The continuing lack of ornithological research capacity in almost all of West Africa

West Africa has high bird diversity and is a crucial non-breeding area for over one-third of European breeding species, yet local capacity for ornithological research and so targeted bird conservation is perceived to be limited. I reviewed all the published literature on the Web of Science^? classified as ‘ornithology’ with an accompanying keyword of a country’s name, over the last three decades, from the 16 countries within West Africa and compared it with that from 16 Western European countries. Inclusion of the country’s name as a search term identified any papers produced by local authors, and so should provide an index of local ornithological capacity. Overall only 129 papers were produced from 1987 to 2016 with West African authors (range: zero Burkina Faso to 45 Nigeria), significantly fewer compared with 12 380 with European authors (range: 71 Greece to 2 745 England). The number of papers produced increased significantly at similar rates over the three-decade period in both continents. The number of papers produced by local authors in West Africa and Europe approximately doubled each decade, but variation between countries was large, particularly in West Africa. The results are broadly the same when paper output is adjusted for the population of each country. Of the three West African countries that showed a consistent increase in numbers of locally authored ornithological papers, only Nigeria showed a highly significant increase and this increase was down to a single ornithological research institute established there in 2002. The results confirm that there is little local ornithological capacity in West Africa and this is not changing except in Nigeria, where even a single new research institute can make a significant difference because of the very low baseline.     

Global research trends on bioflocculant potentials in wastewater remediation from 1990 to 2019 using a bibliometric approach

The preference of biofloculants over chemical flocculants in water and wastewater remediation systems has gained wider attention due to their biodegradability, innocuousness, safety to human and environmental friendliness. The present study aimed to evaluate research outputs on bioflocculant potentials in wastewater remediation from 1990 to 2019 using bibliometric analyses. To the best of our knowledge, this is the first bibliometric report in bioflocculant research. The subject bibliometric dataset was extracted from the Web of Science Core Collection (WoSCC) and Scopus using the Boolean, ‘bioflocculant* and waste*’ and analysed for indicators such as a yearly trend, productivity (authors, articles, country, institution and journal source), conceptual framework and collaboration network. We found 119 documents with 347 authors from 78 journal sources on the subject, an annual growth rate of 12·1%, and average citations/document of 15·08. Guo J. and Wang Y. were the top researchers with 15 and 12 outputs respectively. China (42%) and South Africa (9·24%) ranked the top two dominant countries in the field. The top journals were Bioresource Technology (9 papers, 506 citations), Applied Microbiology and Biotechnology (5 papers, 268 citations), whereas, the top institution was Chengdu University of Information and Technology (n = 9 documents) followed by Sichuan Univ. Sci. & Engn, China (n = 8 documents). This study found that lack of intercountry collaboration and research funding adversely affects research participants in the field.     

A critique of 'countryside biogeography' as a guide to research in human‐dominated landscapes

Proliferation of redundant terms in ecology and conservation slows progress and creates confusion. ‘Countryside biogeography’ has been promoted as a new framework for conservation in production landscapes, so may offer a replacement for other concepts used by landscape ecologists. We conducted a systematic review to assess whether the 'countryside biogeography' concept provides a distinctive framing for conservation in human‐dominated landscapes relative to existing concepts. We reviewed 147 papers referring to countryside biogeography and 81 papers that did not. These papers were divided into categories representing three levels of use of countryside biogeography concepts (strong, weak, cited only) and two categories that did not use countryside biogeography at all but used similar concepts including fragmentation and matrix. We revealed few distinctions among groups of papers. Countryside biogeography papers made more frequent use of the terms 'ecosystem services', 'intensification' and 'land sparing' compared with non‐countryside biogeography papers. Papers that did not refer to countryside biogeography sampled production areas (e.g. farms) less often, and this related to their focus on habitat specialist species for which patch‐matrix assumptions were reasonable. Countryside biogeography offers a conceptual wrapper rather than a distinctive framework for advancing research in human‐modified landscapes. This and similar wrappers such as ‘conservation biogeography’ and ‘agricultural biogeography’ risk creating confusion among new researchers, and can prevent clear communication about research. To improve communication, we recommend using the suite of well‐established terms already applied to conservation in human‐modified landscapes rather than through an interceding conceptual wrapper.     

