Monthly Archives: January 2022

Shining light on wasteful clinical trials | Springer Nature Sustainability Community

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“This year the Health Research Authority (HRA) started submitting to the ISRCTN registry  all clinical trials entered for combined review by the HRA and the Medicines and Healthcare products Regulatory Agency (MHRA). It is one of a series of measures announced in the HRA’s widely welcomed transparency strategy Make It Public. Read on to find out more about the history behind the HRA’s partnership with ISRCTN and the worldwide movement to promote scientific transparency.

The ISRCTN registry is inviting feedback on the way it helps its users achieve complete and understandable registration and reporting of clinical trials. The rich information in the registry can be useful to anyone interested in evidence underpinning health care. It is not just for the nurses, doctors and scientists who run clinical trials and related health research. …”

iNaturalist Systems architect

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“To do this, we need your help to keep iNaturalist’s infrastructure scaling. We’d like to start by offering a 5-month contract to help research, design, and implement improvements or alternatives to help iNaturalist’s core infrastructure, such as our search functionality, to perform at larger scales. We expect to hire a full-time systems architect at the end of the contract period. Depending on the applicant, there may be a possibility to transition from one role to another. POSITION SUMMARY: The systems architect will work alongside our team of five other developers including the member of our team chiefly responsible for dev-ops. The work can be done remotely, but the position will require working closely with the iNaturalist team through weekly iteration meetings and daily Slack and Github communication. The work will require forking and setting up local instances of the iNaturalist infrastructure, implementing changes to the infrastructure, testing at production scales, and helping apply changes to iNaturalist’s production systems. More specifically, we’re looking for someone with experience and ideas to try in order to ensure that iNaturalist users continue to receive fast responses to search queries at larger scales, and will do the work to implement and test these improvements. Search functionality is core to iNaturalist and impacts the response time of most parts of the platform and most new features we have planned. Our goal at the end of this contract is to have an implementation that either performs better than our current system at our current scale, or performs as good as our current system at larger scales….”

Illinois, Rhode Island Introduce New Library E-book Bills

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“Illinois has become the latest state to introduce a library e-book bill, with state legislators last week introducing the Equitable Access to Electronic Literature Act. In addition, Rhode Island legislators have re-introduced their library e-book bill in the new legislative session after a previous effort stalled last year.

The Illinois bill provides that publishers that offer “a contract or license for electronic literary product acquisition to the public shall offer to license the electronic literary product to libraries, if purchased with public funds, on reasonable terms and under reasonable technological protection measures that will permit libraries to provide their patrons with access to the electronic literary products.” 

The bill in Rhode Island is similar, although it specifically expands the law to cover “elementary and secondary schools and educational institutions” in the state.

The bills are also similar to efforts passed in Maryland and New York last year (although New York governor Kathy Hochul vetoed the bill last month.) Similar bills are being considered in several more state legislatures, library leaders tell PW….”

Wiley and SCELC Sign Pilot to Deliver More Open Access Articles

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Global research and education leader Wiley today announced a new pilot agreement with the Statewide California Electronic Library Consortium (SCELC) to accelerate the publication of open access articles across 61 SCELC members and affiliates.

The agreement supports researchers at participating institutions – which span the U.S. states of California, Texas, Hawaii and others – by delivering unrestricted access to all of Wiley’s hybrid and subscription journals and granting the ability to publish accepted articles open access in all of Wiley’s 1,400 hybrid journals.

Senior Research Fellowship ‘Open Data for Open Science and Society’ @ Vrije Universiteit Brussel. End of play: April 15, 2022

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1 – Working at the VUB

For already 50 years, the Vrije Universiteit Brussel has stood for freedom, equality and connectedness. These values are strongly present on our campuses, in our students as well as our staff. At the VUB, you’ll find a diverse collection of personalities: pure innovators and especially people who are 100% their authentic selves. With about 3.500 employees, we are the largest Flemish-speaking employer in Brussels, an international city with which we are all too happy to be connected, and around which our four campuses are located.

Our education and research are grounded in the principles of free research with an eye on human progress. We disapprove of every purely authoritative argument and guarantee the free formation of judgement that is necessary for this basic principle to be incorporated in the community.

The VUB is autonomous and managed democratically. As such, we guarantee fundamental freedoms within our university, as well as the right of the university community to be involved in making and checking university policy.

The mission of the university includes:

the development, the transfer and the application of high-standing academic education and scientific research, free from any prejudice;
community integration of this in a spirit of social compassion;
critical development of everyone in light of the responsibilities borne in the community.

2 – Position description

The Faculty of Social Sciences & Solvay Business School, Department Communication Sciences, is looking for a full-time professor. 

More concretely your work package contains: 

Education and Research domain:

Communication Science: Open Data for Open Science & Society

Education tasks:

You are responsible for teaching courses at the Faculty of Social Sciences and Solvay Business School, for an equivalent of 6 ECTS (credits) per semester in the field of Open Data for Open Science & Society.
The course(s) will address how open data is transforming scientific knowledge and practice – making it more transparent, accessible, democratic, and societally relevant;
You supervise a limited number of bachelor’s and master’s theses.

