Frontiers | neuPrint: An open access tool for EM connectomics

Abstract:  Due to advances in electron microscopy and deep learning, it is now practical to reconstruct a connectome, a description of neurons and the chemical synapses between them, for significant volumes of neural tissue. Smaller past reconstructions were primarily used by domain experts, could be handled by downloading data, and performance was not a serious problem. But new and much larger reconstructions upend these assumptions. These networks now contain tens of thousands of neurons and tens of millions of connections, with yet larger reconstructions pending, and are of interest to a large community of non-specialists. Allowing other scientists to make use of this data needs more than publication—it requires new tools that are publicly available, easy to use, and efficiently handle large data. We introduce neuPrint to address these data analysis challenges. Neuprint contains two major components—a web interface and programmer APIs. The web interface is designed to allow any scientist worldwide, using only a browser, to quickly ask and answer typical biological queries about a connectome. The neuPrint APIs allow more computer-savvy scientists to make more complex or higher volume queries. NeuPrint also provides features for assessing reconstruction quality. Internally, neuPrint organizes connectome data as a graph stored in a neo4j database. This gives high performance for typical queries, provides access though a public and well documented query language Cypher, and will extend well to future larger connectomics databases. Our experience is also an experiment in open science. We find a significant fraction of the readers of the article proceed to examine the data directly. In our case preprints worked exactly as intended, with data inquiries and PDF downloads starting immediately after pre-print publication, and little affected by formal publication later. From this we deduce that many readers are more interested in our data than in our analysis of our data, suggesting that data-only papers can be well appreciated and that public data release can speed up the propagation of scientific results by many months. We also find that providing, and keeping, the data available for online access imposes substantial additional costs to connectomics research.

 

EU/EEA routine surveillance open data policy

“Aggregate EU/EEA epidemiological routine surveillance data shall be:

As open as possible and as closed as necessary to protect personal or commercially sensitive information;
Compatible with the FAIR principles, i.e. findable, accessible, interoperable and reusable;
Publicly and easily accessible to any interested party regardless of their motivation;
Accessible free of charge through a standardised open access license;
Shared as timely as possible….”

Early sharing not the only driver for preprint use | Research Information

“But what is interesting, is that while early sharing came out as important for authors, it is not their only driving motivator when using and selecting such services and adopting more open research practices. Authors are looking for more integrated services and want those platforms to offer multiple features that not only enhance the sharing, development and discoverability of their work, but also enable them to track and monitor its progress:   

Transparency was the top feature for authors when selecting an integrated preprint service:

71 per cent of authors said that greater transparency of the peer review process at journals was useful. Through its integration with peer review, In Review enables authors to see specific details of peer review and track their article, providing a high level of transparency into an often ‘hidden’ process.

50 per cent of authors said that the more transparent the service was, the more they felt it was credible, as it enabled greater accountability for the journal

Integrated early sharing – authors surveyed stated that ease of use (69 per cent) and being able to share their manuscript as a preprint at the same time as submitting it to a journal (BMC/ Springer journals) (83 per cent) had an impact on where they choose to take their work. We also learnt that this type of integrated solution is attractive for researchers in LMICs and early career researchers….”

Modern geoscience publishing – GEOSCIENTIST

“The preprint is the initial version of a research article, often (but not always) before submission to a journal and before formal peer-review. Preprints help modernise geoscience by removing barriers that inhibit broad participation in the scientific process, and which are slowing progress towards a more open and transparent research culture. …

Preprints have many well-documented benefits for both researchers and the public (e.g., Bourne et al., 2017; Sarabipour et al., 2019; Pourret et al., 2020). For example, preprints enable:

 

