应用CiteSpace对生态学科meta分析的文献计量学和可视化分析

Meta分析是针对一系列独立研究结果进行定量综合分析的方法。从20世纪90年代初开始被应用于生态学的研究中,已经对这一学科的数据汇总方式产生重大影响。为了探究meta分析方法在生态学领域的研究现状及热点,以Web of Science论文核心合集为检索数据库,通过输入关键词检索了1992至2018年之间的论文,并利用Web of Science自带的文献分析工具和Histcite对检索的文献信息进行统计分析,分析了不同年份、国家、期刊、学科基础知识论文的发表和被引情况,用CiteSpace软件对其进行热点分析并绘制了知识图谱。研究发现,我国生态学研究在meta分析方法的改进和利用方面与美国、英国等国家相比尚有差距;使用meta分析方法开展研究越来越多,但研究方向上出现了一些转变,越来越多的研究关注全球变化背景下植物光合作用、物种入侵的机理以及模拟氮循环过程对物候和植被生产力的影响及价值评估的研究,并成为本领域的研究前沿。     

Citation Analysis May Severely Underestimate the Impact of Clinical Research as Compared to Basic Research

Background

Citation analysis has become an important tool for research performance assessment in the medical sciences. However, different areas of medical research may have considerably different citation practices, even within the same medical field. Because of this, it is unclear to what extent citation-based bibliometric indicators allow for valid comparisons between research units active in different areas of medical research.

Methodology

A visualization methodology is introduced that reveals differences in citation practices between medical research areas. The methodology extracts terms from the titles and abstracts of a large collection of publications and uses these terms to visualize the structure of a medical field and to indicate how research areas within this field differ from each other in their average citation impact.

Results

Visualizations are provided for 32 medical fields, defined based on journal subject categories in the Web of Science database. The analysis focuses on three fields: Cardiac & cardiovascular systems, Clinical neurology, and Surgery. In each of these fields, there turn out to be large differences in citation practices between research areas. Low-impact research areas tend to focus on clinical intervention research, while high-impact research areas are often more oriented on basic and diagnostic research.

Conclusions

Popular bibliometric indicators, such as the h-index and the impact factor, do not correct for differences in citation practices between medical fields. These indicators therefore cannot be used to make accurate between-field comparisons. More sophisticated bibliometric indicators do correct for field differences but still fail to take into account within-field heterogeneity in citation practices. As a consequence, the citation impact of clinical intervention research may be substantially underestimated in comparison with basic and diagnostic research.     

Identification and characterization of three members of the human metallocarboxypeptidase gene family

Amino acid homology searches of the human genome revealed three members of the metallocarboxypeptidase (metallo-CP) family that had not been described in the literature in addition to the 14 known genes. One of these three, named CPA5, is present in a gene cluster with CPA1, CPA2, and CPA4 on chromosome 7. The cDNA encoding a mouse homolog of human CPA5 was isolated from a testis library and sequenced. The deduced amino acid sequence of human CPA5 has highest amino acid sequence identity (60%) to CPA1. Modeling analysis shows the overall structure to be very similar to that of other members of the A/B subfamily of metallocarboxypeptidases. The active site of CPA5 is predicted to cleave substrates with C-terminal hydrophobic residues, as do CPA1, -2, and -3. Using Northern blot analysis, CPA5 mRNA is detected in testis but not in kidney, liver, brain, or lung. In situ hybridization analysis shows that CPA5 is localized to testis germ cells. Mouse pro-CPA5 protein expressed in Sf9 cells using the baculovirus system was retained in the particulate fraction of the cells and was not secreted into the media. Pro-CPA5 was not enzymatically active toward standard CPA substrates, but after incubation with prohormone convertase 4 the resulting protein was able to cleave furylacryloyl-Gly-Leu, with 3-4-fold greater activity at pH 7.4 than at 5.6. Two additional members of the human CP gene family were also studied. Modeling analysis indicates that both contain the necessary amino acids required for enzymatic activity. The CP on chromosome 8 is predicted to have a CPA-like specificity for C-terminal hydrophobic residues and was named CPA6. The CP on chromosome 2 is predicted to cleave substrates with C-terminal acidic residues and was named CPO.     

