Environmental factors and reproduction in the female hopping mouse, Notomys alexis.

Australian hopping mice (Notomy alexis) were subjected to short or long photoperiods, different social environments and/or water deprivation. The age at which vaginal opening and first oestrus occurred was delayed by short photoperiods and by the absence of male proximity. Water deprivation prevented normal maturation. The normal 7 to 8 day oestrous cycle was prolonged by short photoperiods or water deprivation. Animals deprived of water had lighter body, ovarian and uterine weights, and follicular growth seemed to be impaired. No differences in organ weights were found between animals in the two photoperiods. The significance of the findings is discussed.     

Reproductive response of a tropical mammal, the musk shrew (Suncus murinus), to photoperiod

Musk shrews (Suncus murinus) were maintained for 8 weeks in long (16 h light:8 h darkness) or short (8 h light:16 h darkness) daylengths. Males housed in short daylength had significantly lighter androgen-dependent sex accessory organs than did males kept in long daylengths. This same trend was noted in male sexual behaviour. However, the weights of the testes and epididymides and sperm numbers did not differ. Females housed in short daylengths had significantly lighter cervices and were less likely to demonstrate sex behaviour than animals kept in under long daylengths. Ovarian and uterine weights did not differ. These results suggest that the ability to respond to photoperiod can exist in tropical mammals, even if it is not used as a cue to time seasonal breeding.     

Citation decay in animal science

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

Summary and perspective on evolutionary ecology of fishes

This special issue of Evolutionary Ecology provides ten papers that have been presented at a conference on Evolutionary Ecology of Fishes in 2009. In addition to briefly summarizing the main content of the papers which is related to adaptive radiations, processes of ecological divergence, and fisheries-induced evolution, we review and synthesize in short the recent advance in studies on evolutionary ecology of fishes. We conclude that fishes are excellent model systems to study evolutionary ecology of animals, and suggest three promising new research avenues; (1) the contribution of behavioural processes to evolution, in particular the consideration of animal personalities and predator–prey interactions, (2) metabolic physiology and parasite-host interactions as new niche dimensions to be considered for adaptive diversification, and (3) the opportunities for mechanistic understanding of adaptation and speciation emerging from new genetic tools.     

Learning biology through research papers: a stimulus for question-asking by high-school students

Question-asking is a basic skill, required for the development of scientific thinking. However, the way in which science lessons are conducted does not usually stimulate question-asking by students. To make students more familiar with the scientific inquiry process, we developed a curriculum in developmental biology based on research papers suitable for high-school students. Since a scientific paper poses a research question, demonstrates the events that led to the answer, and poses new questions, we attempted to examine the effect of studying through research papers on students' ability to pose questions. Students were asked before, during, and after instruction what they found interesting to know about embryonic development. In addition, we monitored students' questions, which were asked orally during the lessons. Questions were scored according to three categories: properties, comparisons, and causal relationships. We found that before learning through research papers, students tend to ask only questions of the properties category. In contrast, students tend to pose questions that reveal a higher level of thinking and uniqueness during or following instruction with research papers. This change was not observed during or following instruction with a textbook. We suggest that learning through research papers may be one way to provide a stimulus for question-asking by high-school students and results in higher thinking levels and uniqueness.     

Counting Highly Cited Papers for University Research Assessment: Conceptual and Technical Issues

A Kuhnian approach to research assessment requires us to consider that the important scientific breakthroughs that drive scientific progress are infrequent and that the progress of science does not depend on normal research. Consequently, indicators of research performance based on the total number of papers do not accurately measure scientific progress. Similarly, those universities with the best reputations in terms of scientific progress differ widely from other universities in terms of the scale of investments made in research and in the higher concentrations of outstanding scientists present, but less so in terms of the total number of papers or citations. This study argues that indicators for the 1% high-citation tail of the citation distribution reveal the contribution of universities to the progress of science and provide quantifiable justification for the large investments in research made by elite research universities. In this tail, which follows a power low, the number of the less frequent and highly cited important breakthroughs can be predicted from the frequencies of papers in the upper part of the tail. This study quantifies the false impression of excellence produced by multinational papers, and by other types of papers that do not contribute to the progress of science. Many of these papers are concentrated in and dominate lists of highly cited papers, especially in lower-ranked universities. The h-index obscures the differences between higher- and lower-ranked universities because the proportion of h-core papers in the 1% high-citation tail is not proportional to the value of the h-index.     

