Could This Search Engine Save Your Life? – The Chronicle of Higher Education

One of the Allen Institute’s priorities is an academically oriented search engine, established in 2015, called Semantic Scholar (slogan: “Cut through the clutter”). The need is great, with more than 34,000 peer-reviewed journals publishing 2.5 million articles a year. “What if a cure for an intractable cancer is hidden within the tedious reports on thousands of clinical studies?,” Etzioni once said.

Although Semantic Scholar has focused so far on computer and biomedical sciences, Etzioni says that the engine will soon push into the social sciences and the humanities as well. The Chronicle spoke with him about information overload, impact factors’ imperfect inevitability, and the promise and perils of AI….”

Conservation Biology as an Example of the Dilemmas Facing Scholarly Society Publishing

“An editorial entitled “Open Access and Academic Imperialism” was published in Conservation Biology on November 9, 2018. The editorial was written by Mark Burgman, the editor-in-chief of the journal, but all of Conservation Biology’s editors and the editors-in-chief of the other two journals published by the Society for Conservation Biology (SCB), Conservation Letters and Conservation Science and Practice signed on.1

The editorial was an attack on Plan S, the funder mandate that will require by 2020 the immediate open access publication of articles based on the research supported by the Plan S funding agencies.2 The editorial did not mince words, “We think this policy is a mistake,” it begins, and continues, “Access to journals for authors and readers is a complex and nuanced topic, encompassing the cost of publication, academic freedom, and the potential for conflicts of interest between editors required to guarantee the quality of papers and authors paying for publication. We focus on a single issue, that of equity of access to publication by readers and authors.”3 The argument is that open access, what Burgman terms the “author-pays” model, disadvantages authors who can now publish at no cost in the “reader-pays” or subscription/paywall model. As the editorial puts it, “Enforcing author-pay models will strengthen the hand of those who have resources and weaken the hand of those who do not have, magnifying the north-south academic divide, creating another structural bias, and further narrowing the knowledge-production system.”4 The editorial supports the hybrid open access model, that is offered by Conservation Biology because authors get to decide whether or not to pay to have their article made open access, thus the ability to pay is not an obstacle for publication. The current version of the Plan S implementation guidelines say that hybrid open access journals are not compliant unless they have a plan to become fully open access within three years. Plan S also looks to constrain the article process charges (APCs) authors pay to have their articles published, but Burgman is unmoved by this provision.

Joona Lehtomäki, Johanna Eklund, Tuuli Toivonen write, in a critical response to the editorial, “We wish to express our disappointment with such a narrow and misleading interpretations of the recent attempts to make academic publishing more open, and what consequences this might have for the global conservation community.”5 They point out that reader-pays models are quite expensive and the expense denies access to the articles by many especially those in the global south that Burgman claims to be supporting. They also note that hybrid models can be seen as double-dipping, charging both authors and readers. They note the high profit margins of the large commercial publishers, including Wiley, the publisher of Conservation Biology, whose reported profit margin is nearly 30%. They end by writing, “In conclusion, we fear the approach advocated by Burgman will only bolster the current publishing system where all researchers and national science funders, irrespective of geographies, are being exploited by a few publishing empires.”6

It would be easy to view this argument as an academic tit-for-tat in a narrow subdiscipline of biology, but I think it is a useful example of the dilemmas facing many scholarly societies as they confront the changes taking place in scholarly publishing. In my view these changes are inevitable and irreversible. They are the result of the change in the technologies that drive scholarly communications. The old models were based on print of paper, and the new models are based on digital networkbased documents. This change is at least as revolutionary as printing, the technological change that made scholarly societies and their subscription journals possible in the first place. Scholarly societies are likely to have a difficult time managing this transition this change in technologies requires. To do so, they will have to resolve at least three dilemmas. The first is ethical; the second concerns the value of society membership, and the third is financial. We will address each below, but first it is useful to provide some background….”

The International Tree?Ring Data Bank (ITRDB) revisited: Data availability and global ecological representativity – Zhao – – Journal of Biogeography – Wiley Online Library

Abstract:  Aim. The International Tree?Ring Data Bank (ITRDB) is the most comprehensive database of tree growth. To evaluate its usefulness and improve its accessibility to the broad scientific community, we aimed to: (a) quantify its biases, (b) assess how well it represents global forests, (c) develop tools to identify priority areas to improve its representativity, and (d) make available the corrected database….

Methods. We identified and corrected formatting issues in all individual datasets of the ITRDB. We then calculated the representativity of the ITRDB with respect to species, spatial coverage, climatic regions, elevations, need for data update, climatic limitations on growth, vascular plant diversity, and associated animal diversity. We combined these metrics into a global Priority Sampling Index (PSI) to highlight ways to improve ITRDB representativity.