Assessing metacommunity processes through signatures in spatiotemporal turnover of community composition

Although metacommunity ecology has been a major field of research in the last decades, with both conceptual and empirical outputs, the analysis of the temporal dynamics of metacommunities has only emerged recently and consists mostly of repeated static analyses. Here we propose a novel analytical framework to assess metacommunity processes using path analyses of spatial and temporal diversity turnovers. We detail the principles and practical aspects of this framework and apply it to simulated datasets to illustrate its ability to decipher the respective contributions of entangled drivers of metacommunity dynamics. We then apply it to four empirical datasets. Empirical results support the view that metacommunity dynamics may be generally shaped by multiple ecological processes acting in concert, with environmental filtering being variable across both space and time. These results reinforce our call to go beyond static analyses of metacommunities that are blind to the temporal part of environmental variability.     

生物多样性相关传统知识研究热点与前沿的可视化分析

传统知识研究目前已经成为生物多样性保护研究的热点领域, 并对生态系统服务管理、社区可持续发展等领域产生了重要影响。本文以Web of Science (WoS)数据库为数据源, 应用WoS自带的统计分析功能和可视化分析软件CiteSpace III, 采用关键词共现分析、突现词分析、文献共被引分析等方法对传统知识的研究态势、研究热点以及知识演进进行系统分析。研究发现, 传统知识研究的文献数量呈逐年上升趋势; 中国科学院、墨西哥国立自治大学、印度农业研究理事会、加州大学系统等研究机构在该领域表现出较强的科研实力; 非洲、南美洲的巴西、玻利维亚以及亚洲的印度等地区为传统知识研究的热点区域; Albuquerque UP、Singh R、薛达元在该领域发表的学术论文最多; Berkes F、Drew JA、Gómez-Baggethun E等学者发表的论文为该领域知识基础的构建及相关研究的推进奠定了坚实的基础。与生物资源管理、生物多样性保护、生态系统服务和人类福祉、政策管理等相关的传统知识研究是未来该领域的重要方向。     

The Citation Merit of Scientific Publications

We propose a new method to assess the merit of any set of scientific papers in a given field based on the citations they receive. Given a field and a citation impact indicator, such as the mean citation or the -index, the merit of a given set of articles is identified with the probability that a randomly drawn set of articles from a given pool of articles in that field has a lower citation impact according to the indicator in question. The method allows for comparisons between sets of articles of different sizes and fields. Using a dataset acquired from Thomson Scientific that contains the articles published in the periodical literature in the period 1998–2007, we show that the novel approach yields rankings of research units different from those obtained by a direct application of the mean citation or the -index.     

Inheritance of cleft palate in Italy. Evidence for a major autosomal recessive locus

Although several studies have demonstrated familial aggregation of nonsyndromic cleft palate (CP), the mode of inheritance still remains uncertain. We report the results of complex segregation analysis performed in families of 357 consecutive newborns affected with nonsyndromic CP (i.e., CP not a component feature of malformation syndrome, sequence or association), and registered in the North East Italy and Emilia Romagna congenital malformation registries in the period 1981–1993. This sample, based on a large number of consecutive births, in a well-defined geographical area, with quality control to detect associated anomalies and malformation syndromes, is independent of the number of affected subjects in the family and of CP severity, fitness, and survival. We have analyzed, using the mixed model, the whole sample of nonsyndromic CP, including isolated (i.e., without other anomalies) CP (CPI) and CP associated with at least one other anomaly (CPA), for which a diagnosis of malformation syndrome was not possible. When nonsyndromic CP (including CPA) are considered in the analysis, there is no heterogeneity between CPA and CPI nor between CP including hard palate (CPH) and CP of the soft palate only (CPS). POINTER and COMDS programs cannot discriminate between alternative genetic models; only the hypothesis of non-genetic transmission is rejected. The COMDS analysis two-locus model, which indicates that a modifier locus (or loci) operates in addition to a single major locus (SML), does not show evidence of better fit than SML, polygenic, and multifactorial models. When the severity parameter (defined as CPH and CPS) is added, CPI and CPA show heterogeneity. Eventually, when the analysis is limited to CPI and includes information on severity, a recessive SML, with low penetrance and determining CPH, provides a significant best fit. To have defined a genetic model for CPI and provided evidence for SML inheritance suggests that genetic linkage studies could be implemented. This conclusion is in agreement with previous studies which showed a significant association between alleles of transforming growth factor alpha and CP only in humans, and that single recessive genes may play a crucial role during palatogenesis in mice as well as in Brittany spaniels. Application of the candidate genes to human CPH families could reveal whether these genes are involved. Received: 16 December 1996 / Accepted: 16 March 1997     