• Rapid sharing of research results, which can be critical for time-sensitive studies (such as after disasters), as well as for early career researchers applying for jobs, or any academic applying for grants or a promotion, given that journal-led peer review can take many months to years;
• Greater visibility and accessibility for research outputs, given there is no charge for posting or reading a preprint, especially for those who do not have access to pay-walled journals, or limited access due to remote working (such as during lockdowns);
• Additional peer feedback beyond that provided by journal-led peer review, enhancing the possibility of collaboration via community input and discussion;
• Researchers to establish priority (or a precedent) on their results, mitigating the chance of being ‘scooped’;
• Breakdown of the silos that traditional journals uphold, by exposing us to broader research than we might encounter otherwise, and giving a home to works that do not have a clear destination in a traditional publication;
• Research to be more open and transparent, with the intention of improving the overall quality, integrity, and reproducibility of results. …”

Why preprints are good for patients | Nature Medicine

“Rapid communication of clinical trial results has likely saved lives during the COVID-19 pandemic and should become the new norm….

But during health emergencies, there are many tensions, one of which is the mismatch between the urgent need for information and evidence and the much longer time frames of scientific peer review and publication. The COVID-19 pandemic is the first global health emergency of the new information age, with data and results widely shared via social media. This has resulted in very real difficulties in distinguishing important information from noise, and real news from fake news. How should the research and medical community best manage this new reality?…

Some may argue that the speed advantage of preprints does not outweigh the risks of poor-quality, misleading or even fraudulent research being published and acted upon. I would counter that clinicians should not rely solely on peer review to assess the validity and meaningfulness of research findings. This is because dubious, perhaps fraudulent data can still get through peer review, as was seen with early COVID papers published and then retracted from two of the most prestigious medical journals. In addition, even valid data can be misleading. There has been an avalanche of observational data that passed peer review and was then used to justify treatments, most notably with hydroxychloroquine, but the susceptibility of observational methodology to moderate biases means that such data should not be the basis of patient care.

I take two lessons from our experience running the largest COVID-19 clinical trial over the last two years. The first is that that the preprint system has come of age, demonstrating huge value in rapidly communicating important research findings. Almost daily I am alerted through social media alerts from trusted sources and colleagues of important new findings published as preprints. A degree of immediate peer review is also available by means of the preprint comments section and from colleagues via social media. The full peer-reviewed manuscripts usually appear many weeks or even months later. I cannot envisage a future without such rapid dissemination of new evidence.

 

Given this new reality, the second lesson is that we must ensure that the medical community and policy makers are sufficiently skilled in critical thinking and scientific methods that they can make sensible decisions, regardless of whether an article is peer reviewed or not.”

Need for universal acceptance of preprinting by editors of journals of health professional education | SpringerLink

“While publishers in multiple fields are adopting preprints [2], we have discovered a great deal of confusion about the pros and cons of preprinting as well as disparity in publishers’ policies regarding preprinting in health professions education (HPE). In seeking to resolve this confusion, we documented preprint policies at 74 journals within HPE (e.g. nursing, medicine, pharmacy, dentistry, rehabilitation sciences, nutrition). We culled preprint policies for 43 (58%) journals using journal websites, JISC’s Sherpa Romeo tool, and Wikipedia’s list of academic publishers by preprint policy. We then obtained information from email solicitations for an additional 27 (36%), leaving us without information for 4 (5%). Of the 70 journals for which we have information, 53 (76%) will review/accept preprinted manuscripts; 11 (16%) do not, and 6 (9%) are unclear or make decisions on a case-by-case basis. (For a link to our list of HPE journals and our understanding of their policies regarding preprinted manuscripts, see https://jahse.med.utah.edu/submission/ and select “Where to Publish”.) No wonder there is confusion.

We encourage our colleagues across the health professions to join our call to eliminate this confusion by encouraging all HPE journals to support and promote preprinting. The value of preprinting has only become more important during the COVID-19 pandemic [3]. Being able to preprint scholarship prior to formal submission enhances formative review and revision, augments the benefits of peer coaching, and promotes higher quality publications. Preprinting also makes work available to others more quickly, which can enhance collaboration and uptake of new ideas without compromising the eventual copyright of the final published product.”

The rise of preprints — University Affairs

“Peer review, despite its flaws, is one of the most important pillars of the scientific process. So preprint servers, which make scientific papers that have yet to be reviewed or published available online, have been slow to catch on in many fields.

