A text mining analysis of the climate change literature in industrial ecology

The literature on climate change research has evolved tremendously since the 1990s. The goal of this study is to use text mining to review the climate change literature and study the evolution of the main trends over time. Specific keywords from articles published in the special issue “ Industrial Ecology for Climate Change Adaptation and Resilience” in the Journal of Industrial Ecology are first selected. Details of over 35,000 publications containing these keywords are downloaded from the Web of Science from 1990 to 2018. The number of publications and co‐occurrence of keywords are analyzed. Moreover, latent Dirichlet allocation (LDA)—a probabilistic approach that can retrieve topics from large and unstructured text documents—is applied on the abstracts to uncover the main topics (consisting of new terms) that naturally emerge from them. The evolution in time of the importance of some emerging topics is then analyzed on the basis of their relative frequency. Overall, a rapid growth in climate change publications is observed. Terms such as “climate change adaptation” appear on the rise, whereas other terms are declining such as “pollution.” Moreover, several terms tend to co‐occur frequently, such as “climate change adaptation” and “resilience.” The database collected and the LiTCoF (Literature Topic Co‐occurrence and Frequency) Python‐based tool developed for this study are also made openly accessible. This article met the requirements for a gold – gold JIE data openness badge described http://jie.click/badges .     

Trends in HSPB5 research: a 36-year bibliometric analysis

HSPB5 (heat shock protein B5), also known as αB-crystallin, is one of the most widespread and populous of the ten human small heat shock proteins (sHsps). Over the past decades, extensive research has been conducted on HSPB5. However, few studies have statistically analyzed these publications. Herein, we conducted a bibliometric analysis to track the global research trend and current development status of HSPB5 research from the Web of Science Core Collection (WoSCC) database between 1985 and 2020. Our results demonstrate that 1220 original articles cited 54,778 times in 391 scholarly journals were published. Visualization analyses reveal that the Journal of Biological Chemistry was the most influential journal with 85 articles. The USA dominated this field with 520 publications (42.62%), followed by Japan with 149 publications (12.21%), and Kato contributed the largest number of publications. Most related publications were published in journals focusing on biochemistry molecular biology, cell biology, neurosciences neurology, and ophthalmology. In addition, keyword co-occurrence analyses identify three predominant research topics: expression of HSPB5, chaperone studies for HSPB5, and pathological studies of HSPB5. This study provides valuable guidance for researchers and leads to collaborative opportunities between diverse research interests to be integrated for HSPB5 research.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12192-021-01220-6.     

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...     

Female Mate Choice Can Drive the Evolution of High Frequency Echolocation in Bats: A Case Study with Rhinolophus mehelyi

Animals employ an array of signals (i.e. visual, acoustic, olfactory) for communication. Natural selection favours signals, receptors, and signalling behaviour that optimise the received signal relative to background noise. When the signal is used for more than one function, antagonisms amongst the different signalling functions may constrain the optimisation of the signal for any one function. Sexual selection through mate choice can strongly modify the effects of natural selection on signalling systems ultimately causing maladaptive signals to evolve. Echolocating bats represent a fascinating group in which to study the evolution of signalling systems as unlike bird songs or frog calls, echolocation has a dual role in foraging and communication. The function of bat echolocation is to generate echoes that the calling bat uses for orientation and food detection with call characteristics being directly related to the exploitation of particular ecological niches. Therefore, it is commonly assumed that echolocation has been shaped by ecology via natural selection. Here we demonstrate for the first time using a novel combined behavioural, ecological and genetic approach that in a bat species, Rhinolophus mehelyi: (1) echolocation peak frequency is an honest signal of body size; (2) females preferentially select males with high frequency calls during the mating season; (3) high frequency males sire more off-spring, providing evidence that echolocation calls may play a role in female mate choice. Our data refute the sole role of ecology in the evolution of echolocation and highlight the antagonistic interplay between natural and sexual selection in shaping acoustic signals.     

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.     

DNA Repair: A changing geography? (1964–2008)

This article aims to explain the current state of DNA Repair studies’ global geography by focusing on the genesis of the community. Bibliometric data is used to localize scientific activities related to DNA Repair at the city level. The keyword “DNA Repair” was introduced first by American scientists. It started to spread after 1964 that is to say, after P. Howard-Flanders (Yale University), P. Hanawalt (Stanford University) and R. Setlow (Oak Ridge Laboratories) found evidence for Excision Repair mechanisms. It was the first stage in the emergence of an autonomous scientific community. In this article, we will try to assess to what extent the geo-history of this scientific field is determinant in understanding its current geography. In order to do so, we will localize the places where the first “DNA Repair” publications were signed fifty years ago and the following spatial diffusion process, which led to the current geography of the field. Then, we will focus on the evolution of the research activity of “early entrants” in relation to the activity of “latecomers”. This article is an opportunity to share with DNA Repair scientists some research results of a dynamic field in Science studies: spatial scientometrics.     