LIBRARY LETTERS

Lampert, W. & Sommer, U. (1997) Limnoecology: the ecology of lakes and streams. Oxford University Press, Oxford. xiv+382 pp., figs, tables, index. Hardback: Price £37.50. ISBN 0-19-509592-8. This book is an English translation of a volume that was first published in German in 1992 and is the result of a collaboration between Winfried Lampert, Director at the Max Planck Institute for Limnology at Plon, and Ulrich Sommer, Professor of Biological Oceanography at the University of Kiel. The book was written in response to the criticism that most textbooks in ecology use examples that are drawn, almost exclusively, from terrestrial systems. The authors’ intention was to produce a book on limnology that would highlight fundamental principles and would thus be of interest to a much wider audience. The first chapter, ‘Ecology and evolution’, develops the theme by explaining that one of the main aims of ecology is to investigate not only how organisms are adapted to their environment but also why they have developed particular adaptations. A number of important concepts, such as the difference between proximate and ultimate factors, are discussed and illustrated with examples drawn from the aquatic literature. The second chapter, ‘Methods of ecological research’, describes some of the methods used to test hypotheses and includes advice on the design of laboratory and field experiments. Some of this advice may appear elementary, but experienced researchers would do well to remember that ‘correlation analysis can be used to draw numerical, but not functional, relationships.’ Chapter 3, ‘Special features of aquatic habitats’, has clearly been included for the sake of completeness. The basic physical and chemical characteristics of lakes are discussed in time-honoured fashion and a few pages devoted to the special characteristics of running waters. The organization of Chapter 4, ‘The individual in its habitat’, is rather unbalanced and clearly reflects the authors’ areas of special interest. The best sections in the chapter are those devoted to the functional responses of aquatic organisms and the feeding mechanisms of the microcrustacea. Chapter 5, ‘Populations’, combines an introduction to the basic principles of population ecology with a review of more recent issues, such as the concept of r and K selected organisms. The factors that control population size are discussed in a simple but informative way, and are illustrated with examples drawn from studies of phytoplankton and zooplankton. Chapter 6, ‘Interactions’, is the longest in the book and clearly reflects the author's interest in the temporal dynamics of planktonic crustacea. The chapter starts in a fairly traditional way by reviewing the competition models of Lotka-Volterra and Tilman but then pursues a number of specialist issues, such the impact of chemical signals (kairomones) on the growth of rotifers. Chapter 7, ‘Communities’, is largely devoted to a discussion of the ‘top-down’ versus ‘bottom-up’ controversy that has preoccupied plankton ecologists for several decades. The authors provide a commendably dispassionate overview of the historical argument and highlight some recent studies that try to reconcile these opposing views. The chapter includes a brief discussion of the causes and maintenance of diversity and ends with a somewhat displaced account of the river continuum concept. Chapter 8, ‘Ecosystem perspectives’, is another chapter that appears to have been written as a matter of duty. The carbon, nitrogen, phosphorus and silica cycles are, however, described before the authors return to the terra firma of plankton succession and the ‘climax’ concept. Chapter 9, ‘Final remarks’, is only three pages long but leaves the reader in no doubt as to why this book was written. The authors clearly view the recent trend towards more marketable ‘applied’ research with considerable concern: ‘The objective of this applied ecology is not the development of generalized theories, but the optimization of human living conditions.’ In a concluding paragraph, they point out that the relationship between ecology and environmental science can be compared to the relationship between physics and engineering. ‘Physics provides the fundamental materials from which the engineers make products.’ This is not a new definition of ecology, but we are left with the clear implication that this book would not have been written if the authors had spent most of their time working in the ‘engineering’ department! Like any book, its structure and content is strongly influenced by the specialist knowledge of the writers. The authors are at their best when they describe recent developments in their own fields of interest. The least satisfactory sections are the chapters and sections devoted to lake physics, chemistry and the spatial organization of limnetic systems. For example, in Chapter 3 the authors include a figure that purports to show that small vertical variations in water temperature can produce micro-layers of phytoplankton in the near-surface ‘mixed zone’. Thermally induced layers of this kind are periodically recorded in lakes, but in this example there is no evidence of any physical discontinuities. In 1892, Forel, a Swiss Professor, defined limnology as ‘the oceanography of lakes’. This book has not been designed as a textbook in that classical sense but provides an excellent introduction to those aspects of limnology that have a strong ecological bias. The book is well produced with clear line drawings and includes boxed sections of text that explain some technical issues in more detail. The translater should be congratulated for producing a text that reads very well in English and, as far as I can judge, conveys the philosophical as well as the factual message of the original text. Overall, it is a valuable, indeed elegant, addition to the existing English texts, which I would also recommend to those interested in general ecological theory.     

