive oxygen species (ROS), due to their potentially harmful effect towards cellular constituents, is one of the most frequently cited in biomedical sciences. In fact, the ROS-mediated alterations of biomacromolecules are considered to be essential events in the etiopathogenesis of those diseases where involvement of ROS has been indicated. ROS easily react in vitro with most biological molecules, causing their degradation and destruction. This may implicitly suggest that, when excessively produced in vivo, ROS are deleterious to integral components of the cell and cause their dysfunctions. Some experimental data indicate that ROS-mediated lipid peroxidation, protein oxidation and oxidative alterations to nucleic acids are crucial events of unfavorable actions of ROS. Yet the most convincing evidence, i.e. unambiguous inhibition of tissue injury by pretreatment with antioxidants, has not been provided. On the contrary, there are quite a few papers reporting failure in applying antioxidants to heal those pathologies where the causal role of ROS was supposed. Other papers reported serious complications arising from antioxidant therapy, which is quite in contradiction to its expected effect. On the other hand, an increasing number of recent findings have provided evidence of a key role of ROS in both intracellular signaling and intercellular communication, processes involved in maintaining homeostasis. Hence, some investigators consider excessive production of ROS to be rather a "smoke after the fire" than "a deleterious fire" itself, suggesting the occurrence of overproduced ROS as being the consequence of some primary damage. The present paper aims at summarizing some pros and cons of various opinions with an attempt to help better understand the involvement of ROS in tissue injury.     

《环境昆虫学报》2001-2010年载文被引统计分析

利用"中国学术期刊文献评价统计分析系统",对《环境昆虫学报》载文在2001～2010年所刊载论文的被引用情况进行统计分析。结果表明,在2001～2010年间《环境昆虫学报》10年共载文504篇,有343篇论文,被引率为68.06%;被引用1904次,篇均被引次数为5.55,单篇被引最高次数为40次;被引用5次以下的论文占63.57%;引证期刊262种,引用3次以下的期刊占74.81%。同时,对被引论文作者进行了系统分析,特别阐述了高被引论文的详细信息,从而提出从统计得出的高被引频次论文作者及研究热点着手,加强组稿,突出栏目特色,提高刊物对高质量论文的吸纳能力。     

Impact analysis of a regional scientific journal (1980-2000): supporting promising local researchers pays the greatest dividends

During the past 28 years, the journal "Collegium Antropologicum" has continuously served as one of the main disseminators of anthropological scientific production in Central and Eastern Europe. The journal was committed to its role of a multidisciplinary platform for presenting wide range of research topics relevant to anthropology, from investigations within social and cultural anthropology and archaeology to those covering contemporary population genetics, human evolution and biomedical issues. Two key strategies aimed at sustaining and increasing the impact of this journal were oriented towards: (i) identification of promising local groups of researchers who were at disadvantage by many aspects (e.g. educational curricula, financial supports, language barriers etc.) when trying to publish their research internationally, and (ii) invitation and encouragement of already established international scientists to make contributions for "Collegium Antropologicum". From 1980-2000, 89 articles (or 6.3% of all published papers during that period) were cited 6 or more times, contributing disproportionately to journal's impact (nearly a third of all citations received). In an attempt to identify such papers more readily among the submissions to the journal in the future, we analyzed research topics and affiliations of the authors among the 89 papers receiving most citations in comparison to all papers published. Among the papers most frequently cited, we found greater-than-expected prevalence of Croatian researchers (especially when publishing in collaboration with international scientists) and studies of special populations. Several papers received more than 25 citations or had overall citation intensity greater than 2 per year. This implies that an interesting article from a local group of researchers can still resonate with international audience although published in a regional journal. Present analysis supports current editorial strategy that with a help of the international consulting editorial board continuously improves international recognition of this journal. The results imply that a balanced encouragement to promising local groups of researchers and to contributions of already established international scientists is a strategy superior to others in maintaining and increasing the impact of this regional journal.     

不同国家医患纠纷处理方式研究

现阶段我国的医患纠纷日益增多,医患矛盾尖锐。寻求合理的医患纠纷处理方式具有重要现实意义。对于医患纠纷的处理,世界各国均有较多尝试。美国、德国、日本、中国台湾地区等也出现了诸多处理方式。通过对这些处理方式的比较与分析,旨在吸取经验,为改善医患关系,提高医疗服务质量抛砖引玉。     

Citation decay in animal science

The half-life of literature in animal science is about 5–6 years, which is short in comparison to many other fields of scientific research. Only about 10% of the citations in animal-science articles refer to articles which were published more than 20 years before the appearance of the papers which cite them. Probably only a small proportion of the older works cited deserve to be called classics. Historical reviews of literature in scientific specialisations are likely to recover many still useful data and ideas.     