But then came the pandemic.

“COVID changed everything,” says Jim Handman, executive director of the Science Media Centre of Canada. Scientists, science communicators, and journalists who had been wary of using preprints in the past suddenly felt the urgency to get important new information out as fast as possible to help deal with the unprecedented public health threat. The use of preprint servers skyrocketed. Now, everyone is adapting to this new way of working, developing best practices to harness the benefits of increased speed and wider reach while mitigating the risks of sharing unreviewed science.

Most of the time, the world of scholarly publishing moves at an almost glacial pace. New publications can take months or even years to wind their way through the process of peer review and publication. Even then, they can be hard to access for most people. So 30 years ago, some scientists started posting their work in online repositories before it had been formally reviewed and published. ArXiv, which shares research on math, physics, and astronomy, was the first to launch in 1991. It was followed by repositories for other subject areas over the next few decades….”

Dismantling the ivory tower’s knowledge boundaries

“The major shift to open access during the pandemic began with the Free Read initiative, which launched the petition “

Unlock Coronavirus Research” for scientists in early February of 2020 and to which highly reputable medical publishers quickly responded. Before the pandemic, up to 75 percent of scholarly publications were behind a paywall. By comparison, a preliminary study of over 5,600 articles on PubMed suggests that more than 95 percent of scholarly articles related to COVID-19 are now freely available. This increase in accessibility resulted from the rapid adaptation by biomedical journals and publishers, including Elsevier, Springer Nature, Cell Press, New England Journal of Medicine, and The Lancet. These journals and publishers granted open access to research on COVID-19 research, often making it 

immediately accessible on the platform PubMed Central and similar public repositories. Free and open access to COVID-19 research quickly became the new normal for biomedicine, with available findings directly impacting the development of treatment protocols and vaccines. Yet the pandemic became more than a health crisis. Understanding the social, psychological, and economic implications of the pandemic were imperative to its continued management.

Social science research, which delivers insights into human behaviors, relationships, and institutions, was instrumental to policymaking and healthcare solution development during the COVID-19 pandemic. The importance of social science research to pandemic management was demonstrated by the 

shift in the topic of COVID-19 papers, from the initial focus on disease modeling, hospital mortality, diagnostics, and testing to an increasing focus on topics such as business closure, remote work, geographic mobility and migration, inequality, managerial decision-making, as well as accelerating innovation. Once the basic science on the virus were established, research on creating societal and economic resilience played an even larger role for beating the COVID-19 pandemic. One clear area that demonstrated the importance of social science research in informing COVID-19 management was the rollout of vaccines. Psychological, marketing, and information systems research played a central role in vaccine uptake across communities. A recent report by the National Institutes of Health called for the use of evidence-based strategies, such as 

behavioral nudges and strategic social norms, to increase vaccine uptake….”

 

 

Accelerating Open Science Together; Center for Open Science Impact Reports

“Amid continuing global challenges due to the pandemic, 2021 was another noteworthy year not only for COS, but for the broader research community. The theme, “Accelerating Open Science” is based on our observations of an accelerating shift toward openness-as-default. This shift is being driven by the collective, collaborative actions of researchers and stakeholders committed to providing research progress. The full Impact Report highlights our achievements, our relationships, and our community support, and we hope you’ll take the time to review it. Thank you for your individual and collective actions to change the default to open so that the scientific ideals are manifest and rewarded in everyday practice.”

Opening Up to Open Science

“This way of sharing science has some benefits: peer review, for example, helps to ensure (even if it never guarantees) scientific integrity and prevent inadvertent misuse of data or code. But the status quo also comes with clear costs: it creates barriers (in the form of publication paywalls), slows the pace of innovation, and limits the impact of research. Fast science is increasingly necessary, and with good reason. Technology has not only improved the speed at which science is carried out, but many of the problems scientists study, from climate change to COVID-19, demand urgency. Whether modeling the behavior of wildfires or developing a vaccine, the need for scientists to work together and share knowledge has never been greater. In this environment, the rapid dissemination of knowledge is critical; closed, siloed knowledge slows progress to a degree society cannot afford. Imagine the consequences today if, as in the 2003 SARS disease outbreak, the task of sequencing genomes still took months and tools for labs to share the results openly online didn’t exist. Today’s challenges require scientists to adapt and better recognize, facilitate, and reward collaboration….