Time and space in biogeography: response to Parenti & Ebach (2013)

A recent Guest Editorial by Parenti & Ebach (2013, Journal of Biogeography, 40, 813–820) disagrees with the methods or interpretations in two of our recent papers. In addition, the authors open a debate on biogeographical concepts, and present an alternative philosophy for biogeographical research in the context of their recently described biogeographical subregion called ‘Pandora’. We disagree with their approach and conclusions, and comment on several issues related to our differing conceptual approaches for biogeographical research; namely, our use of molecular phylogenetic analyses, including time estimates; and Parenti & Ebach's reliance on taxon/general area cladograms. Finally, we re‐examine their ‘tests’ supporting the existence of ‘Pandora’.     

Confundiendo al confuso: reflexiones sobre el factor de impacto,el índice h(irsch), el valor Q y otros cofactores que influyen en la felicidad del investigador

BackgroundThe need to evaluate curricula for sponsorship for research projects or professional promotion, has led to the search for tools that allow an objective valuation. However, the total number papers published, or citations of articles of a particular author, or the impact factor of the Journal where they are published are inadequate indicators for the evaluation of the quality and productivity of researchers. The h index, proposed by Hirsch, categorises the papers according to the number of citations per article. This tool appears to lack the limitations of other bibliometric tools but is less useful for non English-speaking authors.AimsTo propose and debate the usefulness of the existing bibliometric indicators and tools for the evaluation and categorization of researchers and scientific journals.MethodsSearch for papers on bibliometric tools.ResultsThere are some hot spots in the debate on the national and international evaluation of researchers’ productivity and quality of scientific journals. Opinions on impact factors and h index have been discussed. The positive discrimination, using the Q value, is proposed as an alternative for the evaluation of Spanish and Iberoamerican researchers.ConclusionsIt is very important de-mystify the importance of bibliometric indicators. The impact factor is useful for evaluating journals from the same scientific area but not for the evaluation of researchers’ curricula. For the comparison of curricula from two or more researchers, we must use the h index or the proposed Q value. the latter allows positive discrimination of the task for Spanish and Iberoamerican researchers.     

JPE Best Paper awards (2020)

Journal of Plant Ecology (JPE) decided to establish awards of JPE Best Papers, in order to thank and encourage authors to submit their valuable research to JPE. This award will be given annually to the first author(s) of 2–5 papers selected by the editors, according to the citation data as well as the impact in the field of plant ecology. We will place extra emphasis on authors who had completed graduate studies not more than 5 years before submission of the paper, to encourage more early-career scientists to submit their work to JPE. It will come with a ‘JPE Best Paper’ certificate, as well as a price money of Chinese RMB 5000. This year, we selected the best papers from all the articles published in the year of 2020. Here, we are delighted to announce the three winners of a ‘JPE Best Paper’ award and highlight the significance of these papers below.     

Unravelling the Philosophies Underlying ‘Animal Personality’ Studies: A Brief Re‐Appraisal of the Field

The last decade has seen lots of studies on ‘animal personality’ (i.e. the study of consistent between‐individual behavioural differences). As timely and promising as this field is, its development has come with a diversity of research questions. As an unfortunate consequence, it now suffers from substantial confusion about what ‘animal personality’ is, and how relevant related research frameworks are. Here, we stress the current inconsistencies and sources of confusion pertaining to the field, and their consequences on terminology used and miscommunication between researchers. In an attempt to unravel and clarify the concepts underlying the field, we identify two distinct, but complementary, theory‐driven conceptual frameworks: the intra‐individual variability (IIV) approach and the life‐history (LH) approach, which we believe encompass the vast majority of existing ‘personality studies’. Finally, we argue in favour of theory‐driven studies of consistent behavioural differences and state that the integrative statistical properties of random regression models should not override the merit of alternative conceptual frameworks. We then provide brief guidelines and warnings for a parsimonious and sound use of terminology.     

