NCube/papyrus huggingface dataset:
The fish or the egg : maternal transfer and subcellular partitioning of mercury and selenium in Yellow Perch (Perca flavescens)

Mercury (Hg) is a trace element of particular concern since it is ubiquitous in the environment and because its methylated form (MeHg) readily bioaccumulates and biomagnifies in food webs. This latter process leads to elevated Hg concentrations in fish and may thus induce toxicity. Maternal transfer of bioaccumulated contaminants to offspring is a suggested mechanism of impaired reproductive success in fish. The purpose of this study was to assess the toxicity potential of Hg during maternal transfer in Yellow Perch from Lake Saint-Pierre (Quebec, Canada) using a subcellular partitioning approach. We also evaluated potential protective effects of selenium, as this element has been shown to alleviate Hg toxicity through sequestration. A customized subcellular partitioning protocol was used to separate liver and gonad of Yellow Perch into various subcellular fractions. Results show that, in the liver, MeHg was primarily (51%) associated to the subcellular fraction containing cytosolic enzymes. Furthermore, 23% and 15% of MeHg was found in hepatic and gonadal mitochondria, respectively, suggesting that Yellow Perch is not effectively detoxifying this metal. There was also a strong relationship (R2 = 0.73) between MeHg bioaccumulation in the liver and MeHg concentrations in gonadal mitochondria, which corroborates the potential risk linked to MeHg maternal transfer. On the other hand, we also found that selenium might have a protective effect on Hg toxicity at a subcellular level. In fact, Se:Hg molar ratios in subcellular fractions were systematically above 1 in all tissues and fractions examined, which corresponds to the suggested protective threshold. This study provides the first assessment of subcellular Se:Hg molar ratios in fish. Since early developmental stages in aquatic biota are particularly sensitive to Hg, this study represents a step forward in understanding the likelihood for toxic effects in wild fish through maternal transfer.

Keyphrases: Methylmercury, Se:Hg molar ratios, Mitochondria, Gravid females, Liver, Gonads
An ecological microsystem to treat waste oil contaminated soil: Using phytoremediation assisted by fungi and local compost, on a mixed-contaminant site, in a cold climate

As a result of anthropization and industrialization, northern remote communities face issues of soil contamination by mixtures of organic and inorganic contaminants. Soil bioremediation in cold environments is particularly challenging because of slower degradation rates, slower production of biomass for phytoextraction of trace elements (TEs), and remoteness, which can complicate logistics and inflate costs. This study evaluated a decontamination approach integrating indigenous willows, fungi and compost in a northern community. The site was a waste oil pit and its soil was initially contaminated with petroleum hydrocarbons (PHC) exceeding 200 g kg-1 and TEs including As, Cd, Co, Cr, Cu, Pb and Zn. In under five years, 65 and 75% of PHC (C6-C50 and >C50) were degraded, compared to 27 and 13% for the untreated control soil. We found contrasting TE translocation patterns to the aboveground biomass for the willow species used (Salix planifolia and Salix alaxensis), as well as distinctive rooting strategies. Hazard quotients were calculated to assess the risk plant material could pose to local wildlife. The highest TE concentration measured was Zn in S. planifolia, which exceeded Canadian soil guidelines. Results indicate toxicity risks to animals linked to TEs in Salix spp. leaves is generally unlikely. The fungus Trametes versicolor inoculated into the soil did not fruit, however fruiting bodies of Psathyrella sp. were observed consistently (four out of five years). Biological tests indicated that in five growing seasons soil toxicity significantly decreased compared to the untreated soil used as control. This was demonstrated by vegetation cover (137 vs 11% cover), toxicity assays on earthworms (Eisenia andrei) (0 vs 33% mortality) and barley seed germination (Hordeum vulgare) (86 vs 62% germination). The proposed decontamination approach, without the use of synthetic fertilizers, is promising for the PHC remediation of mixed-contaminants on cold climate sites.