This tension between individual and institutional incentives and the progress of science must be recognized and resolved in a manner that contributes to solving the great challenges of today and the future. To change the culture, researchers must do more than take a pledge; they must change the game—the structures, the policies, and the criteria for success. In a word, open science must be institutionalized….

A powerful open science story can be found in the World Climate Research Programme’s Coupled Model Intercomparison Project (CMIP), established in 1995. Before CMIP, with the internet in its infancy, climate model results were scattered around the world and difficult to access and use. CMIP inspired 40 modeling groups and about 1,000 researchers to collaborate on advancing modeling techniques and setting guidelines for how and where to share results openly. That simple step led to an unexpected transformation: as more people were able to access the data, the community expanded, and more groups contributed data to CMIP. More people asking questions and pointing out issues in their results helped drive improvements. In its assessment reports, the Intergovernmental Panel on Climate Change relied on research publications using CMIP data to assess climate change. As a platform, CMIP enabled thousands of scientists to work together, self-correct their work, and create further ways to collaborate—a virtuous circle that attracted more scientists and more data, and increased the speed and usefulness of the work….

The most important message from these reports is that all parts of science, from individual researchers to universities and funding agencies, need to coordinate their efforts to ensure that early adopters aren’t jeopardizing their careers by joining the open science community. The whole enterprise has to change to truly realize the full benefits of open science. Creating this level of institutional adoption also requires updating policies, providing training, and recognizing and rewarding collaborative science….”

Is Canada ready for open access? — University Affairs

“Canadian science could benefit enormously if all research articles in the country were made freely available to anyone immediately upon publication. But there are significant barriers that need to be overcome to achieve this.

Last year, 30 per cent of Canadian research was published as paid open access (OA). That’s slightly below the global average of 34 per cent but trailing many other high research output countries such as Sweden (54 per cent), Netherlands (50 per cent) and the United Kingdom (48 per cent), according to the  dimensions.ai database. As one of the top-quality research output countries in the world, according to Nature Index, Canada should be doing better. In our opinion, the fundamental reasons for the slow uptake of open access in Canada are (1) the lack of coordinated funding to support OA publishing, and (2) barriers that researchers face to publish in OA.

The Tri-Councils’ OA policy stipulates that any publications coming from research should be freely accessible within 12 months of publication. However, there is low compliance with this request. Researchers are expected to pay for open access via article publishing charges (APCs). As noted in the “Open Science Dialogues,” organized by the Office of the Chief Science Advisor (OCSA) to gain feedback on their Roadmap for Open Science, researchers are expected to pay these APCs from their research grants. Unfortunately, the APCs commanded by the high impact factor journals can represent an unfeasibly large percentage of the researchers’ total grant. APCs of US$5,000 to $10,000 are not uncommon for the prestige journals published by the large commercial publishers. But even the more moderate APCs of US$1,000 to $3,000 of lesser journals and those of not-for-profit publishers can also quickly deplete smaller research grants. For example, average NSERC grants in 2020 ranged from C$26,000 to $53,000, which leaves little room, if any, for the added expense of APCs….

The slow adoption of OA in Canada is probably not due to a lack of money per se. A back-of-the-envelope calculation of the number of Canadian articles being published as OA multiplied by the average APCs (from publisher websites), suggests that C$30-40 million was spent on OA publishing last year, 80 per cent of which was spent with the large commercial publishers….

So can Canada achieve a national OA strategy? We believe so, but to overcome the barriers we need an approach that captures the following principles:

Unity: bring together all stakeholders in the scientific research enterprise to establish a unified front and determine priorities, requirements and challenges.
Coordination: to move beyond consultation, there is a need for a coordinating body to establish a path forward, timelines, funding needs and to organize this collaborative action.
Evidence: There is an immediate need to assess data on costs, sources of funds being allocated to subscriptions and APCs, trends in OA publishing outputs, and to determine if there is sufficient existing funding to support a full switch to OA….”