Looking for Landmarks: The Role of Expert Review and Bibliometric Analysis in Evaluating Scientific Publication Outputs

Objective

To compare expert assessment with bibliometric indicators as tools to assess the quality and importance of scientific research papers.

Methods and Materials

Shortly after their publication in 2005, the quality and importance of a cohort of nearly 700 Wellcome Trust (WT) associated research papers were assessed by expert reviewers; each paper was reviewed by two WT expert reviewers. After 3 years, we compared this initial assessment with other measures of paper impact.

Results

Shortly after publication, 62 (9%) of the 687 research papers were determined to describe at least a ‘major addition to knowledge’ –6 were thought to be ‘landmark’ papers. At an aggregate level, after 3 years, there was a strong positive association between expert assessment and impact as measured by number of citations and F1000 rating. However, there were some important exceptions indicating that bibliometric measures may not be sufficient in isolation as measures of research quality and importance, and especially not for assessing single papers or small groups of research publications.

Conclusion

When attempting to assess the quality and importance of research papers, we found that sole reliance on bibliometric indicators would have led us to miss papers containing important results as judged by expert review. In particular, some papers that were highly rated by experts were not highly cited during the first three years after publication. Tools that link expert peer reviews of research paper quality and importance to more quantitative indicators, such as citation analysis would be valuable additions to the field of research assessment and evaluation.     

The STAR project: context, objectives and approaches

STAR is a European Commission Framework V project (EVK1-CT-2001-00089). The project aim is to provide practical advice and solutions with regard to many of the issues associated with the Water Framework Directive. This paper provides a context for the STAR research programme through a review of the requirements of the directive and the Common Implementation Strategy responsible for guiding its implementation. The scientific and strategic objectives of STAR are set out in the form of a series of research questions and the reader is referred to the papers in this volume that address those objectives, which include: (a) Which methods or biological quality elements are best able to indicate certain stressors? (b) Which method can be used on which scale? (c) Which method is suited for early and late warnings? (d) How are different assessment methods affected by errors and uncertainty? (e) How can data from different assessment methods be intercalibrated? (f) How can the cost-effectiveness of field and laboratory protocols be optimised? (g) How can boundaries of the five classes of Ecological Status be best set? (h) What contribution can STAR make to the development of European standards? The methodological approaches adopted to meet these objectives are described. These include the selection of the 22 stream-types and 263 sites sampled in 11 countries, the sampling protocols used to sample and survey phytobenthos, macrophytes, macroinvertebrates, fish and hydromorphology, the quality control and uncertainty analyses that were applied, including training, replicate sampling and audit of performance, the development of bespoke software and the project outputs. This paper provides the detailed background information to be referred to in conjunction with most of the other papers in this volume. These papers are divided into seven sections: (1) typology, (2) organism groups, (3) macrophytes and diatoms, (4) hydromorphology, (5) tools for assessing European streams with macroinvertebrates, (6) intercalibration and comparison and (7) errors and uncertainty. The principal findings of the papers in each section and their relevance to the Water Framework Directive are synthesised in short summary papers at the beginning of each section. Additional outputs, including all sampling and laboratory protocols and project deliverables, together with a range of freely downloadable software are available from the project website at www.eu_star.at.     

Evaluating "payback" on biomedical research from papers cited in clinical guidelines: applied bibliometric study

ObjectivesTo develop a methodology for evaluating the impact of research on health care, and to characterise the papers cited on clinical guidelines.DesignThe bibliographic details of the papers cited in 15 clinical guidelines, developed in and for the United Kingdom, were collated and analysed with applied bibliometric techniques.ResultsThe median age of papers cited in clinical guidelines was eight years; most papers were published by authors living in either the United States (36%) or the United Kingdom (25%)—this is two and a half times more than expected as about 10% of all biomedical outputs are published in the United Kingdom; and clinical guidelines do not cite basic research papers.ConclusionAnalysis of the evidence base of clinical guidelines may be one way of tracking the flow of knowledge from the laboratory to the clinic. Moreover, such analysis provides a useful, clinically relevant method for evaluating research outcomes and different strategies in research and development.     