Results. Our refined dataset provides access to a network of >52 million growth data points worldwide. We found, however, that the database is dominated by trees from forests with low diversity, in semi?arid climates, coniferous species, and in western North America. Conifers represented 81% of the ITRDB and even in well?sampled areas, broadleaves were poorly represented. Our PSI stressed the need to increase the database diversity in terms of broadleaf species and identified poorly represented regions that require scientific attention. Great gains will be made by increasing research and data sharing in African, Asian, and South American forests.

Main conclusions. The extensive data and coverage of the ITRDB show great promise to address macroecological questions. To achieve this, however, we have to overcome the significant gaps in the representativity of the ITRDB. A strategic and organized group effort is required, and we hope the tools and data provided here can guide the efforts to improve this invaluable database….”

New study makes 52 million tree stories more accessible to science

“The world’s primary archive of tree ring data, which holds more than 52 million cost-free records spanning 8,000 years of history, has gotten a makeover by scientists from four countries committed to making science more accessible.


The co-authors report in the Journal of Biogeography that the International Tree Ring Data Bank, developed in 1974 and populated by hundreds of contributing scientists and agencies, had only been used for a handful of studies at a global scale due to inconsistent data accessibility and formatting.

The team corrected thousands of formatting issues that prevented files from being read, requiring scientists to either manually correct errors or omit large portions of available data. “The data correction took weeks of intensive work,” says Manzanedo. “In the sample records, any misplaced character or erroneous empty space would make a whole file unreadable. Finding those was sometimes like finding a needle in a haystack. We kept a log with our decisions to ensure the future traceability of the process.” …”

Transparency and reproducibility of biomedical research is improving | EurekAlert! Science News

“This new study builds upon the authors’ previous evaluation of articles published between 2000 and 2014, which demonstrated that the biomedical literature largely lacked transparency. In their second assessment, the authors instead find that the majority of recently published articles provided information on funding and conflicts of interest, and statements related to data-sharing had become more widespread….”

Majority of journal’s editorial board resigns after publisher’s handling of letter about move to open access – Retraction Watch

“A leading journal in ecology and evolution is going through an evolution of its own, following the resignation of its editor in chief and more than half of its editorial board.

The mass exodus at Diversity & Distributionscame after Wiley, which publishes the journal, allegedly blocked it from running a letter protesting the company’s decision to make D & D open access (the company disputes the claim, as we’ll detail in a bit). A letter about the issue, signed by scores of researchers worldwide, decried Wiley’s move….”

Project Data Sphere

Project Data Sphere, LLC (PDS), an independent, not-for-profit initiative of the CEO Roundtable on Cancer’s Life Sciences Consortium (LSC), operates the Project Data Sphere platform, a free digital library-laboratory that provides one place where the research community can broadly share, integrate and analyze historical, patient-level data from academic and industry phase III cancer clinical trials.

The Project Data Sphere platform is available to researchers affiliated with life science companies, hospitals and institutions, as well as independent researchers. Anyone interested in cancer research can apply to become an authorized user….”

Innovating Nanotechnology with Open Science and AI | It’s FOSS

“Excessive patenting in Nanotechnology leads to:

  • increases in costs,
  • slows down technical development and
  • removes fundamental knowledge from the public domain…

Now that we have seen how Open Source revolutionizes Nanotechnology Research, let us discuss in detail about three important initiatives in Open Source Nanotechnology. If we recall from our first Science article, Open Science implies Open Source, Open Access, Open Data and Open Standards….”


Open Source 3D Printing: Exploring Scientific and Medical Solutions

“Open Source 3D Printing eliminates all the issues we just discussed in the proprietary section. Not only does it reduce costs, it enables easier innovation to solve issues faced during 3D manufacturing….

It is now possible for users to completely go Open Source, making it possible to greatly reducing production time and manufacturing costs!…

[I]n this final and most important section, let us pick related applications that we just discussed and look into some examples in detail where we feel Open Source Approach is most necessary…

An Open System that enables such customized Printing of bio-materials that diverse in nature will make it much easier to conduct research in Tissue Engineering….

Finally, we focused on the Scientific and Medical Solutions for Open Source Bioprinting by looking into initiatives for saving our corals, teeth replacement with anti-bacterial abilities, Bioprinting with focus on Open Source Bioprinting and Applied Nanotechnology for Organ Transplant. In our final subsection, we also highlighted the role of 3D Printing in Drug Discovery.

These are only some of the many applications of 3D Printing. We believe there is a need for Proprietary manufacturers to migrate towards Open Source Business Models that would promote better applicability for our planet.”