A review of published wetland research, 1991–2008: Ecological engineering and ecosystem restoration

An effective bibliometric analysis based on the Science Citation Index (SCI) published by the Institute of Scientific Information (ISI) was carried out to identify wetland research between 1991 and 2008. The objective was to conduct a quantitative and qualitative analysis for global trends of wetland-related research. The characteristics related to publications were analyzed. The results showed the significant wetland research issues in the SCI database. From 1991 to 2008, the annual number of journal articles published and the number of articles cited to wetland research increased more than sixfold and ninefold respectively. The USA produced the most single-country articles and international collaborative articles, followed by Canada and UK. The results also showed the significant wetland research issues in SCI database. The most frequently used words were: “water” (or “water quality”), which ranked 3rd, 7th, and 3rd according to the word in article title, author keyword, and keyword plus analysis, respectively. Constructed wetland biodiversity became more active in wetland research. The keywords “constructed wetland” and “constructed wetlands” ranked 58th and 12th in 1991–1996, while they ranked 5th and 4th in 2003–2008; the author keyword “biodiversity” ranked 45th in 1991–1996, while it ranked 23rd in 1997–2002, and 14th in 2003–2008; and keyword plus “diversity” ranked 93rd in 1991–1996, while it ranked 20th in 1997–2002, and 17th in 2003–2008. Moreover, it was proved that article title, author keyword, and keyword plus analysis methods were effective approaches for mapping wetland research. Popular wetland research issues and wetland research changes were also identified by statistical analysis.     

氮肥农学效应与环境效应国际研究发展态势

分析国内外农田氮素农学效应和环境效应研究的发展动态、研究热点,为以后研究农田氮素效应提供参考。基于ISI Web of Science数据库,检索出以"农田氮肥施用"为主题的所有SCI论文(1957—2014年8月),并分别提取出与"农学效应"、"环境效应"、"适宜施氮量"相关的文献,采用计量学方法,分析各研究方向的主要热点、研究机构、发文期刊和高被引论文等。共检索出关于农田施氮研究的SCI文献7460篇,其中与"农学效应"研究相关的文献2773篇,主要涉及到施氮肥对小麦、玉米、水稻、大豆等作物产量、氮素利用率和土壤有机碳的影响;与"环境效应"研究相关的文献1609篇,主要涉及到氮肥施用对氨挥发、硝化反硝化、温室气体排放、硝酸盐淋失、地下水水质等环境因素的影响;与"适宜施氮量"研究相关的文献408篇,主要涉及氮肥施用量、氮肥管理等。刊发各类研究成果最多的机构主要来自欧美发达国家,影响力大的期刊与高被引论文也主要来自欧美国家,中国在该领域的研究发展迅速,以中国科学院、中国农业大学、南京农业大学和中国农业科学院等为代表的中国研究机构的研究水平逐渐进入世界前列。文献计量学可用于分析农田氮素效应主题的研究热点和发展态势,目前氮素农学效应仍是研究的重点,随着当前环境污染问题日益突出,农田氮素环境效应研究越来越多,特别是氮流失对水体水质的影响备受关注,而基于氮素综合效应确定农田适宜施氮量是同时保障粮食安全和环境安全的有效措施。中国在相关研究领域的研究起步较晚,高影响力论文偏少,优秀国际期刊不足,但研究实力不断增加,研究成果也逐渐被国际社会所认可。     

蝙蝠回声定位声波的可塑性及其生态适应

蝙蝠通过调节回声定位声波特征来满足自身的感官需求,表现出回声定位声波的可塑性及其对生态环境与需求的适应。声波频率、强度、脉冲持续时间和间隔时间等特征与蝙蝠所处的生态位密切相关,声波可塑性在蝙蝠进化过程中起着至关重要的作用。本文结合马铁菊头蝠(Rhinolophus ferrumequinum)和大趾鼠耳蝠(Myotis macrodactylus)回声定位声波可塑性的研究,从回声定位声波的方向性、目标距离、环境复杂度和应对干扰4个方面总结了蝙蝠如何通过改变回声定位声波特征来满足自身在导航和捕捉猎物过程中的感官需求与生态适应,并阐述了回声定位声波可塑性的研究现状,为开展蝙蝠声学和行为学研究提供参考。     

Bibliometric analysis of Helicobacter pylori resistance—from 2002 to 2022

Background

Drug resistance in Helicobacter pylori severely affects the efficacy of eradication therapy, and a number of studies have been conducted on this issue. The aim of this study was to assess the progress in this field using a bibliometric approach.

