August 2022 - Listserv For Scientists

OSTP Issues Guidance to Make Federally Funded Research Freely Available Without Delay

by Jason E. Barkeloo

OSTP Issues Guidance to Make Federally Funded Research Freely Available Without Delay AUGUST 25, 2022 PRESS RELEASES Today, the White House Office of Science and Technology Policy (OSTP) updated U.S. policy guidance to make the results of taxpayer-supported research immediately available to the American public at no cost. In a memorandum to federal departments and agencies, Dr. Alondra Nelson, the head of OSTP, delivered guidance for agencies to update their public access policies as soon as possible to make publications and research funded by taxpayers publicly accessible, without an embargo or cost. All agencies will fully implement updated policies, including ending the optional 12-month embargo, no later than December 31, 2025. More… https://therapoid.net/en/forums/forum/policy-news-and-issues-840/topic/ostp…

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Using lessons from Arnstein’s ladder and IAP2 spectrum on community engagement to improve stakeholder engagement in research

by Gabriele Bammer

Using lessons from Arnstein’s ladder and IAP2 spectrum on community engagement to improve stakeholder engagement in research is discussed in https://i2insights.org/2022/08/30/learning-from-arnsteins-ladder-and-iap2-s…. Both influenced the development of the i2S stakeholder engagement options framework. Arnstein’s ladder teaches: beware of manipulation & tokenism; genuine engagement involves access to power. IAP2 spectrum teaches: differing levels of participation are legitimate & depend on goals, time frames, resources & levels of concern in decision to be made, plus seeks to ensure genuine participation through “promise to the public” which gives feedback to those involved about how input used. Do stakeholders need their own framework to alert them to manipulation & tokenism? When is stakeholder-led research best & how can researchers can be supportive? =================================================== Professor Gabriele Bammer National Centre for Epidemiology and Population Health ANU College of Health and Medicine The Australian National University 62 Mills Road Acton ACT 2601 Australia +61 2 6125 0716 Gabriele.Bammer(a)anu.edu.au<mailto:Gabriele.Bammer@anu.edu.au> @GabrieleBammer http://i2s.anu.edu.au<http://www.anu.edu.au/iisn> http://i2Insights.org<http://i2insights.org/> CRICOS Provider # 00120C ===================================================

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Check out this meeting protocol for effectively including online participation in onsite meetings

by Gabriele Bammer

Check out this meeting protocol for effectively including online participation in onsite meetings developed at SESYNC in this revisited blog post at https://i2insights.org/2020/03/24/effective-online-plus-onsite-meetings/ The protocol provides multiple tips such as 1) fully include online participants eg face them, make eye contact & rethink activities they can't join; 2) be aware of the soundscape, as microphones don't work like ears; online participants can hear everything happening onsite & this may be disruptive; 3) attend to camera angles, field of view & zoom in on speakers if possible; 4) delegate someone to monitor chat; 5) online participants should adjust their work schedules & if necessary body clocks to be fully present; 6) plan ahead for good facilitation. =================================================== Professor Gabriele Bammer National Centre for Epidemiology and Population Health ANU College of Health and Medicine The Australian National University 62 Mills Road Acton ACT 2601 Australia +61 2 6125 0716 Gabriele.Bammer(a)anu.edu.au<mailto:Gabriele.Bammer@anu.edu.au> @GabrieleBammer http://i2s.anu.edu.au<http://www.anu.edu.au/iisn> http://i2Insights.org<http://i2insights.org/> CRICOS Provider # 00120C ===================================================