Location,location, location? No. Catalog number

Once you start to read this Editor’s Corner, you might wonder why I have devoted an entire article, albeit a short one, to this topic. Let me assure you there are reasons. First, I want to announce a new policy for the journal that will affect all research papers. Starting with all papers that are not currently in press, we will no longer be asking for geographical locations of research companies that follow the listing of a reagent. In Materials and Methods the authors typically refer to a reagent and then list the company and its location parenthetically. For example, “…p-nitrophenyl phosphate (Sigma-Aldrich, St. Louis, MO).” Instead, we will require catalog numbers. The reason is that it is now quite easy to find a company using the internet, and in fact you rarely need to know the location because it is rare that you would send a written order. On the other hand, knowing the name of the reagent is not always sufficient to narrow down the precise item. For example, if you search for “p-nitrophenyl phosphate” at the Sigma-Aldrich site, you get seven primary choices and it is not at all obvious which one to choose. When my lab uses p-nitrophenyl phosphate for the Pho8?60 assay, we use item N9389, which narrows it down to a precise reagent. Thus, we will start requiring papers to write “…p-nitrophenyl phosphate (Sigma-Aldrich, N9389).

Second, I think this is actually a useful change, and one that many journals will start to institute once they see it being done here. The old style of listing the city and state is a relic that is no longer relevant. Furthermore, it is not even clear in the current global marketplace if this is particularly helpful. For example, if I am ordering an item from Roche Applied Science, why would anyone care where it is coming from? It is highly unlikely that a researcher in Germany or Japan is going to order from Roche Applied Science that happens to be based in Indianapolis, IN when there are much closer sites in Mannheim, Germany and Tokyo, Japan. So, do not be surprised when you start to see more and more journals adopting this approach, and remember that you saw it here first. Autophagy—the cutting edge.     

A human autophagy interaction network

The original “Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes” has been well received and used by many researchers and authors. I consider these to be very important guidelines that require a consensus among the researchers in the field, because they are used by authors to defend against inappropriate reviewers’ comments, and by reviewers to point out to editors the flaws in research papers. Accordingly, I decided it was time to revise and update the guidelines. After all, the field has expanded substantially, as has the range of model systems being used to analyze autophagy. As a result, the list of authors has similarly increased. In addition, this version of the guidelines is not limited to higher eukaryotes nor to macroautophagy. Here, I explain the approach used to invite authors to participate in the revised guidelines, and briefly demonstrate one aspect of their utility.     

A guide into glycosciences: How chemistry,biochemistry and biology cooperate to crack the sugar code

BackgroundThe most demanding challenge in research on molecular aspects within the flow of biological information is posed by the complex carbohydrates (glycan part of cellular glycoconjugates). How the ‘message’ encoded in carbohydrate ‘letters’ is ‘read’ and ‘translated’ can only be unraveled by interdisciplinary efforts.Scope of reviewThis review provides a didactic step-by-step survey of the concept of the sugar code and the way strategic combination of experimental approaches characterizes structure–function relationships, with resources for teaching.Major conclusionsThe unsurpassed coding capacity of glycans is an ideal platform for generating a broad range of molecular ‘messages’. Structural and functional analyses of complex carbohydrates have been made possible by advances in chemical synthesis, rendering production of oligosaccharides, glycoclusters and neoglycoconjugates possible. This availability facilitates to test the glycans as ligands for natural sugar receptors (lectins). Their interaction is a means to turn sugar-encoded information into cellular effects. Glycan/lectin structures and their spatial modes of presentation underlie the exquisite specificity of the endogenous lectins in counterreceptor selection, that is, to home in on certain cellular glycoproteins or glycolipids.General significanceUnderstanding how sugar-encoded ‘messages’ are ‘read’ and ‘translated’ by lectins provides insights into fundamental mechanisms of life, with potential for medical applications.     