Keyphrases: Co-contamination, North, Bioremediation, Phytoremediation, Mycoremediation
On the topicality and research impact of special issues

The publication of special issues constitute an important yet underinvestigated phenomenon of scholarly communication. In an attempt to draw attention to the proliferation of special issues, Priem (2006) suggested that their commissioning has an underestimated opportunity cost, given the relative scarcity of publication space: by distorting the “marketplace for ideas” through the commanding of preselected topical distributions, special issues undermine the total research output by “squeezing out” high-quality but topically unrelated articles. The present paper attempts to test this hypothesis by providing a topicality and research impact analysis of conference-based, monographic, and regular issues published between 2010 and 2015 inclusive and indexed in Clarivate Analytics’ Web of Science. The results show that the titles and abstracts of articles copublished are topically closer to each other than those copublished in regular issues, which suggests that their relative importance might influence the total topical distribution. However, disciplinary and overall comparison of relative citations for both special and regular issues shows that intraissue averages and variances in the former case are respectively higher and lower than in the regular issue context, which undermines not only the abovementioned hypothesis, but also the belief that editors often “fill up” special issues by accepting substandard papers.

Keyphrases: Scholarly publishing, Journals, Issues, Special issues, Citation impact, Vector semantics
An analysis of direct reciprocal borrowing among Québec university libraries

An analysis of Quebec academic libraries’ direct reciprocal borrow- ´ ing statistics from 2005 to 2010 reveals that the physical distance separating universities plays an important role in determining the amount of direct reciprocal borrowing activity conducted between institutions. Significant statistical correlations were also seen between the amount of direct reciprocal borrowing/lending as well as institution size and library collection size. Given their proximity, Montreal-area libraries have a higher ratio of direct reciprocal bor- ´ rowing activity compared to interlibrary loan consortial borrowing activity, whereas libraries located outside of Montreal have higher ´ interlibrary loan activity compared to direct reciprocal borrowing. It was found that institutions’ net lender and borrower status can shift depending on whether one is looking at direct reciprocal borrowing versus interlibrary loan activity. An exploratory social network analysis of direct reciprocal borrowing among Quebec ´ academic libraries was performed, and it affirmed the important role of physical distance in determining direct reciprocal borrowing activity. Language may also play a role in affecting the amount of direct reciprocal borrowing.

Keyphrases: Direct reciprocal borrowing, Resource sharing, Library cooperation, Library consortia, Academic libraries, Statistics, Distance, Correlation, Collection size, Interlibrary loan, Institution size
Scientific mobility indicators in practice : international mobility profiles at the country level

This paper presents and describes the methodological opportunities offered by bibliometric data to produce indicators of scientific mobility. Large bibliographic datasets of disambiguated authors and their affiliations allow for the possibility of tracking the affiliation changes of scientists. Using the Web of Science as data source, we analyze the distribution of types of mobile scientists for a selection of countries. We explore the possibility of creating profiles of international mobility at the country level, and discuss potential interpretations and caveats. Five countries—Canada, The Netherlands, South Africa, Spain, and the United States—are used as examples. These profiles enable us to characterize these countries in terms of their strongest links with other countries. This type of analysis reveals circulation among and between countries with strong policy implications. Este trabajo presenta y describe las oportunidades metodológicas que ofrecen los datos bibliográficos para producir indicadores de movilidad científica. El uso de grandes conjuntos de datos bibliográficos con autores y afiliaciones desambiguadas, abren la posibilidad de rastrear cambios de afiliación de investigadores. Empleando la Web of Science como base de datos, desarrollamos distintas perspectivas para mostrar la movilidad observable de una selección de países. Exploramos la posibilidad de crear perfiles de movilidad internacional a nivel de países y discutimos cómo interpretar estos indicadores así como sus potenciales limitaciones. Para ello, estudiamos los casos de Canadá, Países Bajos, Sudáfrica, España y Estados Unidos. Sus perfiles no solo nos permiten identificar a grupos de investigadores que muestran distintos tipos de movilidad, pero también nos permiten caracterizar los países según aquellos otros con los que tienen mayores vínculos. Este tipo de análisis permiten realizar comparaciones entre países de origen y destino de cada uno de los países analizados, especialmente relevantes en el contexto de política cientifica.

