Mapping open knowledge institutions: an exploratory analysis of Australian universities

While the movement for open research has gained momentum in recent years, there remain concerns about the broader commitment to openness in knowledge production and dissemination. Increasingly, universities are under pressure to transform themselves to engage with the wider community and to be more inclusive. Open knowledge institutions (OKIs) provide a framework that encourages universities to act with the principles of openness at their centre; not only should universities embrace digital open access (OA), but also lead actions in cultivating diversity, equity, transparency and positive changes in society. This leads to questions of whether we can evaluate the progress of OKIs and what are potential indicators for OKIs. As an exploratory study, this article reports on the collection and analysis of a list of potential OKI indicators. Data for these indicators are gathered for 43 Australian universities. The indicators provide high-dimensional and complex signals about university performances. They show evidence of large disparities in characteristics such as Indigenous employment and gender equity, and a preference for repository-mediated OA across Australian universities. We demonstrate use of the OKI evaluation framework to categorise these indicators into three platforms of diversity, communication and coordination. The analysis provides new insights into the Australian open knowledge landscape and ways of mapping different paths of OKIs.

MyCites: a proposal to mark and report inaccurate citations in scholarly publications

Background

Inaccurate citations are erroneous quotations or instances of paraphrasing of previously published material that mislead readers about the claims of the cited source. They are often unaddressed due to underreporting, the inability of peer reviewers and editors to detect them, and editors' reluctance to publish corrections about them. In this paper, we propose a new tool that could be used to tackle their circulation.

Methods

We provide a review of available data about inaccurate citations and analytically explore current ways of reporting and dealing with these inaccuracies. Consequently, we make a distinction between publication (i.e., first occurrence) and circulation (i.e., reuse) of inaccurate citations. Sloppy reading of published items, literature ambiguity and insufficient quality control in the editorial process are identified as factors that contribute to the publication of inaccurate citations. However, reiteration or copy-pasting without checking the validity of citations, paralleled with lack of resources/motivation to report/correct inaccurate citations contribute to their circulation.

Results and discussion

We propose the development of an online annotation tool called "MyCites" as means with which to mark and map inaccurate citations. This tool allows ORCID users to annotate citations and alert authors (of the cited and citing articles) and also editors of journals where inaccurate citations are published. Each marked citation would travel with the digital version of the document (persistent identifiers) and be visible on websites that host peer-reviewed articles (journals' websites, Pubmed, etc.). In the future development of MyCites, challenges such as the conditions of correct/incorrect-ness and parties that should adjudicate that, and, the issue of dealing with incorrect reports need to be addressed.

Evaluating the impact of open access policies on research institutions

The proportion of research outputs published in open access journals or made available on other freely-accessible platforms has increased over the past two decades, driven largely by funder mandates, institutional policies, grass-roots advocacy, and changing attitudes in the research community. However, the relative effectiveness of these different interventions has remained largely unexplored. Here we present a robust, transparent and updateable method for analysing how these interventions affect the open access performance of individual institutes. We studied 1,207 institutions from across the world, and found that, in 2017, the top-performing universities published around 80-90% of their research open access. The analysis also showed that publisher-mediated (gold) open access was popular in Latin American and African universities, whereas the growth of open access in Europe and North America has mostly been driven by repositories.

A longitudinal analysis of university rankings

Pressured by globalization and demand for public organizations to be accountable, efficient, and transparent, university rankings have become an important tool for assessing the quality of higher education institutions. It is therefore important to assess exactly what these rankings measure. Here, the three major global university rankings—the Academic Ranking of World Universities, the Times Higher Education ranking and the Quacquarelli Symonds World University Rankings—are studied. After a description of the ranking methodologies, it is shown that university rankings are stable over time but that there is variation between the three rankings. Furthermore, using principal component analysis and exploratory factor analysis, we demonstrate that the variables used to construct the rankings primarily measure two underlying factors: a university’s reputation and its research performance. By correlating these factors and plotting regional aggregates of universities on the two factors, differences between the rankings are made visible. Last, we elaborate how the results from these analysis can be viewed in light of often-voiced critiques of the ranking process. This indicates that the variables used by the rankings might not capture the concepts they claim to measure. The study provides evidence of the ambiguous nature of university rankings quantification of university performance.