Reporting the implementation of the Three Rs in European primate and mouse research papers: are we making progress?

It is now more than 20 years since both Council of Europe Convention ETS123 and EU Directive 86/609/EEC were introduced, to promote the implementation of the Three Rs in animal experimentation and to provide guidance on animal housing and care. It might therefore be expected that reports of the implementation of the Three Rs in animal research papers would have increased during this period. In order to test this hypothesis, a literature survey of animal-based research was conducted. A randomly-selected sample from 16 high-profile medical journals, of original research papers arising from European institutions that featured experiments which involved either mice or primates, were identified for the years 1986 and 2006 (Total sample = 250 papers). Each paper was scored out of 10 for the incidence of reporting on the implementation of Three Rs-related factors corresponding to Replacement (justification of non-use of non-animal methods), Reduction (statistical analysis of the number of animals needed) and Refinement (housing aspects, i.e. increased cage size, social housing, enrichment of cage environment and food; and procedural aspects, i.e. the use of anaesthesia, analgesia, humane endpoints, and training for procedures with positive reinforcement). There was no significant increase in overall reporting score over time, for either mouse or primate research. By 2006, mouse research papers scored an average of 0 out of a possible 10, and primate research papers scored an average of 1.5. This review provides systematic evidence that animal research is still not properly reported, and supports the call within the scientific community for action to be taken by journals to update their policies.     

Misconduct Policies,Academic Culture and Career Stage,Not Gender or Pressures to Publish,Affect Scientific Integrity

The honesty and integrity of scientists is widely believed to be threatened by pressures to publish, unsupportive research environments, and other structural, sociological and psychological factors. Belief in the importance of these factors has inspired major policy initiatives, but evidence to support them is either non-existent or derived from self-reports and other sources that have known limitations. We used a retrospective study design to verify whether risk factors for scientific misconduct could predict the occurrence of retractions, which are usually the consequence of research misconduct, or corrections, which are honest rectifications of minor mistakes. Bibliographic and personal information were collected on all co-authors of papers that have been retracted or corrected in 2010-2011 (N=611 and N=2226 papers, respectively) and authors of control papers matched by journal and issue (N=1181 and N=4285 papers, respectively), and were analysed with conditional logistic regression. Results, which avoided several limitations of past studies and are robust to different sampling strategies, support the notion that scientific misconduct is more likely in countries that lack research integrity policies, in countries where individual publication performance is rewarded with cash, in cultures and situations were mutual criticism is hampered, and in the earliest phases of a researcher’s career. The hypothesis that males might be prone to scientific misconduct was not supported, and the widespread belief that pressures to publish are a major driver of misconduct was largely contradicted: high-impact and productive researchers, and those working in countries in which pressures to publish are believed to be higher, are less-likely to produce retracted papers, and more likely to correct them. Efforts to reduce and prevent misconduct, therefore, might be most effective if focused on promoting research integrity policies, improving mentoring and training, and encouraging transparent communication amongst researchers.     

Do Scientific Advancements Lean on the Shoulders of Giants? A Bibliometric Investigation of the Ortega Hypothesis

Background

In contrast to Newton''s well-known aphorism that he had been able “to see further only by standing on the shoulders of giants,” one attributes to the Spanish philosopher Ortega y Gasset the hypothesis saying that top-level research cannot be successful without a mass of medium researchers on which the top rests comparable to an iceberg.

Methodology/Principal Findings

The Ortega hypothesis predicts that highly-cited papers and medium-cited (or lowly-cited) papers would equally refer to papers with a medium impact. The Newton hypothesis would be supported if the top-level research more frequently cites previously highly-cited work than that medium-level research cites highly-cited work. Our analysis is based on (i) all articles and proceedings papers which were published in 2003 in the life sciences, health sciences, physical sciences, and social sciences, and (ii) all articles and proceeding papers which were cited within these publications. The results show that highly-cited work in all scientific fields more frequently cites previously highly-cited papers than that medium-cited work cites highly-cited work.

Conclusions/Significance

We demonstrate that papers contributing to the scientific progress in a field lean to a larger extent on previously important contributions than papers contributing little. These findings support the Newton hypothesis and call into question the Ortega hypothesis (given our usage of citation counts as a proxy for impact).     