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[CfP] First Workshop on Information Extraction from Scientific Publications (WIESP) at AACL-IJCNLP 2022

by Tirthankar Ghosal

*** First Workshop on Information Extraction from Scientific Publications ( WIESP) at AACL-IJCNLP 2022 *** *** Website: https://ui.adsabs.harvard.edu/WIESP/ *** Twitter: https://twitter.com/wiesp_nlp The number of scientific papers published per year has exploded in recent years. Indexing the article's full text in search engines helps discover and retrieve vital scientific information to continue building on the shoulders of giants, informing policy, and making evidence-based decisions. Nevertheless, it is difficult to navigate this ocean of data. Using simple string matching has substantial limitations: human language is ambiguous in nature, context matters, and we frequently use the same word and acronyms to represent a multitude of different meanings. Extracting structured and semantically relevant information from scientific publications (e.g., named-entity recognition, summarization, citation intention, linkage to knowledge graphs) allows for better selection and filter articles. The First Workshop on Information Extraction from Scientific Publications ( WIESP) will create the necessary forum to foster discussion and research using Natural Language Processing and Machine Learning. WIESP would specifically focus on topics related to information extraction from scientific publications, including (but not limited to): - Scientific document parsing - Scientific named-entity recognition - Scientific article summarization - Question-answering on scientific articles - Citation context/span extraction - Structured information extraction from full-text, tables, figures, bibliography - Novel datasets curated from scientific publications - Argument extraction and mining - Challenges in information extraction from scientific articles - Building knowledge graphs via mining scientific literature; querying scientific knowledge graphs - Novel tools for IE on scientific literature and interaction with users - Mathematical information extraction - Scientific concepts, facts extraction - Visualizing scientific knowledge - Bibliometric and Altmetric studies via information extraction from scientific articles and metadata - Information extraction from COVID-19 articles to inform public health policy In addition to research paper presentations, WIESP would also feature keynote talks, a panel discussion, and a shared task. We will update the details on our website as and when they become available. We especially welcome participation from academic and research institutions, government and industry labs, publishers, and information service providers. Projects and organizations using NLP/ML techniques in their text mining and enrichment efforts are also welcome to participate. ***Call for Papers*** We invite papers of the following categories: ***Long papers*** must describe substantial, original, completed, and unpublished work. Wherever appropriate, concrete evaluation and analysis should be included. Papers must not exceed eight (8) pages of content, plus unlimited pages of references. The final versions of long papers will be given one additional page of content (up to 9 pages) so that reviewers' comments can be taken into account. ***Short papers*** must describe original and unpublished work. Please note that a short paper is not a shortened long paper. Instead, short papers should have a point that can be made in a few pages, such as a small, focused contribution, a negative result, or an interesting application nugget. Short papers must not exceed four (4) pages, plus unlimited pages of references. The final versions of short papers will be given one additional page of content (up to 5 pages) so that reviewers' comments can be taken into account. ***Position papers*** will give voice to authors who wish to take a position on a topic listed above or the field of scholarly information extraction. Submissions need not present original work and should be two to four pages in length, including title, text, figures and tables, and references. ***Demo papers*** should be no more than four (4) pages in length, including references, and should describe implemented systems that are of relevance to the theme of the workshop. Authors of demo papers should be willing to present a demo of their system during WIESP at AACL-IJCNLP 2022. ***Extended Abstracts*** We welcome submissions of extended abstracts (2 pages max) related to the research topics mentioned above. Submissions may include previously published results, late-breaking results, or a description of ongoing projects in the broad field of information extraction and mining from scientific publications. Extended abstracts can also summarize existing work, work in progress, or a collection of works under a unified theme (e.g., a series of closely related papers that build on each other or tackle a common problem). ***Shared Task: Detecting Entities in the Astrophysics Literature (DEAL)*** A good amount of astrophysics research makes use of data coming from missions and facilities such as ground observatories in remote locations or space telescopes, as well as digital archives that hold large amounts of observed and simulated data. These missions and facilities are frequently named after historical figures or use some ingenious acronym which, unfortunately, can be easily confused when searching for them in the literature via simple string matching. For instance, Planck can refer to the person, the mission, the constant, or several institutions. Automatically recognizing entities such as missions or facilities would help tackle this word sense disambiguation problem. The shared task consists of Named Entity Recognition (NER) on samples of text extracted from astrophysics publications. The labels were created by domain experts and designed to identify entities of interest to the astrophysics community. They range from simple to detect (ex: URLs) to highly unstructured (ex: Formula), and from useful to researchers (ex: Telescope) to more useful to archivists and administrators (ex: Grant). Overall, 31 different labels are included, and their distribution is highly unbalanced (ex: ~100x more Citations than Proposals). Submissions will be scored using both the CoNLL-2000 shared task seqeval F1-Score at the entity level and scikit-learn's Matthews correlation coefficient method at the token level. We also encourage authors to propose their own evaluation metrics. A sample dataset and more instructions can be found at: https://ui.adsabs.harvard.edu/WIESP/2022/SharedTasks Participants (individuals or groups) will have the opportunity to present their findings during the workshop and write a short paper. The best performant or interesting approaches might be invited to further collaborate with the NASA Astrophysical Data System ( https://ui.adsabs.harvard.edu/). ***Important Dates*** - Paper/Abstract Submission Deadline: August 25, 2022 - Notification of workshop paper/abstract acceptance: September 25, 2022 - Camera-ready Submission Deadline: October 10, 2022 - Workshop: November 20, 2021 (online) ***All submission deadlines are 11.59 pm UTC -12h ("Anywhere on Earth")*** ***Submission Website and Format*** Submission Link: softconf.com/aacl2022/WIESP Submission will be via softconf. Submissions should follow the ACLPUB formatting guidelines (https://acl-org.github.io/ACLPUB/formatting.html) and template files (https://github.com/acl-org/acl-style-files/tree/master). Submissions (Long and Short Papers) will be subject to a double-blind peer-review process. Position papers, Demo papers, and Extended Abstracts need not be anonymized. The authors will present accepted papers at the workshop either as a talk or a poster. All accepted papers will be published in the workshop proceedings. We follow the same policies as AACL-IJCNLP 2022 regarding preprints and double submissions. The anonymity period for WIESP 2022 is from July 15 to September 25. ***Organizers*** - Tirthankar Ghosal, Charles University, CZ - Sergi Blanco-Cuaresma, Center for Astrophysics | Harvard & Smithsonian, USA - Alberto Accomazzi, Center for Astrophysics | Harvard & Smithsonian, USA - Robert M. Patton, Oak Ridge National Laboratory, USA - Felix Grezes, Center for Astrophysics | Harvard & Smithsonian, USA - Thomas Allen, Center for Astrophysics | Harvard & Smithsonian, USA -- +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Tirthankar Ghosal Researcher at UFAL, Charles University, CZ https://member.acm.org/~tghosal +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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SESYNC Team Science Resources