Comparison of bibliographic data sources: Implications for the robustness of university rankings

Universities are increasingly evaluated on the basis of their outputs. These are often converted to simple and contested rankings with substantial implications for recruitment, income, and perceived prestige. Such evaluation usually relies on a single data source to define the set of outputs for a university. However, few studies have explored differences across data sources and their implications for metrics and rankings at the institutional scale. We address this gap by performing detailed bibliographic comparisons between Web of Science (WoS), Scopus, and Microsoft Academic (MSA) at the institutional level and supplement this with a manual analysis of 15 universities. We further construct two simple rankings based on citation count and open access status. Our results show that there are significant differences across databases. These differences contribute to drastic changes in rank positions of universities, which are most prevalent for non-English-speaking universities and those outside the top positions in international university rankings. Overall, MSA has greater coverage than Scopus and WoS, but with less complete affiliation metadata. We suggest that robust evaluation measures need to consider the effect of choice of data sources and recommend an approach where data from multiple sources is integrated to provide a more robust data set.

A multi-disciplinary perspective on emergent and future innovations in peer review

Peer review of research articles is a core part of our scholarly communication system. In spite of its importance, the status and purpose of peer review is often contested. What is its role in our modern digital research and communications infrastructure? Does it perform to the high standards with which it is generally regarded? Studies of peer review have shown that it is prone to bias and abuse in numerous dimensions, frequently unreliable, and can fail to detect even fraudulent research. With the advent of web technologies, we are now witnessing a phase of innovation and experimentation in our approaches to peer review. These developments prompted us to examine emerging models of peer review from a range of disciplines and venues, and to ask how they might address some of the issues with our current systems of peer review. We examine the functionality of a range of social Web platforms, and compare these with the traits underlying a viable peer review system: quality control, quantified performance metrics as engagement incentives, and certification and reputation. Ideally, any new systems will demonstrate that they out-perform and reduce the biases of existing models as much as possible. We conclude that there is considerable scope for new peer review initiatives to be developed, each with their own potential issues and advantages. We also propose a novel hybrid platform model that could, at least partially, resolve many of the socio-technical issues associated with peer review, and potentially disrupt the entire scholarly communication system. Success for any such development relies on reaching a critical threshold of research community engagement with both the process and the platform, and therefore cannot be achieved without a significant change of incentives in research environments.

A multi-disciplinary perspective on emergent and future innovations in peer review

Peer review of research articles is a core part of our scholarly communication system. In spite of its importance, the status and purpose of peer review is often contested. What is its role in our modern digital research and communications infrastructure? Does it perform to the high standards with which it is generally regarded? Studies of peer review have shown that it is prone to bias and abuse in numerous dimensions, frequently unreliable, and can fail to detect even fraudulent research. With the advent of Web technologies, we are now witnessing a phase of innovation and experimentation in our approaches to peer review. These developments prompted us to examine emerging models of peer review from a range of disciplines and venues, and to ask how they might address some of the issues with our current systems of peer review. We examine the functionality of a range of social Web platforms, and compare these with the traits underlying a viable peer review system: quality control, quantified performance metrics as engagement incentives, and certification and reputation. Ideally, any new systems will demonstrate that they out-perform current models while avoiding as many of the biases of existing systems as possible. We conclude that there is considerable scope for new peer review initiatives to be developed, each with their own potential issues and advantages. We also propose a novel hybrid platform model that, at least partially, resolves many of the technical and social issues associated with peer review, and can potentially disrupt the entire scholarly communication system. Success for any such development relies on reaching a critical threshold of research community engagement with both the process and the platform, and therefore cannot be achieved without a significant change of incentives in research environments.