Substantial delays in clinical data published by the European Medicines Agency – a cross sectional study – Journal of Clinical Epidemiology

Abstract:  

Background

Reporting bias poses a fundamental threat to the transparency and validity of interpretations of clinical trials, which may, in part, be mitigated through access Clinical Study Reports (CSRs). The European Medicines Agency (EMA), under their Policy 0070, prospectively publishes clinical data, including CSRs, submitted as part of marketing authorization applications or post-authorization procedures, although this practice is currently suspended for non-COVID-19 medicines, and have set out planned timelines for publication.

 

Methods

We conducted a cross-sectional study assessing the content and characteristics of all clinical data packages released by the EMA under Policy 0070 and the time to their publication. We extracted the number and characteristics of trials included in the clinical packages, assessed the delay to publication relative to the EMAs planned timeline and whether it differed between the EMAs various transparency measures and types of application procedures.

 

Results

We identified 148 clinical data packages that contained data on a total of 1,005 clinical trials, of which 261 (26%) were labelled as phase 3 trials. Full CSRs were available for 913 (90•8%) of the trials. The median time to publication was 511 (IQR 411 to 574) days. Only 2 (1•4%) of the clinical data packages were published within the EMA’s planned timeline. The delay was shorter for clinical data packages released under the EMAs transparency measures for COVID.19 medicines compared with their standard transparency measure.

 

Conclusion

The clinical data packages released by the EMA under Policy 0070 contained CSRs on many trials but were published with considerable delays relative to the timeline set forth by the EMA, reducing their potential impact on reporting bias.

Highlights from 5 years of publishing | Wellcome Open Research Blog

“2021 marked another successful year for the Wellcome Open Research (WOR) publishing platform. Publication output on WOR continued to grow, with the diversity of research outputs published increasing. The Platform showcases the broad portfolio of research that Wellcome funds.

In this blog, Hannah Hope, Open Research Lead at Wellcome Trust, provides an overview of WOR’s publishing activity of the past year as well as the initiatives we plan to implement in 2022….

This growth has enabled us to continue to be the most used publication venue (by volume of articles) for Wellcome-funded researchers according to Europe PMC and Dimensions data….”

 

Accelerating Open Research: A Multi-stakeholder Discussion – The Scholarly Kitchen

“As we move through a transition to a fully open research environment, there are challenges for all stakeholders in the ecosystem. Many funders have taken a leadership role in driving this transition, yet even with funder mandates in place for nearly two decades, the transition to open research globally has been slow (Larivière and Sugimoto, 2018). 

A recent study led by the Research on Research Institute (Waltman et al., 2021 ) found that commitments to open research and data sharing fell short during the pandemic and that lack of collaboration was a key factor. 

On the 10th February 2022, the Society for Scholarly Publishing (SSP) Publisher-Funder Task Force convened a closed forum of funders, publishers, librarians and academics to discuss how collaborating among stakeholder groups may accelerate a transition to open research. The meeting was conducted under the Chatham House Rule, enabling 22 international participants to freely express opinions and ideas without fear of comments being attributed to those present. …

To this end, they discussed these questions:

Where have funder policies and mandates succeeded as tools for change? What are some of the challenges?
How might we collaborate to ensure that researchers are able to engage constructively with this transition?
How might we collaborate to ensure that we are building a truly equitable global system of open research? 
How might we collaborate to ensure a sustainable approach to accelerating the transition to open research, allowing for stakeholders to thrive amidst a culture of openness? …”

Preprints and preregistration: making your research or research plans publicly available at an early stage. – Digital Scholarship Leiden

“We explored two different ways of opening up research at an early stage: preprints and pre-registration. How to go about making your research or research plans publicly available at an early stage, and what can you expect to happen after you have done so?…”