by Fiore, Steve

Dear Team Science Colleagues - I wanted to let you know that the National Socio-Environmental Synthesis Center (SESYNC) has online a set of resources that will be of value to this community. If you recall, Dr. Margaret Palmer, director of SESYNC, was a keynote speaker at the SciTS 2022 conference (https://www.inscits.org/2022-keynote-speakers), where she shared with us the important collaborative and interdisciplinary research they've been doing. This set of resources is part of SESYNC's new website (www.sesync.org<http://www.sesync.org/>) that contains a vast collection of lessons and learning materials for the classroom, videos, case studies, data lessons and guides, explainer articles, and more. The materials cover a range of unique and innovative topics, including the science of team science. They will continue to add to this collection in order to help those at all career stages and experience levels engage in socio-environmental and interdisciplinary research. Best, Steve -------- Stephen M. Fiore, Ph.D. Past President, International Network for the Science of Team Science<https://www.inscits.org/> Professor, Cognitive Sciences, Department of Philosophy <https://philosophy.cah.ucf.edu/> <http://philosophy.cah.ucf.edu/staff.php?id=134> Director, Cognitive Sciences Laboratory<http://csl.ist.ucf.edu>, Institute for Simulation & Training<https://www.ist.ucf.edu/> <http://philosophy.cah.ucf.edu/staff.php?id=134> <http://philosophy.cah.ucf.edu/staff.php?id=134> University of Central Florida<https://www.ucf.edu/> sfiore(a)ist.ucf.edu

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Hypocritical or not? | Impacts of U.S. Section 1498, a compulsory patent license that was used for COVID19 vaccines.