A review of the effectiveness of oral health promotion activities among elderly people

Objectives: This study aimed to review the effectiveness of oral health promotion studies conducted among elderly people between 1997 and 2007. Methods: Four electronic databases were searched and papers were rated for level of evidence and scientific quality. Key findings of the papers were summarised. Results: Thirteen thousand nine hundred and four papers were retrieved and 17 studies (18 papers) met the criteria for the review: 13 were randomised controlled studies, three were quasi‐experimental studies and one was a pre‐/post‐single group intervention study. According to the Levels of Evidence, 11 studies could be categorised as 1b and six studies could be categorised as 2b. The quality of the evidence of the 17 studies ranged from 12 to 19; 13 of the studies had a score of 15 or above; four of the studies ranged from 12 to 14. Evidence from oral health promotion activities aimed at preventing caries, improving periodontal health and altering oral health behaviours were reviewed. The use of fluoride, antimicrobial agents and health‐care provider education has important roles within oral health promotion activities for elderly people. Studies have tended to be of short‐term duration and rely on surrogate outcome measures of oral health. Conclusion: In the last 10 years, increasing attention has been paid to oral health promotion activities among the elderly population and high quality evidence has emerged. However, there is a need for even higher‐quality research to provide more definitive guidelines on oral health promotion practices for elderly people.     

Pattern perception and computational complexity: introduction to the special issue

Research on pattern perception and rule learning, grounded in formal language theory (FLT) and using artificial grammar learning paradigms, has exploded in the last decade. This approach marries empirical research conducted by neuroscientists, psychologists and ethologists with the theory of computation and FLT, developed by mathematicians, linguists and computer scientists over the last century. Of particular current interest are comparative extensions of this work to non-human animals, and neuroscientific investigations using brain imaging techniques. We provide a short introduction to the history of these fields, and to some of the dominant hypotheses, to help contextualize these ongoing research programmes, and finally briefly introduce the papers in the current issue.     

Phylogenetic biogeography and taxonomy of disjunctly distributed bryophytes

More than 200 research papers on the molecular phylogeny and phylogenetic biogeography ofbryophytes have been published since the beginning of this millenium. These papers corroborated assumptions of a complex genetic structure of morphologically circumscribed bryophytes, and raised reservations against many morphologically justified species concepts, especially within the mosses. However, many molecular studies allowed for corrections and modifications of morphological classification schemes. Several studies reported that the phylogenetic structure of disjunctly distributed bryophyte species reflects their geographical ranges rather than morphological disparities. Molecular data led to new appraisals of distribution ranges and allowed for the reconstruction of refugia and migration routes. Intercontinental ranges of bryophytes are often caused by dispersal rather than geographical vicariance. Many distribution patterns of disjunct bryophytes are likely formed by processes such as short distance dispersal, rare long distance dispersal events, extinction, recolonization and diversification.     

Evolutionary approaches to cultural and linguistic diversity

Evolutionary approaches to cultural change are increasingly influential, and many scientists believe that a 'grand synthesis' is now in sight. The papers in this Theme Issue, which derives from a symposium held by the AHRC Centre for the Evolution of Cultural Diversity (University College London) in December 2008, focus on how the phylogenetic tree-building and network-based techniques used to estimate descent relationships in biology can be adapted to reconstruct cultural histories, where some degree of inter-societal diffusion will almost inevitably be superimposed on any deeper signal of a historical branching process. The disciplines represented include the three most purely 'cultural' fields from the four-field model of anthropology (cultural anthropology, archaeology and linguistic anthropology). In this short introduction, some context is provided from the history of anthropology, and key issues raised by the papers are highlighted.     

Is There a Relationship between Research Sponsorship and Publication Impact? An Analysis of Funding Acknowledgments in Nanotechnology Papers

This study analyzes funding acknowledgments in scientific papers to investigate relationships between research sponsorship and publication impacts. We identify acknowledgments to research sponsors for nanotechnology papers published in the Web of Science during a one-year sample period. We examine the citations accrued by these papers and the journal impact factors of their publication titles. The results show that publications from grant sponsored research exhibit higher impacts in terms of both journal ranking and citation counts than research that is not grant sponsored. We discuss the method and models used, and the insights provided by this approach as well as it limitations.