The Measurement of the Effect on Citation Inequality of Differences in Citation Practices across Scientific Fields

This paper has two aims: (i) to introduce a novel method for measuring which part of overall citation inequality can be attributed to differences in citation practices across scientific fields, and (ii) to implement an empirical strategy for making meaningful comparisons between the number of citations received by articles in 22 broad fields. The number of citations received by any article is seen as a function of the article’s scientific influence, and the field to which it belongs. A key assumption is that articles in the same quantile of any field citation distribution have the same degree of citation impact in their respective field. Using a dataset of 4.4 million articles published in 1998–2003 with a five-year citation window, we estimate that differences in citation practices between the 22 fields account for 14% of overall citation inequality. Our empirical strategy is based on the strong similarities found in the behavior of citation distributions. We obtain three main results. Firstly, we estimate a set of average-based indicators, called exchange rates, to express the citations received by any article in a large interval in terms of the citations received in a reference situation. Secondly, using our exchange rates as normalization factors of the raw citation data reduces the effect of differences in citation practices to, approximately, 2% of overall citation inequality in the normalized citation distributions. Thirdly, we provide an empirical explanation of why the usual normalization procedure based on the fields’ mean citation rates is found to be equally successful.     

An Analysis of Peer-Reviewed Scores and Impact Factors with Different Citation Time Windows: A Case Study of 28 Ophthalmologic Journals

Background

An important attribute of the traditional impact factor was the controversial 2-year citation window. So far, several scholars have proposed using different citation time windows for evaluating journals. However, there is no confirmation whether a longer citation time window would be better. How did the journal evaluation effects of 3IF, 4IF, and 6IF comparing with 2IF and 5IF? In order to understand these questions, we made a comparative study of impact factors with different citation time windows with the peer-reviewed scores of ophthalmologic journals indexed by Science Citation Index Expanded (SCIE) database.

Methods

The peer-reviewed scores of 28 ophthalmologic journals were obtained through a self-designed survey questionnaire. Impact factors with different citation time windows (including 2IF, 3IF, 4IF, 5IF, and 6IF) of 28 ophthalmologic journals were computed and compared in accordance with each impact factor’s definition and formula, using the citation analysis function of the Web of Science (WoS) database. An analysis of the correlation between impact factors with different citation time windows and peer-reviewed scores was carried out.

Results

Although impact factor values with different citation time windows were different, there was a high level of correlation between them when it came to evaluating journals. In the current study, for ophthalmologic journals’ impact factors with different time windows in 2013, 3IF and 4IF seemed the ideal ranges for comparison, when assessed in relation to peer-reviewed scores. In addition, the 3-year and 4-year windows were quite consistent with the cited peak age of documents published by ophthalmologic journals.

Research Limitations

Our study is based on ophthalmology journals and we only analyze the impact factors with different citation time window in 2013, so it has yet to be ascertained whether other disciplines (especially those with a later cited peak) or other years would follow the same or similar patterns.

Originality/ Value

We designed the survey questionnaire ourselves, specifically to assess the real influence of journals. We used peer-reviewed scores to judge the journal evaluation effect of impact factors with different citation time windows. The main purpose of this study was to help researchers better understand the role of impact factors with different citation time windows in journal evaluation.     