by Jason E. Barkeloo

“A compulsory license allows the use of patented inventions without the permission of patent holders. In the case of the statute, such broad suspension of traditional patent rights are granted as long as the patented invention is used in service of a critical government function, typically in areas of national security or a national emergency.” American-made coronavirus treatments were accelerated using the very type of involuntary patent sharing the drug industry has decried. Lee Fang August 23 2022, 5:26 p.m. Vials containing the Moderna Covid-19 booster at a vaccination center. Photo: Dinendra Haria / Sipa via AP Images DURING THE HEIGHT of the coronavirus pandemic, when South Africa, India, and many lower-income countries requested a special waiver on the enforcement of patents that would allow them to manufacture cheap Covid-19 vaccines and therapeutic medicine, the U.S. pharmaceutical industry snarled. American drug executives and lobbyists countered that the U.S. should not only vigorously oppose any patent sharing, but also move to sanction any country that dared to violate corporate patent rights. “Patents are the reason that Covid-19 vaccines exist. Waiving them would undermine our response to this pandemic and future health emergencies,” wrote Michelle McMurray-Heath, a top biotech lobbyist and head of the Biotechnology Innovation Organization, or BIO, in an opinion column scorning the South Africa-led waiver request. McMurray-Heath, in her column, referenced the success of Moderna Inc., in which “licensing technology, not abrogating patents” made vaccines possible. That tough talk belies an unprecedented suspension of patent enforcement granted to select pharmaceutical and medical device companies — including Moderna. We now know that drug companies like Moderna took advantage of emergency conditions to waive patent rights for components of Covid-19 mRNA vaccines. Despite the drug industry’s rhetoric around the sanctity of patent protections, newly disclosed government pandemic contracts and a contentious patent infringement lawsuit against Moderna showcase the extent to which American-made coronavirus treatments were accelerated using the very type of involuntary patent sharing the drug industry has decried. Knowledge Ecology International, an advocacy group that campaigns for access to medicine, recently released the results of a Freedom of Information Act request showing that the Trump administration quietly invoked a World War I-era law to give companies racing to produce Covid-19 medications, vaccines, tests, and other pandemic-related products special authority to seize virtually any patent they wished without authorization. KEI has identified 62 federal pandemic-related contracts — including with major companies such as Corning Inc., Eli Lilly and Co., Merck & Co. Inc., Qiagen, Sanofi, Moderna, and Siemens — with clauses that reference regulations associated with Section 1498, a statute that grants a compulsory license for the completion of the contract. A compulsory license allows the use of patented inventions without the permission of patent holders. In the case of the statute, such broad suspension of traditional patent rights are granted as long as the patented invention is used in service of a critical government function, typically in areas of national security or a national emergency. The contracts flowed to companies that swiftly developed products needed to respond to the pandemic. Qiagen’s federal funding helped it produce the QIAstat-Dx line of PCR testing equipment to detect Covid-19 pathogens in human samples. The Corning contract identified by KEI supported the manufacturing of medical-grade vials and glass tubing used for coronavirus response efforts. More... https://theintercept.com/2022/08/23/covid-vaccine-patents-moderna-big-pharm…

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Transforming transdisciplinarity with art and literature

by Gabriele Bammer

Transforming transdisciplinarity with art and literature is described by Jane Palmer and Dena Fam in https://i2insights.org/2022/08/23/art-and-literature-transform-transdiscipl…. Art and literature offer a way to imagine less anthroprocentric ways of being in the world & to decentre humans to achieve sustainability, as well as ways to 'pause' accustomed thought processes by mindfulness, 'mindwandering' & solitude to change relations with others, human & nonhuman. Exposure to subversive & immersive imaginaries shifts perspectives & openness to others' value premises & belief systems and enables us to see agency & aliveness of the other, & possibility of other, even incommensurate, knowledges. Finally art and literature provide a way into Nicolescu's "zone of non-resistance" & openness to new transdisciplinary forms of collaboration. =================================================== Professor Gabriele Bammer National Centre for Epidemiology and Population Health ANU College of Health and Medicine The Australian National University 62 Mills Road Acton ACT 2601 Australia +61 2 6125 0716 Gabriele.Bammer(a)anu.edu.au<mailto:Gabriele.Bammer@anu.edu.au> @GabrieleBammer http://i2s.anu.edu.au<http://www.anu.edu.au/iisn> http://i2Insights.org<http://i2insights.org/> CRICOS Provider # 00120C ===================================================