Modelling the radiotherapy effect in the reaction-diffusion equation

PurposeIn recent years, the reaction-diffusion (Fisher-Kolmogorov) equation has received much attention from the oncology research community due to its ability to describe the infiltrating nature of glioblastoma multiforme and its extraordinary resistance to any type of therapy. However, in a number of previous papers in the literature on applications of this equation, the term (R) expressing the ‘External Radiotherapy effect’ was incorrectly derived. In this note we derive an analytical expression for this term in the correct form to be included in the reaction-diffusion equation.MethodsThe R term has been derived starting from the Linear-Quadratic theory of cell killing by ionizing radiation. The correct definition of R was adopted and the basic principles of differential calculus applied.ResultsThe compatibility of the R term derived here with the reaction-diffusion equation was demonstrated. Referring to a typical glioblastoma tumour, we have compared the results obtained using our expression for the R term with the ‘incorrect’ expression proposed by other authors.     

The Pagerank-Index: Going beyond Citation Counts in Quantifying Scientific Impact of Researchers

Quantifying and comparing the scientific output of researchers has become critical for governments, funding agencies and universities. Comparison by reputation and direct assessment of contributions to the field is no longer possible, as the number of scientists increases and traditional definitions about scientific fields become blurred. The h-index is often used for comparing scientists, but has several well-documented shortcomings. In this paper, we introduce a new index for measuring and comparing the publication records of scientists: the pagerank-index (symbolised as π). The index uses a version of pagerank algorithm and the citation networks of papers in its computation, and is fundamentally different from the existing variants of h-index because it considers not only the number of citations but also the actual impact of each citation. We adapt two approaches to demonstrate the utility of the new index. Firstly, we use a simulation model of a community of authors, whereby we create various ‘groups’ of authors which are different from each other in inherent publication habits, to show that the pagerank-index is fairer than the existing indices in three distinct scenarios: (i) when authors try to ‘massage’ their index by publishing papers in low-quality outlets primarily to self-cite other papers (ii) when authors collaborate in large groups in order to obtain more authorships (iii) when authors spend most of their time in producing genuine but low quality publications that would massage their index. Secondly, we undertake two real world case studies: (i) the evolving author community of quantum game theory, as defined by Google Scholar (ii) a snapshot of the high energy physics (HEP) theory research community in arXiv. In both case studies, we find that the list of top authors vary very significantly when h-index and pagerank-index are used for comparison. We show that in both cases, authors who have collaborated in large groups and/or published less impactful papers tend to be comparatively favoured by the h-index, whereas the pagerank-index highlights authors who have made a relatively small number of definitive contributions, or written papers which served to highlight the link between diverse disciplines, or typically worked in smaller groups. Thus, we argue that the pagerank-index is an inherently fairer and more nuanced metric to quantify the publication records of scientists compared to existing measures.     

On the future contents of a small journal of histochemistry

In the last three years, more than 70,000 scientific articles have been published in peer reviewed journals on the application of histochemistry in the biomedical field: most of them did not appear in strictly histochemical journals, but in others dealing with cell and molecular biology, medicine or biotechnology. This proves that histochemistry is still an active and innovative discipline with relevance in basic and applied biological research, but also demonstrates that especially the small histochemical journals should likely reconsider their scopes and strategies to preserve their authorship. A review of the last three years volumes of the European Journal of Histochemistry, taken as an example of a long-time established small journal, confirmed that the published articles were widely heterogeneous in their topics and experimental models, as in this journal''s tradition. This strongly suggests that a journal of histochemistry should keep its role as a forum open to an audience as broad as possible, publishing papers on cell and tissue biology in a wide variety of models. This will improve knowledge of the basic mechanisms of development and differentiation, while helping to increase the number of potential authors since scientists who generally do not use histochemistry in their research will find hints for the applications of histochemical techniques to novel still unexplored subjects.Key words: Basic and applied histochemistry     

Symposium introduction: The importance of scale in ecology

Abstract Conceptual issues about scale, both spatial and temporal, have had considerable influence on the way in which ecologists view populations, communities and ecosystems. Scale includes two aspects: the extent over which a community or ecosystem is studied, and the resolution or ‘grain’ at which measurements or experiments are conducted. We illustrate the influence of extent and grain on perceptions of ecological patterns and processes, derived from fundamental measurements, field experiments and theory and modelling. These concepts provide background for a series of subsequent papers that were presented at a symposium on spatial and temporal scaling in freshwater systems. These papers conclude that multi-scale measurements and experiments plus novel methodologies for analysing large-scale surveys and manipulations should be priorities for future research in freshwater systems.