Examining the Impact of the National Institutes of Health Public Access Policy on the Citation Rates of Journal Articles

PurposeTo examine whether National Institutes of Health (NIH) funded articles that were archived in PubMed Central (PMC) after the release of the 2008 NIH Public Access Policy show greater scholarly impact than comparable articles not archived in PMC.MethodsA list of journals across several subject areas was developed from which to collect article citation data. Citation information and cited reference counts of the articles published in 2006 and 2009 from 122 journals were obtained from the Scopus database. The articles were separated into categories of NIH funded, non-NIH funded and whether they were deposited in PubMed Central. An analysis of citation data across a five-year timespan was performed on this set of articles.ResultsA total of 45,716 articles were examined, including 7,960 with NIH-funding. An analysis of the number of times these articles were cited found that NIH-funded 2006 articles in PMC were not cited significantly more than NIH-funded non-PMC articles. However, 2009 NIH funded articles in PMC were cited 26% more than 2009 NIH funded articles not in PMC, 5 years after publication. This result is highly significant even after controlling for journal (as a proxy of article quality and topic).ConclusionOur analysis suggests that factors occurring between 2006 and 2009 produced a subsequent boost in scholarly impact of PubMed Central. The 2008 Public Access Policy is likely to be one such factor, but others may have contributed as well (e.g., growing size and visibility of PMC, increasing availability of full-text linkouts from PubMed, and indexing of PMC articles by Google Scholar).     

Cryo-Electron Microscopy: The field of 1,000+ methods

Cryo-Electron Microscopy (CryoEM) is currently a well-established method to elucidate a biological macromolecule’s three-dimensional (3D) structure. Its success is due to technological and methodological advances in several fronts: sample preparation, electron optics and detection, image acquisition, image processing, and map interpretation. The first methods started in the late 1960s and, since then, new methods on all fronts have continuously been published, maturating the field as we know it now.In terms of publications, we can distinguish several periods, witnessing a substantial acceleration of methodological publications in recent years, pointing out to an increased interest in the domain. On the other hand, this accelerated increase of methods development may confuse practitioners about which method they should be using (and how) and highlight the importance of paying attention to establishing best practices for methods reporting and usage.In this paper, we analyze the trends identified in over 1,000 methodological papers. Our focus is primarily on computational image processing methods. However, our list also covers some aspects of sample preparation and image acquisition.Several interesting ideas stem out from this study: (1) Single Particle Analysis (SPA) has largely accelerated in the last decade and sample preparation methods in the last five years; (2) Electron Tomography is not yet in a rapidly growing phase, but it is foreseeable that it will soon be; (3) the work horses of SPA are 3D classification, 3D reconstruction, and 3D alignment, and there have been many papers on these topics, which are not considered to be solved yet, but ever improving; and (4) since the resolution revolution, atomic modelling has also caught on as a hot topic.     

Traditional Plants Used in Southern Brazil as a Source to Wound Healing Therapies

In southern Brazil, the biodiversity is great and the traditional use of medicinal plants for wound healing has been documented in ethnobotanical studies and pharmacological studies have assessed their wound properties and phytochemistry. Therefore, this study evaluated ethnobotanical surveys regarding medicinal plants used in southern Brazil for wound healing and studies about the healing properties of these plants published between 2000 and 2022. To retrieve articles related to the study, Web of Science, PubMed (NLM), Open Access Journals, Scielo, Lilacs, and Google Scholar, with keywords including medicinal plants, wound healing, and South of Brazil, have been used. As a result, 73 medicinal plants belonging to 39 families were found in ethnobotanical surveys as a traditional resource used for wound healing in southern Brazil, 15 of which were cited more than once. Besides, 14 of these 15 plants were also used as healing agents worldwide. The most cited plant with healing actions in southern Brazil was Symphytum officinale L. (comfrey). From 2000 to date, 44 articles scientifically demonstrated the wound-healing effects of the southern Brazilian plants found in ethnobotanical surveys reviewed. The folk medicine of southern Brazil presents a variety of medicinal plants for wound-healing purposes, and scientific data were found for some of those plants. However, the wound-healing properties of many plants have yet to be investigated, and the current literature still needs more phytochemical information about the plants studied. Aside from this, the future focus should be on the standardization of herbal extracts, and further research is required to investigate the pharmacological mechanisms. Clinical research in this area remains in its infancy and warrants more robust further clinical studies.     

Characterizing Social Media Metrics of Scholarly Papers: The Effect of Document Properties and Collaboration Patterns

A number of new metrics based on social media platforms—grouped under the term “altmetrics”—have recently been introduced as potential indicators of research impact. Despite their current popularity, there is a lack of information regarding the determinants of these metrics. Using publication and citation data from 1.3 million papers published in 2012 and covered in Thomson Reuters’ Web of Science as well as social media counts from Altmetric.com, this paper analyses the main patterns of five social media metrics as a function of document characteristics (i.e., discipline, document type, title length, number of pages and references) and collaborative practices and compares them to patterns known for citations. Results show that the presence of papers on social media is low, with 21.5% of papers receiving at least one tweet, 4.7% being shared on Facebook, 1.9% mentioned on blogs, 0.8% found on Google+ and 0.7% discussed in mainstream media. By contrast, 66.8% of papers have received at least one citation. Our findings show that both citations and social media metrics increase with the extent of collaboration and the length of the references list. On the other hand, while editorials and news items are seldom cited, it is these types of document that are the most popular on Twitter. Similarly, while longer papers typically attract more citations, an opposite trend is seen on social media platforms. Finally, contrary to what is observed for citations, it is papers in the Social Sciences and humanities that are the most often found on social media platforms. On the whole, these findings suggest that factors driving social media and citations are different. Therefore, social media metrics cannot actually be seen as alternatives to citations; at most, they may function as complements to other type of indicators.