Characterizing interdisciplinarity of researchers and research topics using web search engines

Researchers' networks have been subject to active modeling and analysis. Earlier literature mostly focused on citation or co-authorship networks reconstructed from annotated scientific publication databases, which have several limitations. Recently, general-purpose web search engines have also been utilized to collect information about social networks. Here we reconstructed, using web search engines, a network representing the relatedness of researchers to their peers as well as to various research topics. Relatedness between researchers and research topics was characterized by visibility boost-increase of a researcher's visibility by focusing on a particular topic. It was observed that researchers who had high visibility boosts by the same research topic tended to be close to each other in their network. We calculated correlations between visibility boosts by research topics and researchers' interdisciplinarity at the individual level (diversity of topics related to the researcher) and at the social level (his/her centrality in the researchers' network). We found that visibility boosts by certain research topics were positively correlated with researchers' individual-level interdisciplinarity despite their negative correlations with the general popularity of researchers. It was also found that visibility boosts by network-related topics had positive correlations with researchers' social-level interdisciplinarity. Research topics' correlations with researchers' individual- and social-level interdisciplinarities were found to be nearly independent from each other. These findings suggest that the notion of "interdisciplinarity" of a researcher should be understood as a multi-dimensional concept that should be evaluated using multiple assessment means.     

Empirical Study of Data Sharing by Authors Publishing in PLoS Journals

Background

Many journals now require authors share their data with other investigators, either by depositing the data in a public repository or making it freely available upon request. These policies are explicit, but remain largely untested. We sought to determine how well authors comply with such policies by requesting data from authors who had published in one of two journals with clear data sharing policies.

Methods and Findings

We requested data from ten investigators who had published in either PLoS Medicine or PLoS Clinical Trials. All responses were carefully documented. In the event that we were refused data, we reminded authors of the journal''s data sharing guidelines. If we did not receive a response to our initial request, a second request was made. Following the ten requests for raw data, three investigators did not respond, four authors responded and refused to share their data, two email addresses were no longer valid, and one author requested further details. A reminder of PLoS''s explicit requirement that authors share data did not change the reply from the four authors who initially refused. Only one author sent an original data set.

Conclusions

We received only one of ten raw data sets requested. This suggests that journal policies requiring data sharing do not lead to authors making their data sets available to independent investigators.     

DO AID AGENCIES HAVE AN ETHICAL DUTY TO COMPLY WITH RESEARCHERS? A RESPONSE TO RENNIE1

Medical AID organisations such as Médecins Sans Frontières receive several requests from individuals and international academic institutions to conduct research at their implementation sites in Africa. Do AID agencies have an ethical duty to comply with research requests? In this paper we respond to the views and constructed theories (albeit unfounded) of one such researcher, whose request to conduct research at one of our sites in the Democratic Republic of Congo was turned down.     

If We Share Data,Will Anyone Use Them? Data Sharing and Reuse in the Long Tail of Science and Technology

Research on practices to share and reuse data will inform the design of infrastructure to support data collection, management, and discovery in the long tail of science and technology. These are research domains in which data tend to be local in character, minimally structured, and minimally documented. We report on a ten-year study of the Center for Embedded Network Sensing (CENS), a National Science Foundation Science and Technology Center. We found that CENS researchers are willing to share their data, but few are asked to do so, and in only a few domain areas do their funders or journals require them to deposit data. Few repositories exist to accept data in CENS research areas.. Data sharing tends to occur only through interpersonal exchanges. CENS researchers obtain data from repositories, and occasionally from registries and individuals, to provide context, calibration, or other forms of background for their studies. Neither CENS researchers nor those who request access to CENS data appear to use external data for primary research questions or for replication of studies. CENS researchers are willing to share data if they receive credit and retain first rights to publish their results. Practices of releasing, sharing, and reusing of data in CENS reaffirm the gift culture of scholarship, in which goods are bartered between trusted colleagues rather than treated as commodities.     

How Are Academic Age,Productivity and Collaboration Related to Citing Behavior of Researchers?