Knowledge graphs of ethical concerns of cerebral organoids

ObjectivesThe rapid development of cerebral organoid technology and the gradual maturity of cerebral organoids highlight the necessity of foresighted research on relevant ethical concerns. We employed knowledge graphs and conducted statistical analysis with CiteSpace for a comprehensive analysis of the status quo of the research on the ethical concerns of cerebral organoids from a bibliometric perspective.Materials and MethodsWe performed a statistical analysis of published papers on cerebral organoid ethics, keyword co‐occurrence graph, literature co‐citation and knowledge clustering graph to examine the status of the ethics research, internal relationship between technological development and ethical research, and ethical concerns of the academia. Finally, we used a keyword time zone graph and related statistics to analyze and predict the trends and popular topics of future cerebral organoids ethics research.ResultsWe demonstrated that although the ethical concerns of cerebral organoids have long been discussed, it was not until 2017 that the ethical issues began to receive more attention, when cerebral organoids were gradually mimicking the human brain more closely and increasingly being combined with chimera research. The recent key ethical concerns are primarily divided into three categories: concerns that are common in life sciences, specific to cerebral organoids, and present in cross‐fields. These increasing ethical concerns are inherently related to the continual development of technology. The analysis pointed out that future research should focus on the ethical concerns of consciousness that are unique to cerebral organoids, ethical concerns of cross‐fields, and construction and improvement of legislative and regulatory systems.ConclusionsAlthough research on cerebral organoids can benefit the biomedicine field, the relevant ethical concerns are significant and have received increasing attention, which are inherently related to the continual development of technology. Future studies in ethics regarding cerebral organoid research should focus on the ethical concerns of consciousness, and cross‐fields, as well as the improvement of regulatory systems.

We performed a statistical analysis of published papers on cerebral organoid ethics, keyword co‐occurrence graph, literature co‐citation and knowledge clustering graph to examine the status of the ethics research. We also used a keyword time zone graph and related statistics to analyse and predict the trends and popular topics of future cerebral organoids ethics research.     

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.     

Computational Approaches for Predicting Biomedical Research Collaborations

Biomedical research is increasingly collaborative, and successful collaborations often produce high impact work. Computational approaches can be developed for automatically predicting biomedical research collaborations. Previous works of collaboration prediction mainly explored the topological structures of research collaboration networks, leaving out rich semantic information from the publications themselves. In this paper, we propose supervised machine learning approaches to predict research collaborations in the biomedical field. We explored both the semantic features extracted from author research interest profile and the author network topological features. We found that the most informative semantic features for author collaborations are related to research interest, including similarity of out-citing citations, similarity of abstracts. Of the four supervised machine learning models (naïve Bayes, naïve Bayes multinomial, SVMs, and logistic regression), the best performing model is logistic regression with an ROC ranging from 0.766 to 0.980 on different datasets. To our knowledge we are the first to study in depth how research interest and productivities can be used for collaboration prediction. Our approach is computationally efficient, scalable and yet simple to implement. The datasets of this study are available at https://github.com/qingzhanggithub/medline-collaboration-datasets.     

Identification of Bicluster Regions in a Binary Matrix and Its Applications

Biclustering has emerged as an important approach to the analysis of large-scale datasets. A biclustering technique identifies a subset of rows that exhibit similar patterns on a subset of columns in a data matrix. Many biclustering methods have been proposed, and most, if not all, algorithms are developed to detect regions of “coherence” patterns. These methods perform unsatisfactorily if the purpose is to identify biclusters of a constant level. This paper presents a two-step biclustering method to identify constant level biclusters for binary or quantitative data. This algorithm identifies the maximal dimensional submatrix such that the proportion of non-signals is less than a pre-specified tolerance δ. The proposed method has much higher sensitivity and slightly lower specificity than several prominent biclustering methods from the analysis of two synthetic datasets. It was further compared with the Bimax method for two real datasets. The proposed method was shown to perform the most robust in terms of sensitivity, number of biclusters and number of serotype-specific biclusters identified. However, dichotomization using different signal level thresholds usually leads to different sets of biclusters; this also occurs in the present analysis.     

Relative contributions of crown and phenological traits to growth of a pseudo-backcross pine family ((slash?×?loblolly)?×?slash) and its pure species progenitors

One pseudo-backcross [(slash?×?loblolly)?×?slash] (BC1) and open-pollinated families of the pure species progenitors were established in a single test in North Central Florida. Multivariate analysis was used to estimate the intra-trait correlation among the taxa, and path analyses were used to determine the relative contributions of crown architectural and phenological traits to first-year height growth. The multivariate analysis indicated that BC1, slash, and loblolly pine have different relationships among the traits studied, suggesting that a separate path analysis was required for each taxon. Path analysis coefficients of determination of the final models were 0.69, 0.73, and 0.65 for the pseudo-backcross, loblolly, and slash pine families, respectively. The ranking of traits by relative magnitude of effect on total growth was, for the pseudo-backcross crown projected area (CPA), fascicle length (FL), number of nodes (NN), number of branches (NB), number of needles per fascicle (NF), and fascicle diameter. For loblolly, this was CPA, NB, FL, NN, NF, initiation, and specific leaf area. For slash, this was CPA, NN, FL, NF, and NB. The study indicated that all crown traits considered in the path analysis had moderate effects on first-year height growth, with the exceptions of the consistently large effect of CPA and the minimal effect of the phenological traits.     