Research tasks:

You conduct research in the domain of Open Data for Open Science & Society and develop an interdisciplinary, multi-track, internationally oriented research programme on the subject area. More specifically, you focus on topics such as:

Data brokerage, data stewardship and data governance. Research into new levers for data access, re-use and collaboration, e.g. innovative tools and methods, knowledge and capacity development, and policy requirements;
Replicability, transparency, trust and ethics in open science, e.g. in a context of the use of big data and artificial intelligence;
Economic and social impact: cost-benefit analyses of open data and open science policies and programmes, e.g. the evaluation of metrics used to document impact, and the exploration of new deliberation mechanisms to establish a “social contract” related to open data and open science;

You supervise PhD students;
To implement this programme, you combine fundamental and applied research tracks and acquire external funding on a global (private foundations and international organizations), regional (SBO/FWO/ICON), national (BELSPO) and European (Horizon, ERC, Marie Curie, European Science Cloud) level;
You embed the research in the Data & Society programme of the Centre for Studies on Media, Innovation and Technology (SMIT), seeking connection to VUB-wide valorising initiatives such as the AI Institute for the Common Good (FARI), the AI Experience Centre and the Knowledge Centre Data & Society.

Other tasks:

You are responsible for research related service tasks at the level of the research group, the department, the faculty and/or the university;
You develop and maintain an international research network;
You contribute to creating external visibility for the research group, the department, the faculty and the university.
Additionally, you actively contribute to the faculty and the university’s open science and open data initiatives (incl. the University’s Open Science Board), and represent the research group and university in high-level impact forums and communities.

For this function, our Brussels Humanities, Sciences & Engineering Campus (Elsene) will serve as your home base. 

3 – Profile

What do we expect from you?

You hold a PhD award

Opening The Book: SSP Charleston Pre-Conference Video Now Available

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For your viewing from the Society for Scholarly Publishing (SSP) On Demand Library, today we offer the SSP Pre-Conference Session from the 2021 Charleston Conference. The panel featured librarians, publishers, and other experts weighing in on the state of open access book publishing, particularly in light of new initiatives, new business models, and new regulations and requirements on authors that are planned to go into effect.

Making Biomedical Sciences publications more accessible for machines | SpringerLink

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Abstract:  With the rapidly expanding catalogue of scientific publications, especially within the Biomedical Sciences field, it is becoming increasingly difficult for researchers to search for, read or even interpret emerging scientific findings. PubMed, just one of the current biomedical data repositories, comprises over 33 million citations for biomedical research, and over 2500 publications are added each day. To further strengthen the impact biomedical research, we suggest that there should be more synergy between publications and machines. By bringing machines into the realm of research and publication, we can greatly augment the assessment, investigation and cataloging of the biomedical literary corpus. The effective application of machine-based manuscript assessment and interpretation is now crucial, and potentially stands as the most effective way for researchers to comprehend and process the tsunami of biomedical data and literature. Many biomedical manuscripts are currently published online in poorly searchable document types, with figures and data presented in formats that are partially inaccessible to machine-based approaches. The structure and format of biomedical manuscripts should be adapted to facilitate machine-assisted interrogation of this important literary corpus. In this context, it is important to embrace the concept that biomedical scientists should also write manuscripts that can be read by machines. It is likely that an enhanced human–machine synergy in reading biomedical publications will greatly enhance biomedical data retrieval and reveal novel insights into complex datasets.

 

The Brazilian compound library (BraCoLi) database: a repository of chemical and biological information for drug design | SpringerLink

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Abstract:  The Brazilian Compound Library (BraCoLi) is a novel open access and manually curated electronic library of compounds developed by Brazilian research groups to support further computer-aided drug design works, available on https://www.farmacia.ufmg.br/qf/downloads/. Herein, the first version of the database is described comprising 1176 compounds. Also, the chemical diversity and drug-like profiles of BraCoLi were defined to analyze its chemical space. A significant amount of the compounds fitted Lipinski and Veber’s rules, alongside other drug-likeness properties. A comparison using principal component analysis showed that BraCoLi is similar to other databases (FDA-approved drugs and NuBBEDB) regarding structural and physicochemical patterns. Furthermore, a scaffold analysis showed that BraCoLi presents several privileged chemical skeletons with great diversity. Despite the similar distribution in the structural and physicochemical spaces, Tanimoto coefficient values indicated that compounds present in the BraCoLi are generally different from the two other databases, where they showed different kernel distributions and low similarity. These facts show an interesting innovative aspect, which is a desirable feature for novel drug design purposes.