A multi-disciplinary perspective on emergent and future innovations in peer review

Peer review of research articles is a core part of our scholarly communication system. In spite of its importance, the status and purpose of peer review is often contested. What is its role in our modern digital research and communications infrastructure? Does it perform to the high standards with which it is generally regarded? Studies of peer review have shown that it is prone to bias and abuse in numerous dimensions, frequently unreliable, and can fail to detect even fraudulent research. With the advent of web technologies, we are now witnessing a phase of innovation and experimentation in our approaches to peer review. These developments prompted us to examine emerging models of peer review from a range of disciplines and venues, and to ask how they might address some of the issues with our current systems of peer review. We examine the functionality of a range of social Web platforms, and compare these with the traits underlying a viable peer review system: quality control, quantified performance metrics as engagement incentives, and certification and reputation. Ideally, any new systems will demonstrate that they out-perform and reduce the biases of existing models as much as possible. We conclude that there is considerable scope for new peer review initiatives to be developed, each with their own potential issues and advantages. We also propose a novel hybrid platform model that could, at least partially, resolve many of the socio-technical issues associated with peer review, and potentially disrupt the entire scholarly communication system. Success for any such development relies on reaching a critical threshold of research community engagement with both the process and the platform, and therefore cannot be achieved without a significant change of incentives in research environments.

On the origin of nonequivalent states: How we can talk about preprints

Increasingly, preprints are at the center of conversations across the research ecosystem. But disagreements remain about the role they play. Do they “count” for research assessment? Is it ok to post preprints in more than one place? In this paper, we argue that these discussions often conflate two separate issues, the history of the manuscript and the status granted it by different communities. In this paper, we propose a new model that distinguishes the characteristics of the object, its “state”, from the subjective “standing” granted to it by different communities. This provides a way to discuss the difference in practices between communities, which will deliver more productive conversations and facilitate negotiation, as well as sharpening our focus on the role of different stakeholders on how to collectively improve the process of scholarly communications not only for preprints, but other forms of scholarly contributions.

Architecting the future of research communication: building the models and analytics for an open access future

As part of our Tenth Anniversary PLOS Biology Collection, PLOS' director of advocacy, Cameron Neylon, expounds on the need to improve and focus on our sharing infrastructure to maximize the reach of research communication.

Expert failure: re-evaluating research assessment

It is unlikely that there is any single objective measure of merit, so research assessment therefore requires new multivariate metrics that reflect the context of research, regardless of discipline.

LabTrove: a lightweight, web based, laboratory "blog" as a route towards a marked up record of work in a bioscience research laboratory

BACKGROUND

The electronic laboratory notebook (ELN) has the potential to replace the paper notebook with a marked-up digital record that can be searched and shared. However, it is a challenge to achieve these benefits without losing the usability and flexibility of traditional paper notebooks. We investigate a blog-based platform that addresses the issues associated with the development of a flexible system for recording scientific research.

METHODOLOGY/PRINCIPAL FINDINGS

We chose a blog-based approach with the journal characteristics of traditional notebooks in mind, recognizing the potential for linking together procedures, materials, samples, observations, data, and analysis reports. We implemented the LabTrove blog system as a server process written in PHP, using a MySQL database to persist posts and other research objects. We incorporated a metadata framework that is both extensible and flexible while promoting consistency and structure where appropriate. Our experience thus far is that LabTrove is capable of providing a successful electronic laboratory recording system.

CONCLUSIONS/SIGNIFICANCE

LabTrove implements a one-item one-post system, which enables us to uniquely identify each element of the research record, such as data, samples, and protocols. This unique association between a post and a research element affords advantages for monitoring the use of materials and samples and for inspecting research processes. The combination of the one-item one-post system, consistent metadata, and full-text search provides us with a much more effective record than a paper notebook. The LabTrove approach provides a route towards reconciling the tensions and challenges that lie ahead in working towards the long-term goals for ELNs. LabTrove, an electronic laboratory notebook (ELN) system from the Smart Research Framework, based on a blog-type framework with full access control, facilitates the scientific experimental recording requirements for reproducibility, reuse, repurposing, and redeployment.