Keyphrases: Scientific mobility, Bibliometric indicators, Iinternational mobility, Internationalization, Research policy, Movilidad científica, Indicadores bibliométricos, Movilidad internacional, Internacionalización, Política científica
Les paradigmes de la revue Criminologie : auteurs, revues et disciplines qui ont marqué son histoire

Cet article vise à décrire les influences intellectuelles de la revue Criminologie. Pour ce faire, les 19 813 références faites par les articles publiés dans la revue Criminologie au cours des 40 dernières années sont analysées de manière à dégager l’influence qu’elles ont pu avoir sur les auteurs de la revue. Les auteurs, revues et disciplines les plus influents sont répertoriés et mis en relation avec les caractéristiques des articles qui les citent. Les résultats montrent que le savoir qui inspire les auteurs de la revue est très décentralisé : aucun auteur ou revue ne peut prétendre avoir un ascendant sur un nombre important d’auteurs de Criminologie. Les auteurs et les revues les plus cités sont ceux qui ont su se diversifier et retenir l’attention d’un large auditoire qui travaille avec des traditions de recherches différentes.

Keyphrases: Influences intellectuelles, Citations, Criminologie
Modeling a century of citation distributions

The prevalence of uncited papers or of highly cited papers, with respect to the bulk of publications, provides important clues as to the dynamics of scientific research. Using 25 million papers and 600 million references from the Web of Science over the 1900–2006 period, this paper proposes a simple model based on a random selection process to explain the “uncitedness” phenomenon and its decline over the years. We show that the proportion of cited papers is a function of (1) the number of articles available (the competing papers), (2) the number of citing papers and (3) the number of references they contain. Using uncitedness as a departure point, we demonstrate the utility of the stretched-exponential function and a form of the Tsallis q-exponential function to fit complete citation distributions over the 20th century. As opposed to simple power-law fits, for instance, both these approaches are shown to be empirically well-grounded and robust enough to better understand citation dynamics at the aggregate level. On the basis of these models, we provide quantitative evidence and provisional explanations for an important shift in citation practices around 1960. We also propose a revision of the “citation classic” category as a set of articles which is clearly distinguishable from the rest of the field.

Keyphrases: Citations, Bibliometrics, Citation distributions, Uncitedness, History of science
On the prevalence and scientific impact of duplicate publications in different scientific fields (1980‐2007)

The issue of duplicate publications has received a lot of attention in the medical literature, but much less in the information science community. This paper aims at analyzing the prevalence and scientific impact of duplicate publications across all fields of research between 1980 and 2007, using a definition of duplicate papers based on their metadata. It shows that in all fields combined, the prevalence of duplicates is one out of two-thousand papers, but is higher in the natural and medical sciences than in the social sciences and humanities. A very high proportion (>85%) of these papers are published the same year or one year apart, which suggest that most duplicate papers were submitted simultaneously. Furthermore, duplicate papers are generally published in journals with impact factors below the average of their field and obtain a lower number of citations. This paper provides clear evidence that the prevalence of duplicate papers is low and, more importantly, that the scientific impact of such papers is below average.

Keyphrases: Ethics, Medical sciences, Intellectual property, Publications, Information science
On the shoulders of students? The contribution of PhD students to the advancement of knowledge

Using the participation in peer reviewed publications of all doctoral students in Quebec over the 2000–2007 period, this paper provides the first large scale analysis of their research effort. It shows that PhD students contribute to about a third of the publication output of the province, with doctoral students in the natural and medical sciences being present in a higher proportion of papers published than their colleagues of the social sciences and humanities. Collaboration is an important component of this socialization: disciplines in which student collaboration is higher are also those in which doctoral students are the most involved in peer-reviewed publications. In terms of scientific impact, papers co-signed by doctorate students obtain significantly lower citation rates than other Quebec papers, except in natural sciences and engineering. Finally, this paper shows that involving doctoral students in publications is positively linked with degree completion and ulterior career in research.