A reversed-phase high-performance liquid chromatographic method for the simultaneous determination of serum concentrations of cyproterone acetate and 15 beta-hydroxycyproterone acetate

A reversed-phase high-performance liquid chromatographic method for the simultaneous determination of cyproterone acetate (CPA), 15 beta-hydroxycyproterone acetate (15 beta-OH-CPA) and cyproterone (CP) was reported. This method was specific, sensitive, precise, easy and rapid for determination of the serum concentrations of these steroids in patients receiving CPA. Although no peak corresponding to CP was observed for serum, peaks corresponding to CPA and 15 beta-OH-CPA were detected and well separated in all subjects undergoing long-term CPA therapy. In these patients, there seemed to be a dose-dependent relationship between the amount of CPA administered and the serum concentrations of these steroids, and the serum concentrations of CPA were either similar or low compared with those of 15 beta-OH-CPA. In conclusion, this simplified method is thought to be very valuable for studies on the pharmacokinetics of CPA and 15 beta-OH-CPA, and on the relationship between the CPA dosage and the therapeutic or side effects on adrenal and gonadal steroid production.     

Electrophysiological Explorations of the Bilingual Advantage: Evidence from a Stroop Task

Bilinguals have been shown to exhibit a performance advantage on executive control tasks, outperforming their monolingual counterparts. Although a wealth of research has investigated this ‘bilingual advantage’ behaviourally, electrophysiological correlates are lacking. Using EEG with a Stroop task that manipulated the stimulus onset asynchrony (SOA) of word and colour presentation, the current study addressed two facets of the bilingual advantage. The possibility that bilinguals experience superior conflict processing relative to monolinguals (a ‘conflict-specific advantage’) was investigated by comparing behavioural interference effects as well as the amplitude of the N_inc, a conflict-related ERP component occurring from approximately 300–500 ms after the onset of conflict. In contrast, the hypothesis that bilinguals experience domain-general, conflict-independent enhancements in executive processing (a ‘non-conflict-specific advantage’) was evaluated by comparing the control condition (symbol strings) between groups. There was some significant, but inconsistent, evidence for a conflict-specific bilingual advantage. In contrast, strong evidence emerged for a non-conflict-specific advantage, with bilinguals demonstrating faster RTs and reduced ERP amplitudes on control trials compared to monolinguals. Importantly, when the control stimulus was presented before the colour, ERPs to control trials revealed group differences before the onset of conflict, suggesting differences in the ability to ignore or suppress distracting irrelevant information. This indicates that bilinguals experience superior executive processing even in the absence of conflict and semantic salience, and suggests that the advantage extends to more efficient proactive management of the environment.     

Scientometric sorting by importance for literatures on life cycle assessments and some related methodological discussions

Purpose

This paper aims to sort the literatures on life cycle assessments (LCA) by their respective importance through citation and co-citation analysis and to further discuss the strengths and weaknesses of these kinds of scientometric methods in the case of LCA research.

Methods

CiteSpace II was used to generate document co-citation networks based on 3,824 articles retrieved from the ISI Web of Science database on this topic.

Results

Table 1 provides the top 50 highest cited documents in the LCA field. Here, we use two indicators, i.e., citation frequency in citation analysis and betweenness centrality metric in co-citation analysis, to measure the importance of these LCA literatures.

Conclusions

Citation and co-citation analysis are useful for environmental scientists and engineers to get a better understanding of the inner structure of LCA research. However, like all other research methods, this kind of analysis has some limitations. On the one hand, Scientometric studies and related software are very dependent on ISI Web of Science database, but considering the ISI Web of Science only began to track the LCA field fairly recently, the Scopus database would probably give a fuller picture. On the other hand, since the essence of scientometrics analysis is outsiders commenting insiders, so with only citation and co-citation analysis, to our understanding of the past, present, and future of LCA field, is insufficient.