Materials and Methods

Publications related to H. pylori resistance from 2002 to 2022 were retrieved from the Web of Science database. Relevant information including titles, authors, countries, and keywords was extracted, and the data were processed using Excel, VOSviewer, and CiteSpace software for co-authorship, co-citation, and co-occurrence analysis.

Results

From 2002 to 2022 (as of 09/24/2022), the field of H. pylori–resistance research produced a total of 2677 publications with a total of 75217 citations, with an overall upward trend in the annual number of articles published, reaching a peak of 204 in 2019. Articles were mainly published in Q1 or Q2 journals, with Helicobacter (TP = 261) publishing the most literature, Baylor College of Medicine (TP = 68) and Deng-chyang wu (TP = 38) being the most prolific institutions and authors, respectively. China and the United States were the locations of most of the articles, accounting for 35.08% of the global publication volume. Keyword co-occurrence analysis divided H. pylori-resistance research into four clusters: “Therapeutic Strategies,” “Diseases,” “Mechanism Research and Epidemiology,” and “Drug Research.” “Drug research” and burst detection indicate that the current research hotspot involves the selection and analysis of treatment strategies.

Conclusions

H. pylori–resistance research has become a popular research field, and although there are significant contributions from Europe, the United States, and East Asia, there are significant imbalances between regions that cannot be ignored. In addition, the exploration of treatment strategies remains a key issue for research at the current stage.     

Trend words in ecological core journals over the last 25 years (1978–2002)

Ecological research has been repeatedly criticized for its general lack of progress. While it has proved difficult to reveal scientific progress, from a subjective view trends in ecology seems evident. In order to objectively detect principal trends in this broad discipline during the past 25 years (1978–2002), we performed several word and co-word analyses on titles and abstracts of articles that appeared in five core journals of ecology: «Ecology>>, «Oecologia>>, «Oikos>>, «Journal of Animal Ecology>> and «Journal of Ecology>>. A general time gradient in the use of words was evident and words with a positive trend dominated. Trend words derived from article titles were used to perform co-word analyses on abstracts available since 1991. Besides a trend towards the study of processes most important ecological fields found are landscape ecology, biodiversity, ecosystem research, modelling, and food-web/predator–prey interactions. A semantic map of trend words was built by ordination. In the map, words formed a continuous space with the three thematic directions «biotic>>, «abiotic>> and «temporal & spatial>> representing the classic aspects of ecological research. With respect to the obvious trends and features derived from our analyses, we suggest that the results represent real scientific progress in ecology as a pluralistic, multi-aspect and multiple-causation discipline. Such a progress could hardly be observed from details in sub-disciplines.     

Extremely high frequency sensitivity in a ‘simple’ ear

An evolutionary war is being played out between the bat, which uses ultrasonic calls to locate insect prey, and the moth, which uses microscale ears to listen for the approaching bat. While the highest known frequency of bat echolocation calls is 212 kHz, the upper limit of moth hearing is considered much lower. Here, we show that the greater wax moth, Galleria mellonella, is capable of hearing ultrasonic frequencies approaching 300 kHz; the highest frequency sensitivity of any animal. With auditory frequency sensitivity that is unprecedented in the animal kingdom, the greater wax moth is ready and armed for any echolocation call adaptations made by the bat in the on-going bat–moth evolutionary war.     

Adaptive Evolution of the Myo6 Gene in Old World Fruit Bats (Family: Pteropodidae)