Keyphrases: Doctorate, Bibliometrics, Publications, Citations, Québec, Canada
The state of OA : a large-scale analysis of the prevalence and impact of Open Access articles

Despite growing interest in Open Access (OA) to scholarly literature, there is an unmet need for large-scale, up-to-date, and reproducible studies assessing the prevalence and characteristics of OA. We address this need using oaDOI, an open online service that determines OA status for 67 million articles. We use three samples, each of 100,000 articles, to investigate OA in three populations: (1) all journal articles assigned a Crossref DOI, (2) recent journal articles indexed in Web of Science, and (3) articles viewed by users of Unpaywall, an open-source browser extension that lets users find OA articles using oaDOI. We estimate that at least 28% of the scholarly literature is OA (19M in total) and that this proportion is growing, driven particularly by growth in Gold and Hybrid. The most recent year analyzed (2015) also has the highest percentage of OA (45%). Because of this growth, and the fact that readers disproportionately access newer articles, we find that Unpaywall users encounter OA quite frequently: 47% of articles they view are OA. Notably, the most common mechanism for OA is not Gold, Green, or Hybrid OA, but rather an under-discussed category we dub Bronze: articles made freeto-read on the publisher website, without an explicit Open license. We also examine the citation impact of OA articles, corroborating the so-called open-access citation advantage: accounting for age and discipline, OA articles receive 18% more citations than average, an effect driven primarily by Green and Hybrid OA. We encourage further research using the free oaDOI service, as a way to inform OA policy and practice.

Keyphrases: Open access, Open science, Scientometrics, Publishing, Libraries, Scholarly communication, Bibliometrics, Science policy
Authorial and institutional stratification in open access publishing : the case of global health research

Using a database of recent articles published in the field of Global Health research, we examine institutional sources of stratification in publishing access outcomes. Traditionally, the focus on inequality in scientific publishing has focused on prestige hierarchies in established print journals. This project examines stratification in contemporary publishing with a particular focus on subscription vs. various Open Access (OA) publishing options. Findings show that authors working at lower-ranked universities are more likely to publish in closed/paywalled outlets, and less likely to choose outlets that involve some sort of Article Processing Charge (APCs; gold or hybrid OA). We also analyze institutional differences and stratification in the APC costs paid in various journals. Authors affiliated with higher-ranked institutions, as well as hospitals and non-profit organizations pay relatively higher APCs for gold and hybrid OA publications. Results suggest that authors affiliated with high-ranked universities and well-funded institutions tend to have more resources to choose pay options with publishing. Our research suggests new professional hierarchies developing in contemporary publishing, where various OA publishing options are becoming increasingly prominent. Just as there is stratification in institutional representation between different types of publishing access, there is also inequality within access types.

Keyphrases: Open access, Publishing economics, Libraries, Global health, Stratification, Article processing charges, Universities
The kiss of death? : the effect of being cited in a reviewon subsequent citations

This article inquires into recent claims that citation in a review article provokes a decline in a paper’s later citation count, these being instead given to the review. Using the Science Citation Index Expanded, we looked at the yearly percentages of lifetime citations of papers published in 1990 first cited in review articles in 1992 and 1995 in the field of biomedical research, and found no significant change to occur following review, regardless of the papers’ citation activity or specialty. Further comparison was made with papers from the field of clinical research, but yielded no meaningful results to support the notion that review articles have any substantial effect on the citation count of the papers they review.