References are an essential component of research articles and therefore of scientific communication. In this study we investigate referencing (citing) behavior in five diverse fields (astronomy, mathematics, robotics, ecology and economics) based on 213,756 core journal articles. At the macro level we find: (a) a steady increase in the number of references per article over the period studied (50 years), which in some fields is due to a higher rate of usage, while in others reflects longer articles and (b) an increase in all fields in the fraction of older, foundational references since the 1980s, with no obvious change in citing patterns associated with the introduction of the Internet. At the meso level we explore current (2006–2010) referencing behavior of different categories of authors (21,562 total) within each field, based on their academic age, productivity and collaborative practices. Contrary to some previous findings and expectations we find that senior researchers use references at the same rate as their junior colleagues, with similar rates of re-citation (use of same references in multiple papers). High Modified Price Index (MPI, which measures the speed of the research front more accurately than the traditional Price Index) of senior authors indicates that their research has the similar cutting-edge aspect as that of their younger colleagues. In all fields both the productive researchers and especially those who collaborate more use a significantly lower fraction of foundational references and have much higher MPI and lower re-citation rates, i.e., they are the ones pushing the research front regardless of researcher age. This paper introduces improved bibliometric methods to measure the speed of the research front, disambiguate lead authors in co-authored papers and decouple measures of productivity and collaboration.     

C-ME: a 3D community-based, real-time collaboration tool for scientific research and training

The need for effective collaboration tools is growing as multidisciplinary proteome-wide projects and distributed research teams become more common. The resulting data is often quite disparate, stored in separate locations, and not contextually related. Collaborative Molecular Modeling Environment (C-ME) is an interactive community-based collaboration system that allows researchers to organize information, visualize data on a two-dimensional (2-D) or three-dimensional (3-D) basis, and share and manage that information with collaborators in real time. C-ME stores the information in industry-standard databases that are immediately accessible by appropriate permission within the computer network directory service or anonymously across the internet through the C-ME application or through a web browser. The system addresses two important aspects of collaboration: context and information management. C-ME allows a researcher to use a 3-D atomic structure model or a 2-D image as a contextual basis on which to attach and share annotations to specific atoms or molecules or to specific regions of a 2-D image. These annotations provide additional information about the atomic structure or image data that can then be evaluated, amended or added to by other project members.     

The dilemma of the honest researcher

Most agree that without honest and trustworthy practitioners, research has no value. Yet high standards present a dilemma for honest researchers, because successful practices often clash with ethically impeccable behaviour.The honesty and trustworthiness of researchers is increasingly scrutinized as high-profile stories of research misconduct become public. Researchers, politicians and funders agree that dishonest and untrustworthy research has no value. However, the standards for judging integrity and the core values to which researchers should adhere are less clear.To help efforts to promote research integrity around the world, the second World Conference on Research Integrity in Singapore developed a statement as a checklist for researchers to assess their own behaviour, and to provide a framework for developing national and organizational guides, codes of conduct and research-integrity policies (World Conferences on Research Integrity, 2010).Yet standards for responsible behaviour in research pose a dilemma for the honest researcher, because many commonly accepted practices are at odds with ‘ideal'' behaviour. Although outright dishonesty is not the norm and for the most part not tolerated, less-than-honest behaviour is, and might even be necessary in today''s competitive research environment.To be funded, research must be innovative and important. The need to ‘sell'' a grant proposal can encourage overselling of the significance of data or the importance of likely outcomes. Support for basic research to decode the human genome was gained on the basis of claims of benefits to human health that many now regard as overly optimistic and unrealistic (Marshall, 2011). Clinical trials are often inconclusive, owing to overestimation of the effects of treatment (Djulbegovic et al, 2010). However, an honest researcher who makes modest claims or honestly describes likely obstacles might not be as competitive as one who provides the most-generous estimates of long-term benefits.The many rules that define best practice can seem to be counter-productive and burdensome. Securing funding requires the provision of compelling preliminary data, but research agencies often do not fund mere data collection. Is it therefore acceptable to collect preliminary data for the next project with funds awarded for the current project? If an institutional review board or research ethics committee places seemingly burdensome requirements on research with human subjects, is it acceptable to bend the rules to complete the project? Studies have shown that a significant number of researchers use this excuse for minor violations of requirements for human subjects (Keith-Spiegel & Koocher, 2005).Ideally, research should be collaborative. Public interest should take precedence over self interest, once intellectual and property interests have been protected. Nonetheless, researchers sometimes do not share information—a practice that has been shown to slow progress (Blumenthal, 2006). It is also alleged, but has not been confirmed empirically, that researchers sometimes provide insufficient or misleading information to slow the work of competitors. On the receiving end, researchers have been known to take unfair advantage of privileged information from peer review.Honesty in research is particularly strained during formal publication. Less-than-honest practices include adding honorary names to the author list; failing to include the names of individuals who made significant contributions, such as industry ghostwriters; misrepresenting findings in abstracts; dividing one project into several publications to enhance a resume; failing to list conflicts of interest; and publishing the same work more than once without adequate notification. Research publications are sliced, diced and wrapped in many ways. When these practices come to be common, it is difficult for the honest researcher not to fall in line.However, before falling into line too quickly, there are two consequences that scientists ought to consider. All questionable practices could, under particular circumstances, be classed as misconduct, particularly if they are engaged in widely and often. One small compromise might not be important, but several larger ones could be. Moreover, acting less than honestly can be a first step down a slippery slope towards misconduct. When researchers engage in common, but not necessarily proper, practices, they need to be aware of what they are doing and the possible consequences. Right and wrong can be too easily confused.Misconduct in research was not new when it first received public attention in the 1970s and 1980s. The fact that it had been either ignored or tolerated by researchers and research institutions led governments around the world to implement regulations. Much the same scenario has followed in relation to conflicts of interest, dual-use research, and other areas in which integrity and the professional conduct of researchers have been questioned. Researchers need to face up to the conflict between professed commitments to high standards for research integrity and widespread tolerance of practices that fall short of these standards. Doing so is essential to preserving public confidence in research and to reducing, if not eliminating, the dilemma faced by the honest researcher.     