The Online Coalition Game: A tool for online interactive coalition formation research | SpringerLink

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Abstract:  In this paper, we present the Online Coalition Game (OCG): an open-source tool written for the open-access research platform oTree that enables high-powered interactive coalition formation experiments. Besides containing a tutorial on conducting and configuring studies using the OCG, we discuss two previous implementations. With these examples, we demonstrate that online use of the OCG provides the benefits of large sample sizes and fast data collection, while leading to convergent and robust findings. Moreover, we show that small changes in the experimental setup offer interesting opportunities to expand coalition formation theory by including insights from, amongst others, literature on bargaining, ostracism, and communication, and vice versa.

 

COVID-19 and the Research Community: It is time for open access in clinical care | eLife

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Abstract:  A healthcare center widely sharing its internal guidelines on how to treat COVID-19 patients “just wasn’t done.” As the pandemic raged at a Boston hospital, the next generation of clinical leaders pushed for change.

From the body of the paper: “Around mid-March, our hospital had put together its first internal guidelines to treat COVID-19 patients. We were about to upload them as a PDF to our hospital’s internal server for our staff to download and print them, when the next generation of clinical leaders spoke up. As pulmonary fellow-in-training Dr C Lee Cohen pointed out, how could paper printouts possibly keep up with the rapidly evolving data on COVID-19? Just as importantly, she and others suggested that we had a responsibility to share our findings with the world, not just with our staff. In anticipation, Cohen built the website COVIDprotocols.org to host our guidelines: this platform was web and mobile-based, searchable and could be continually updated. Evolving recommendations, accessible on our smartphones? That idea was an instant hit. Sharing them outside our hospital was not. What if we were wrong and misled professionals around the globe? Making internal guidelines widely public just wasn’t done. I hesitated. As the individual who had put together the interdisciplinary team working on our COVID-19 protocols, I felt ultimately responsible for any negative fallout. But the pandemic was too massive, and the global confusion too overwhelming; it wasn’t perfect, but it just had to be done. Despite our doubts, on March 20, 2020, we launched the website Cohen had built, and released our first set of guidelines to the public.

Evolving recommendations, accessible on our smartphones? That idea was an instant hit. Sharing them outside our hospital was not. What if we were wrong and misled professionals around the globe? Making internal guidelines widely public just wasn’t done. I hesitated. …”

 

What to expect from post-pandemic publishing – Research Professional News

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“Luckily for the world, as the world’s scientists grappled to understand Covid-19, the publishing situation is very different to Sars. The Covid-19 pandemic prompted what Barbour calls “an outpouring of research”, and most of it was rapidly available online and on preprint servers.

This time around scientists were able to disseminate early data and release initial findings in preprints, publications which are not peer reviewed and are a relatively recent innovation in the research landscape. Traditional journal publishing processes could not keep pace with the pandemic.

Post-Covid, says Barbour, publishing should be heading for a permanent change.

“My view is that the pandemic has reinforced [the view] that traditional journals on their own can’t respond to the rapid flow of information that’s needed in an emergency,” she says. “Traditional journals will have a role in that system, but it’s a limited one and should not be the dominant method.”

The tide appears to be turning in favour of novel forms of academic publishing. In December 2021, the Australian Research Council performed a major U-turn and uncancelled 32 applicants who had been disqualified from entry to the ARC Future Fellowships and Discovery Early Career Researcher Awards because their applications contained references to preprints.

If this is progress, though, there are already questions about whether it can be maintained….”

PARROT: A Pilot Study on the Open Access Provision of Particle-Discrete Tomographic Datasets | Microscopy and Microanalysis | Cambridge Core

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Abstract:  In the present paper, as part of an interdisciplinary research project (Priority Programme SPP2045), we propose a possible way to design an open access archive for particle-discrete tomographic datasets: the PARROT database (https://parrot.tu-freiberg.de). This archive is the result of a pilot study in the field of particle technology and three use cases are presented for illustrative purposes. Instead of providing a detailed instruction manual, we focus on the methodologies of such an archive. The presented use cases stem from our working group and are intended to demonstrate the advantage of using such an archive with concise and consistent data for potential and ongoing studies. Data and metadata merely serve as examples and need to be adapted for disciplines not concerned here. Since all datasets within the PARROT database and its source code are freely accessible, this study represents a starting point for similar projects.

Open Access Publishing: Issues and Way Forward – Predatory Journals and Conferences

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“One of the major challenges the world has faced the past two years has been the onset of the COVID-19 pandemic. With scientists putting up lot of research on COVID, the World Health Organization (WHO) came up with a WHO: COVID-19 Literature on corona virus disease. This database provides a way for the general public, along with scientists, to check the scientific literature on COVID-19, in one place, and this also results in wider reach/dissemination.

However, we do not have a common database for other important research areas concerning the general public, such as “Cancer Research” or “Climate Change”. When we say open access, the main aim should be open science to all, and we need more such databases by international agencies like the United Nations to collate research articles on important areas such as the 17 UN Sustainable Development Goals, which should be the need of the hour. Such initiatives will help in the real dissemination of science to the general public, and give authors of important research contributions, the visibility they deserve. This will be unlike publishers asking authors to promote their articles and measuring them with their commercial metrics….”