Keyphrases: Bibliometrics
A multidimensional analysis of Aslib proceedings – using everything but the impact factor

Purpose – The purpose of this paper is to show that the journal impact factor (IF) is not able to reflect the full impact of scholarly journals and provides an overview of alternative and complementary methods in journal evaluation. Design/methodology/approach – Aslib Proceedings (AP) is exemplarily analyzed with a set of indicators from five dimensions of journal evaluation, i.e. journal output, content, perception and usage, citations and management to accurately reflect its various strengths and weaknesses beyond the IF. Findings – AP has become more international in terms of authors and more diverse regarding its topics. Citation impact is generally low and, with the exception of a special issue on blogs, remains world average. However, an evaluation of downloads and Mendeley readers reveals that the journal is an important source of information for professionals and students and certain topics are frequently read but not cited. Research limitations/implications – The study is limited to one journal. Practical implications – An overview of various indicators and methods is provided that can be applied in the quantitative evaluation of scholarly journals (and also to articles, authors and institutions). Originality/value – After a publication history of more than 60 years, this analysis takes stock of AP, highlighting strengths and weaknesses and developments over time. The case study provides an example and overview of the possibilities of multidimensional journal evaluation.

Keyphrases: Citation analysis, Scholarly communication, Usage statistics, Impact factor, Journal evaluation, Mendeley
On the citation lifecycle of papers with delayed recognition

Delayed recognition is a concept applied to articles that receive very few to no citations for a certain period of time following publication, before becoming actively cited. To determine whether such a time spent in relative obscurity had an effect on subsequent citation patterns, we selected articles that received no citations before the passage of ten full years since publication, investigated the subsequent yearly citations received over a period of 37 years and compared them with the citations received by a group of papers without such a latency period. Our study finds that papers with delayed recognition do not exhibit the typical early peak, then slow decline in citations, but that the vast majority enter decline immediately after their first – and often only – citation. Middling papers’ citations remain stable over their lifetime, whereas the more highly cited papers, some of which fall into the “sleeping beauty” subtype, show non-stop growth in citations received. Finally, papers published in different disciplines exhibit similar behavior and did not differ significantly.

Keyphrases: Delayed recognition, Sleeping beauties, Citation lifecycle
Authorship, citations, acknowledgments and visibility in social media : symbolic capital in the multifaceted reward system of science

The reward system of science is undergoing significant changes, as traditional indicators compete with initiatives that offer novel means of disseminating and assessing scholarly impact. This paper considers a number of aspects of this reward system, including   authorship, citations, acknowledgements, and the growing use of social media platforms by academics, with an eye towards identifying contemporary issues relating to scholarly communication practices, as understood through the perspectives of Bourdieu’s symbolic capital and Merton’s recognition paradigms. This paper posits that, while scientific capital remains the foundation upon which the reward system of science is built, this system is revealing itself to be more and more multifaceted, extremely complex, and facing increasing tension between its traditional means of evaluation and the potential of new indicators in the digital era. The paper presents an extended literature review, as well as recommendations for further considerations and empirical research. A better understanding of the perceptions of academics would be necessary to properly assess the effects of these new indicators on scholarly communication practices and the reward system of science.

Keyphrases: Acknowledgements, Altmetrics, Authorship, Citation analysis, Impact, Inventorship, Reward system of science, Scholarly communication, Social media, Symbolic capital
Tweets vs. Mendeley readers : how do these two social media metrics differ?

A set of 1.4 million biomedical papers was analyzed with regards to how often articles are mentioned on Twitter or saved by users on Mendeley. While Twitter is a microblogging platform used by a general audience to distribute information, Mendeley is a reference manager targeted at an academic user group to organize scholarly literature. Both platforms are used as sources for so-called “altmetrics” to measure a new kind of research impact. This analysis shows in how far they differ and compare to traditional citation impact metrics based on a large set of PubMed papers.

Keyphrases: Altmetrics, Social media, Twitter, Mendeley, Citation analysis, Scholarly communication