Selected wheat seed defense proteins exhibit competitive binding to model microbial lipid interfaces

Puroindolines (Pins) and purothionins (Pths) are basic, amphiphilic, cysteine-rich wheat proteins that play a role in plant defense against microbial pathogens. This study examined the co-adsorption and sequential addition of Pins (Pin-a, Pin-b, and a mutant form of Pin-b with Trp-44 to Arg-44 substitution) and β-purothionin (β-Pth) model anionic lipid layers using a combination of surface pressure measurements, external reflection FTIR spectroscopy, and neutron reflectometry. Results highlighted differences in the protein binding mechanisms and in the competitive binding and penetration of lipid layers between respective Pins and β-Pth. Pin-a formed a blanket-like layer of protein below the lipid surface that resulted in the reduction or inhibition of β-Pth penetration of the lipid layer. Wild-type Pin-b participated in co-operative binding with β-Pth, whereas the mutant Pin-b did not bind to the lipid layer in the presence of β-Pth. The results provide further insight into the role of hydrophobic and cationic amino acid residues in antimicrobial activity.

The role of protein hydrophobicity in thionin-phospholipid interactions: a comparison of α1 and α2-purothionin adsorbed anionic phospholipid monolayers

The plant defence proteins α1- and α2-purothionin (Pth) are type 1 thionins from common wheat (Triticum aestivum). These highly homologous proteins possess characteristics common amongst antimicrobial peptides and proteins, that is, cationic charge, amphiphilicity and hydrophobicity. Both α1- and α2-Pth possess the same net charge, but differ in relative hydrophobicity as determined by C18 reversed phase HPLC. Brewster angle microscopy, X-ray and neutron reflectometry, external reflection FTIR and associated surface pressure measurements demonstrated that α1 and α2-Pth interact strongly with condensed phase 1,2-dipalmitoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DPPG) monolayers at the air/liquid interface. Both thionins disrupted the in-plane structure of the anionic phospholipid monolayers, removing lipid during this process and both penetrated the lipid monolayer in addition to adsorbing as a single protein layer to the lipid head-group. However, analysis of the interfacial structures revealed that the α2-Pth showed faster disruption of the lipid film and removed more phospholipid (12%) from the interface than α1-Pth. Correlating the protein properties and lipid binding activity suggests that hydrophobicity plays a key role in the membrane lipid removal activity of thionins.

Three stories about the conduct of science: Past, future, and present

In this piece I would like to tell a few stories; three stories to be precise. Firstly I want to explain where I am, where I've come from and what has led me to the views that I hold today. I find myself at an interesting point in my life and career at the same point as the research community is undergoing massive change. The second story is one of what the world might look like at some point in the future. What might we achieve? What might it look like? And what will be possible? Finally I want to ask the question of how we get there from here. What is the unifying idea or movement that actually has the potential to carry us forward in a positive way? At the end of this I'm going to ask you, the reader, to commit to something as part of the process of making that happen.

Applying neutral drift to the directed molecular evolution of a β-glucuronidase into a β-galactosidase: Two different evolutionary pathways lead to the same variant

Background

Directed protein evolution has been used to modify protein activity and research has been carried out to enhance the production of high quality mutant libraries. Many theoretical approaches suggest that allowing a population to undergo neutral selection may be valuable in directed evolution experiments.

Findings

Here we report on an investigation into the value of neutral selection in a classical model system for directed evolution, the conversion of the E. coli β-glucuronidase to a β-galactosidase activity. We find that neutral selection, i.e. selection for retaining glucuronidase activity, can efficiently identify the majority of sites of mutation that have been identified as beneficial for galactosidase activity in previous experiments. Each variant demonstrating increased galactosidase activity identified by our neutral drift experiments contained a mutation at one of four sites, T509, S557, N566 or W529. All of these sites have previously been identified using direct selection for beta galactosidase activity.

Conclusions

Our results are consistent with others that show that a neutral selection approach can be effective in selecting improved variants. However, we interpret our results to show that neutral selection is, in this case, not a more efficient approach than conventional directed evolution approaches. However, the neutral approach is likely to be beneficial when the resulting library can be screened for a range of related activities. More detailed statistical studies to resolve the apparent differences between this system and others are likely to be a fruitful avenue for future research.