Review by a local medical research ethics committee of the conduct of approved research projects,by examination of patients' case notes,consent forms,and research records and by interview.

OBJECTIVE: To monitor the conduct of medical research projects that have already been approved by the local medical research ethics committee. DESIGN: Follow up study of ethically approved studies (randomly selected from all the studies approved in the previous year) by examination of patients'' case notes, consent forms, and research records and by interview of the researchers at their workplace. SETTING: Tayside, Scotland (mixed rural and urban population). SUBJECTS: 30 research projects approved by Tayside local medical research ethics committee. MAIN OUTCOME MEASURES: Adherence to the agreed protocol, particularly for recruitment (obtaining and recording informed consent) and for specific requirements of the ethics committee, including notification of changes to the protocol and of adverse events. RESULTS: In one project only oral consent had been obtained, and in a quarter of the studies one or more consent forms were incorrectly completed. Inadequate filing of case notes in five studies and of consent forms in six made them unavailable for scrutiny. Adverse events were reported, but there was a general failure to report the abandoning or non-starting of projects in two studies the investigators failed to notify a change in the responsible researcher. CONCLUSIONS: Monitoring of medical research by local medical research ethics committees promotes and preserves ethical standards, protects subjects and researchers, discourages fraud, and has the support of investigators. We recommend that 10% of projects should undergo on-site review, with all others monitored by questionnaire. This would require about six person hours of time and a salary bill of 120 pounds per study monitored.     

The protein kinase resource and other bioinformation resources

The Internet, especially the World Wide Web has transformed how today's researchers communicate, share information, and analyze their data. Unfortunately, the vast number of online databases, information resources and analytical tools, some of them masked by unfamiliar titles and Internet addresses, has hindered their universal and effective use by the research community. To overcome these hurdles, subject- and function-specific compendiums are now available which organize information and online tolls in a manner familiar to the biological researcher. The Protein Kinase Resource and the CMS Molecular Biology Resource are two excellent examples of web compendia.     

Funding resources for rare disease research

Research is an expensive venture requiring multiple sources of funding for small projects that test new theories, large projects to make major advancements, training the next generation of researchers and facilitating meetings to share findings and support collaboration. For rare conditions, such as Batten disease, research funds can be difficult to find.To see how investigators supported their work in the past, we did a key word search of the Acknowledgement Section of peer-reviewed literature published in Batten disease in the last 6.5 years. Interestingly, we discovered 193 separate funding sources. The authors hope that, by showing where funds are available, we will enable Batten disease researchers to continue their pursuits and expand their studies; moving key findings from discovery to application phases. This article is part of a Special Issue entitled: The Neuronal Ceroid Lipofuscinoses or Batten Disease.     

Researcher Perspectives on Publication and Peer Review of Data

Data “publication” seeks to appropriate the prestige of authorship in the peer-reviewed literature to reward researchers who create useful and well-documented datasets. The scholarly communication community has embraced data publication as an incentive to document and share data. But, numerous new and ongoing experiments in implementation have not yet resolved what a data publication should be, when data should be peer-reviewed, or how data peer review should work. While researchers have been surveyed extensively regarding data management and sharing, their perceptions and expectations of data publication are largely unknown. To bring this important yet neglected perspective into the conversation, we surveyed ∼ 250 researchers across the sciences and social sciences– asking what expectations“data publication” raises and what features would be useful to evaluate the trustworthiness, evaluate the impact, and enhance the prestige of a data publication. We found that researcher expectations of data publication center on availability, generally through an open database or repository. Few respondents expected published data to be peer-reviewed, but peer-reviewed data enjoyed much greater trust and prestige. The importance of adequate metadata was acknowledged, in that almost all respondents expected data peer review to include evaluation of the data’s documentation. Formal citation in the reference list was affirmed by most respondents as the proper way to credit dataset creators. Citation count was viewed as the most useful measure of impact, but download count was seen as nearly as valuable. These results offer practical guidance for data publishers seeking to meet researcher expectations and enhance the value of published data.     