Myosin VI (encoded by the Myo6 gene) is highly expressed in the inner and outer hair cells of the ear, retina, and polarized epithelial cells such as kidney proximal tubule cells and intestinal enterocytes. The Myo6 gene is thought to be involved in a wide range of physiological functions such as hearing, vision, and clathrin-mediated endocytosis. Bats (Chiroptera) represent one of the most fascinating mammal groups for molecular evolutionary studies of the Myo6 gene. A diversity of specialized adaptations occur among different bat lineages, such as echolocation and associated high-frequency hearing in laryngeal echolocating bats, large eyes and a strong dependence on vision in Old World fruit bats (Pteropodidae), and specialized high-carbohydrate but low-nitrogen diets in both Old World and New World fruit bats (Phyllostomidae). To investigate what role(s) the Myo6 gene might fulfill in bats, we sequenced the coding region of the Myo6 gene in 15 bat species and used molecular evolutionary analyses to detect evidence of positive selection in different bat lineages. We also conducted real-time PCR assays to explore the expression levels of Myo6 in a range of tissues from three representative bat species. Molecular evolutionary analyses revealed that the Myo6 gene, which was widely considered as a hearing gene, has undergone adaptive evolution in the Old World fruit bats which lack laryngeal echolocation and associated high-frequency hearing. Real-time PCR showed the highest expression level of the Myo6 gene in the kidney among ten tissues examined in three bat species, indicating an important role for this gene in kidney function. We suggest that Myo6 has undergone adaptive evolution in Old World fruit bats in relation to receptor-mediated endocytosis for the preservation of protein and essential nutrients.     

Are research efforts on Animalia in the South Pacific associated with the conservation status or population trends?

Analyses of knowledge gaps can highlight imbalances in research, encouraging greater proportionality in the distribution of research efforts. In this research we used generalized linear mixed models (GLMM) with the aim to determine if research efforts for the period 2005–2015 for terrestrial vertebrates of Amphibia, Aves, Mammalia and Reptilia in the South Pacific region were correlated with conservation status (critically endangered (CR), endangered (EN), vulnerable (VU), least concern (LC) and near threatened (NT)) or population trends (increasing, stable, decreasing and unknown) through the International Union for Conservation of Nature (IUCN) database. Our results showed that research distribution was uneven across different classes. Out of 633623 investigated papers, the average number of publications per species was 43.7, 306.7, 717.6 and 115.3 for Amphibia (284 species), Aves (1306 species), Mammalia (243 species) and Reptilia (400 species), respectively. Consistently, the lower publication effort on Amphibia compared to other taxonomic classes was revealed as significant by GLMM analysis. There was no significant differences in research effort among levels of conservation status. However, we found significantly different publication efforts among population trends of all examined species in that species with “unknown” population trends gained significantly lower researchers’ attention compared to species with “decreasing” trend. Results also indicated that, although it was not significant, the highest attention is given to species with “increasing” population trend over all taxonomic classes. Using the Information Theoretic approach we also generated a set of competing models to identify most important factors influencing research efforts, revealing that the highest ranked model included taxonomic class and population trend.     

Origins of Life Research: a Bibliometric Approach

This study explores the collaborative nature and interdisciplinarity of the origin(s) of life (OoL) research community. Although OoL research is one of the oldest topics in philosophy, religion, and science; to date there has been no review of the field utilizing bibliometric measures. A dataset of 5647 publications that are tagged as OoL, astrobiology, exobiology, and prebiotic chemistry is analyzed. The most prolific authors (Raulin, Ehrenfreund, McKay, Cleaves, Cockell, Lazcano, etc.), most cited scholars and their articles (Miller 1953, Gilbert 1986, Chyba & Sagan 1992, W?chtersh?user 1988, etc.), and popular journals (Origins of Life and Evolution of Biospheres and Astrobiology) for OoL research are identified. Moreover, interdisciplinary research conducted through research networks, institutions (NASA, Caltech, University of Arizona, University of Washington, CNRS, etc.), and keywords & concepts (astrobiology, life, Mars, amino acid, prebiotic chemistry, evolution, RNA) are explored.     

Acoustic characterization of bats from Malta: setting a baseline for monitoring and conservation of bat populations

Bioacoustic research has made several advancements in developing systems to record extensive acoustic data and classify bat echolocation calls to species level using automated classifiers. These systems are useful as echolocation calls give valuable information on bat behaviour and ecology and hence are widely used for research and conservation of bat populations. Despite the challenges associated with automated classifiers, due to the interspecific differences in call characteristics of bat species found in the Maltese Islands, the use of a quantitative and automated approach is investigated. The sound analysis pipeline involved the use of an algorithm to clean sound files from background noise and measure temporal and spectral parameters of bat echolocation calls. These parameters were then fed to a trained and validated artificial neural network using a bat call library built from reference bat calls from Malta. The automatic classifier achieved an overall correct classification rate of 98%. This high correct classification rate for reliable species identification may have benefitted from the absence of typically problematic species, such as species in the genus Myotis, in the analyses. This study’s results pave the way for efficient and reliable bat acoustic surveys in Malta in aid of necessary monitoring and conservation by providing an updated bat species list and their echolocation characteristics.