Puroindoline-a, a lipid binding protein from common wheat, spontaneously forms prolate protein micelles in solution

The self-assembly in solution of puroindoline-a (Pin-a), an amphiphilic lipid binding protein from common wheat, was investigated by small angle neutron scattering, dynamic light scattering and size exclusion chromatography. Pin-a was found to form monodisperse prolate ellipsoidal micelles with a major axial radius of 112 ± 4.5 Å and minor axial radius of 40.4 ± 0.18 Å. These protein micelles were formed by the spontaneous self-assembly of 38 Pin-a molecules in solution and were stable over a wide pH range (3.5-11) and at elevated temperatures (20-65 °C). Pin-a micelles could be disrupted upon addition of the non-ionic surfactant dodecyl-β-maltoside, suggesting that the protein self-assembly is driven by hydrophobic forces, consisting of intermolecular interactions between Trp residues located within a well-defined Trp-rich domain of Pin-a.

Introducing structural flexibility into porphyrin-DNA zipper arrays

A more flexible nucleotide building block for the synthesis of new DNA based porphyrin-zipper arrays is described. Changing the rigid acetylene linker between the porphyrin substituent and the 2'-deoxyuridine to a more flexible propargyl amide containing linkage leads in part to an increased duplex stability. The CD spectra reveal different electronic interactions between the porphyrins depending on the type of linker used. Molecular modelling suggests large variation of the relative orientation of the porphyrins within the major groove of the DNA. The porphyrins can be metallated post-synthetically with different metals as shown with zinc, cobalt and copper. The spectroscopic features do not alter drastically upon metallation apart from the CD spectra, and the stability of the metal complex is highly dependent on the nature of the metal. As shown by CD spectroscopy, the zinc porphyrin is rapidly demetallated at high temperatures. Globular structure determination using SAXS indicates that a molecular assembly comprised of a two to four helical bundle dominates in solution at higher concentrations (≥50 μM) which is not observed by spectroscopy at lower concentrations (≤1 μM).

Article-level metrics and the evolution of scientific impact

The authors discuss the value of article-level metrics in determining an article's scientific impact.

Head in the clouds: Re-imagining the experimental laboratory record for the web-based networked world

The means we use to record the process of carrying out research remains tied to the concept of a paginated paper notebook despite the advances over the past decade in web based communication and publication tools. The development of these tools offers an opportunity to re-imagine what the laboratory record would look like if it were re-built in a web-native form. In this paper I describe a distributed approach to the laboratory record based which uses the most appropriate tool available to house and publish each specific object created during the research process, whether they be a physical sample, a digital data object, or the record of how one was created from another. I propose that the web-native laboratory record would act as a feed of relationships between these items. This approach can be seen as complementary to, rather than competitive with, integrative approaches that aim to aggregate relevant objects together to describe knowledge. The potential for the recent announcement of the Google Wave protocol to have a significant impact on realizing this vision is discussed along with the issues of security and provenance that are raised by such an approach.

Thermal equivalence of DNA duplexes for probe design

We present the theory of thermal equivalence in the framework of the Peyrard-Bishop model and some of its anharmonic variants. The thermal equivalence gives rise to a melting index τ which maps closely the experimental DNA melting temperatures for short DNA sequences. We show that the efficient calculation of the melting index can be used to analyse the parameters of the Peyrard-Bishop model and propose an improved set of Morse potential parameters. With this new set we are able to calculate some of the experimental melting temperatures to ± 1.2 °C. We review some of the concepts of sequencing probe design and show how to use the melting index to explore the possibilities of gene coverage by tuning the model parameters.

New sources and instrumentation for neutrons in biology

Neutron radiation offers significant advantages for the study of biological molecular structure and dynamics. A broad and significant effort towards instrumental and methodological development to facilitate biology experiments at neutron sources worldwide is reviewed.

Open Science: tools, approaches, and implications

Open Science is gathering pace both as a grass roots effort amongst scientists to enable them to share the outputs of their research more effectively, and as a policy initiative for research funders to gain a greater return on their investment. In this workshop, we will discuss the current state of the art in collaborative research tools, the social challenges facing those adopting and advocating more openness, and the development of standards, policies and best practices for Open Science.