Mapping Public Engagement with Research in a UK University

Notwithstanding that ‘public engagement’ is conceptualised differently internationally and in different academic disciplines, higher education institutions largely accept the importance of public engagement with research. However, there is limited evidence on how researchers conceptualise engagement, their views on what constitutes engagement and the communities they would (or would not) like to engage with. This paper presents the results of a survey of researchers in the Open University that sought to gather data to fill these gaps. This research was part of an action research project designed to embed engagement in the routine practices of researchers at all levels. The findings indicate that researchers have a relatively narrow view of public engagement with research and the communities with which they interact. It also identified that very few strategically evaluate their public engagement activities. We conclude by discussing some of the interventions we have introduced with the aim of broadening and deepening future researcher engagement.     

To Share or Not to Share? A Survey of Biomedical Researchers in the U.S. Southwest,an Ethnically Diverse Region

Background

Cancer health disparities research depends on access to biospecimens from diverse racial/ethnic populations. This multimethodological study, using mixed methods for quantitative and qualitative analysis of survey results, assessed barriers, concerns, and practices for sharing biospecimens/data among researchers working with biospecimens from minority populations in a 5 state region of the United States (Arizona, Colorado, New Mexico, Oklahoma, and Texas). The ultimate goals of this research were to understand data sharing barriers among biomedical researchers; guide strategies to increase participation in biospecimen research; and strengthen collaborative opportunities among researchers.

Methods and Population

Email invitations to anonymous participants (n = 605 individuals identified by the NIH RePORT database), resulted in 112 responses. The survey assessed demographics, specimen collection data, and attitudes about virtual biorepositories. Respondents were primarily principal investigators at PhD granting institutions (91.1%) conducting basic (62.3%) research; most were non-Hispanic White (63.4%) and men (60.6%). The low response rate limited the statistical power of the analyses, further the number of respondents for each survey question was variable.

Results

Findings from this study identified barriers to biospecimen research, including lack of access to sufficient biospecimens, and limited availability of diverse tissue samples. Many of these barriers can be attributed to poor annotation of biospecimens, and researchers’ unwillingness to share existing collections. Addressing these barriers to accessing biospecimens is essential to combating cancer in general and cancer health disparities in particular. This study confirmed researchers’ willingness to participate in a virtual biorepository (n = 50 respondents agreed). However, researchers in this region listed clear specifications for establishing and using such a biorepository: specifications related to standardized procedures, funding, and protections of human subjects and intellectual property. The results help guide strategies to increase data sharing behaviors and to increase participation of researchers with multiethnic biospecimen collections in collaborative research endeavors

Conclusions

Data sharing by researchers is essential to leveraging knowledge and resources needed for the advancement of research on cancer health disparities. Although U.S. funding entities have guidelines for data and resource sharing, future efforts should address researcher preferences in order to promote collaboration to address cancer health disparities.     

PSI:Biology-materials repository: a biologist’s resource for protein expression plasmids

The Protein Structure Initiative:Biology-Materials Repository (PSI:Biology-MR; MR; ) sequence-verifies, annotates, stores, and distributes the protein expression plasmids and vectors created by the Protein Structure Initiative (PSI). The MR has developed an informatics and sample processing pipeline that manages this process for thousands of samples per month from nearly a dozen PSI centers. DNASU (), a freely searchable database, stores the plasmid annotations, which include the full-length sequence, vector information, and associated publications for over 130,000 plasmids created by our laboratory, by the PSI and other consortia, and by individual laboratories for distribution to researchers worldwide. Each plasmid links to external resources, including the PSI Structural Biology Knowledgebase (), which facilitates cross-referencing of a particular plasmid to additional protein annotations and experimental data. To expedite and simplify plasmid requests, the MR uses an expedited material transfer agreement (EP-MTA) network, where researchers from network institutions can order and receive PSI plasmids without institutional delays. As of March 2011, over 39,000 protein expression plasmids and 78 empty vectors from the PSI are available upon request from DNASU. Overall, the MR’s repository of expression-ready plasmids, its automated pipeline, and the rapid process for receiving and distributing these plasmids more effectively allows the research community to dissect the biological function of proteins whose structures have been studied by the PSI.     