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Knowledge overconfidence is associated with anti-consensus views on controversial scientific issues

by Jason E. Barkeloo

Knowledge overconfidence is associated with anti-consensus views on controversial scientific issues NICHOLAS LIGHT HTTPS://ORCID.ORG/0000-0003-4703-1026 PHILIP M. FERNBACH[...] STEVEN A. SLOMAN HTTPS://ORCID.ORG/0000-0001-8223-3788 Authors Info & Affiliations SCIENCE ADVANCES 20 Jul 2022 Vol 8, Issue 29 DOI: 10.1126/sciadv.abo0038 Abstract Public attitudes that are in opposition to scientific consensus can be disastrous and include rejection of vaccines and opposition to climate change mitigation policies. Five studies examine the interrelationships between opposition to expert consensus on controversial scientific issues, how much people actually know about these issues, and how much they think they know. Across seven critical issues that enjoy substantial scientific consensus, as well as attitudes toward COVID-19 vaccines and mitigation measures like mask wearing and social distancing, results indicate that those with the highest levels of opposition have the lowest levels of objective knowledge but the highest levels of subjective knowledge. Implications for scientists, policymakers, and science communicators are discussed. INTRODUCTION Uncertainty is inherent to science. More… https://therapoid.net/en/forums/forum/policy-news-and-issues-840/topic/know…

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Superb article considering the origins and policy implications of SARS-CoV-2 (COVID-19).

by Jason E. Barkeloo

Policy and intercultural scientific implications for future collaborations…. The COVID lab leak theory is dead. Here’s how we know the virus came from a Wuhan market By: Jason E. B. on Aug. 18, 2022, 1:28 p.m. Published: August 14, 2022 4.04pm EDT Edward C Holmes, University of Sydney My colleagues and I published the most detailedstudies of the earliest events in the COVID-19 pandemic last month in the journal Science. Together, these papers paint a coherent evidence-based picture of what took place in the city of Wuhan during the latter part of 2019. The take-home message is the COVID pandemic probably did begin where the first cases were detected – at the Huanan Seafood Wholesale Market. At the same time this lays to rest the idea that the virus escaped from a laboratory. More… https://therapoid.net/en/forums/forum/covid19-887/topic/the-covid-lab-leak-…

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Requirements for genuine transdisciplinary collaborations

by Gabriele Bammer

Requirements for genuine transdisciplinary collaborations are described by Gabriela Alonso-Yanez, Lily House-Peters and Martin Garcia Cartagena in their revisited blog post at: https://i2insights.org/2020/02/04/decentering-and-unlearning/. They are 1) make decisions with stakeholders about processes & resource allocation in a way that gives everyone equal power, 2) reflect upon & intentionally discard conventional avenues of designing & conducting research, 3) unlearn disciplinary practices & behaviours by confronting & grappling with their own identities, 4) recognise deeply embedded language, postures & experiences that are part of disciplinary identity & need to be unlearnt, 5) intentionally discard conventional research design & conduct to be authentically open to other ways of exploring questions. =================================================== Professor Gabriele Bammer National Centre for Epidemiology and Population Health ANU College of Health and Medicine The Australian National University 62 Mills Road Acton ACT 2601 Australia +61 2 6125 0716 Gabriele.Bammer(a)anu.edu.au<mailto:Gabriele.Bammer@anu.edu.au> @GabrieleBammer http://i2s.anu.edu.au<http://www.anu.edu.au/iisn> http://i2Insights.org<http://i2insights.org/> CRICOS Provider # 00120C ===================================================

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Listserv For Scientists August 2022