Evaluating the Consent Preferences of UK Research Volunteers for Genetic and Clinical Studies

Objectives

To establish the views of research volunteers on the consent process; to explore their views on the consent process in different research scenarios; to inform debate on emerging models of consent for participation in research.

Design, Setting and Participants

2,308 adult volunteers from the TwinsUK Registry (www.twinsuk.ac.uk) completed an online survey about their views on the consent process for use of their DNA and medical information in research. Their views on the re-consenting process in different scenarios were assessed.

Results

The majority of volunteers preferred to be informed of the identity of the main researcher of a study in which they are participating, which is contrary to current practice. Over 80% were willing to complete the consent process online instead of face to face. On the whole, respondents did not view their DNA differently from their medical information with regard to the consent process. Research participants were more willing to give broad consent to cover future research if their DNA was to be used by the original researcher than by another researcher, even if the disease under investigation varied, in contrast to the traditional ‘gold standard’ whereby specific consent is required for all new research projects.

Discussion

In some scenarios, research participants reported that they would be comfortable with not signing a new consent form for future research uses of their data and DNA, and are comfortable with secure, online consent processes rather than traditional face-to-face consent processes. Our findings indicate that the perceived relationship between research participants and researchers plays an important role in shaping preferences regarding the consent process and suggest that this relationship is not captured by traditional consent processes. We argue that the development of new formats of consent should be informed by empirical research on volunteers’ perceptions and preferences regarding the consent process.     

Share the details of your experimental methods

Incomplete methods sections have made it difficult for researchers to replicate and build on the work of others, contributing to problems in reproducibility. It is important to increase the level of detail in our methods sections and to share step-by-step protocols in protocol repositories or journals. Request a Protocol is a new feature in Molecular Biology of the Cell that allows readers to request detailed protocols directly from the methods section of the research article, with links between the protocols and the research articles, and has the potential to improve research reproducibility and help everyone design and execute robust life science experiments.     

ISBP: Understanding the Security Rule of Users' Information-Sharing Behaviors in Partnership

The rapid growth of social network data has given rise to high security awareness among users, especially when they exchange and share their personal information. However, because users have different feelings about sharing their information, they are often puzzled about who their partners for exchanging information can be and what information they can share. Is it possible to assist users in forming a partnership network in which they can exchange and share information with little worry? We propose a modified information sharing behavior prediction (ISBP) model that can help in understanding the underlying rules by which users share their information with partners in light of three common aspects: what types of items users are likely to share, what characteristics of users make them likely to share information, and what features of users’ sharing behavior are easy to predict. This model is applied with machine learning techniques in WEKA to predict users’ decisions pertaining to information sharing behavior and form them into trustable partnership networks by learning their features. In the experiment section, by using two real-life datasets consisting of citizens’ sharing behavior, we identify the effect of highly sensitive requests on sharing behavior adjacent to individual variables: the younger participants’ partners are more difficult to predict than those of the older participants, whereas the partners of people who are not computer majors are easier to predict than those of people who are computer majors. Based on these findings, we believe that it is necessary and feasible to offer users personalized suggestions on information sharing decisions, and this is pioneering work that could benefit college researchers focusing on user-centric strategies and website owners who want to collect more user information without raising their privacy awareness or losing their trustworthiness.     

Surface EMG recordings and pain-related disorders: A diagnostic framework

Surface electromyography provides a very valuable set of information when used diagnostically with pain-related disorders. Unfortunately, most researchers and clinicians limit their investigation to only one level of diagnostic information available concerning the neuromuscular system. This article develops and encourages the clinician/researcher to consider three levels of diagnostic information: emotional, organ-related, and postural aspects. The theoretical background and diagnostic procedures used to investigate each is presented. Differential treatment considerations, given differential diagnostic findings, are discussed.     

Surface EMG recordings and pain-related disorders: a diagnostic framework

Surface electromyography provides a very valuable set of information when used diagnostically with pain-related disorders. Unfortunately, most researchers and clinicians limit their investigation to only one level of diagnostic information available concerning the neuromuscular system. This article develops and encourages the clinician/researcher to consider three levels of diagnostic information: emotional, organ-related, and postural aspects. The theoretical background and diagnostic procedures used to investigate each is presented. Differential treatment considerations, given differential diagnostic findings, are discussed.     

Case studies in reproducibility

Reproducible research is a concept of providing access to data and software along with published scientific findings. By means of some case studies from different disciplines, we will illustrate reasons why readers should be given the possibility to look at the data and software independently from the authors of the original publication. We report results of a survey comprising 100 papers recently published in Bioinformatics. The main finding is that authors of this journal share a culture of making data available. However, the number of papers where source code for simulation studies or analyzes is available is still rather limited.