commonmeta-ruby 3.3.12 → 3.3.14
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- checksums.yaml +4 -4
- data/Gemfile.lock +1 -1
- data/lib/commonmeta/crossref_utils.rb +2 -2
- data/lib/commonmeta/readers/json_feed_reader.rb +5 -1
- data/lib/commonmeta/version.rb +1 -1
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/substack_post_with_broken_reference.yml +2566 -1
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/syldavia_gazette_post_with_references.yml +323 -1
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/upstream_post_with_references.yml +1777 -1
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post_with_many_references.yml +6465 -0
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_with_references.yml +1777 -1
- data/spec/readers/json_feed_reader_spec.rb +4 -3
- data/spec/writers/crossref_xml_writer_spec.rb +1 -1
- metadata +2 -2
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to the preregistration plan may not always be feasible and even is not necessarily
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desirable, but without disclosure of deviations, readers who do not carefully
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consult the preregistration plan might get the incorrect impression that the
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study was exactly conducted and reported as planned. In this paper, we have
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investigated adherence and disclosure of deviations for all articles published
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with the Preregistered badge in\n <jats:italic>Psychological Science<\/jats:italic>\n between
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February 2015 and November 2017 and shared our findings with the corresponding
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authors for feedback. Two out of 27 preregistered studies contained no deviations
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from the preregistration plan. In one study, all deviations were disclosed.
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Nine studies disclosed none of the deviations. We mainly observed (un)disclosed
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deviations from the plan regarding the reported sample size, exclusion criteria
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and statistical analysis. This closer look at preregistrations of the first
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generation reveals possible hurdles for reporting preregistered studies and
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provides input for future reporting guidelines. We discuss the results and
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possible explanations, and provide recommendations for preregistered research.\n <\/jats:p>","DOI":"10.1098\/rsos.211037","type":"journal-article","created":{"date-parts":[[2021,10,27]],"date-time":"2021-10-27T07:05:32Z","timestamp":1635318332000},"update-policy":"http:\/\/dx.doi.org\/10.1098\/crossmark-policy","source":"Crossref","is-referenced-by-count":18,"title":"Comparing
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dream to reality: an assessment of adherence of the first generation of preregistered
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be a problem even when there is no \u2018fishing expedition\u2019 or \u2018p-hacking\u2019
|
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and the research hypothesis was posited ahead of time. Dep Stat Columbia Univ
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FL. 2016. Dear colleague letter: Robust and reliable research in the social,
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behavioral, and economic sciences. National Science Foundation. https:\/\/www.nsf.gov\/pubs\/2016\/nsf16137\/nsf16137.jsp
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and the Research Hypothesis Was Posited Ahead of Time. Department of Statistics,
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microRNA miR-34a inhibits prostate cancer stem cells and metastasis by directly
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retraction penalty: Evidence from the Web of Science","volume":"3","author":"Lu","year":"2013","journal-title":"Scientific
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MDAR (Materials Design Analysis Reporting) Framework for transparent reporting
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(lack of) impact of retraction on citation networks","volume":"21","author":"Madlock-Brown","year":"2015","journal-title":"Science
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prejudices: An experimental study of confirmatory bias in the peer review
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in psychology research: How often do they really occur?","volume":"7","author":"Makel","year":"2012","journal-title":"Perspectives
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are more important than novelty: Replication in the education sciences","volume":"43","author":"Makel","year":"2014","journal-title":"Educational
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between cancer stem cells and their niche govern metastatic colonization","volume":"481","author":"Malanchi","year":"2011","journal-title":"Nature"},{"key":"bib110","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.17584","article-title":"Replication
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glutamine metabolism by IDH1 mediates lipogenesis under hypoxia","volume":"481","author":"Metallo","year":"2011","journal-title":"Nature"},{"key":"bib116","doi-asserted-by":"publisher","DOI":"10.1186\/1741-7015-6-13","article-title":"Helping
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of germinal-center origin","volume":"42","author":"Morin","year":"2010","journal-title":"Nature
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acquire resistance to B-RAF(V600E) inhibition by RTK or N-RAS upregulation","volume":"468","author":"Nazarian","year":"2010","journal-title":"Nature"},{"key":"bib123","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1037\/1089-2680.2.2.175","article-title":"Confirmation
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bias: A ubiquitous phenomenon in many guises","volume":"2","author":"Nickerson","year":"1998","journal-title":"Review
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Utopia: II. Restructuring incentives and practices to promote truth over publishability","volume":"7","author":"Nosek","year":"2012","journal-title":"Perspectives
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preregistration revolution","volume":"115","author":"Nosek","year":"2018","journal-title":"PNAS"},{"key":"bib128","article-title":"Preregistration
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Becoming the Norm in Psychological Science","author":"Nosek","year":"2018","unstructured":"Nosek
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BA, Lindsay DS. 2018. Preregistration Becoming the Norm in Psychological Science.
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|
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https:\/\/www.psychologicalscience.org\/observer\/preregistration-becoming-the-norm-in-psychological-science
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|
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[Accessed August 5, 2021]."},{"key":"bib129","doi-asserted-by":"publisher","first-page":"815","DOI":"10.1016\/j.tics.2019.07.009","article-title":"Preregistration
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best time to argue about what a replication means? Before you do it","volume":"583","author":"Nosek","year":"2020","journal-title":"Nature"},{"key":"bib131","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3000691","article-title":"What
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2673
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|
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|
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endogenous tumour-promoting ligand of the human aryl hydrocarbon receptor","volume":"478","author":"Opitz","year":"2011","journal-title":"Nature"},{"key":"bib134","doi-asserted-by":"publisher","first-page":"883","DOI":"10.1038\/nm.2753","article-title":"Melanoma
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|
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2680
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2681
|
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Study: RAF Inhibitors Prime Wild-Type RAF to Activate the MAPK Pathway and
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continued use of retracted, invalid scientific literature","volume":"263","author":"Pfeifer","year":"1990","journal-title":"JAMA"},{"key":"bib138","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.12470","article-title":"Registered
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endogenous mRNAs","volume":"5","author":"Phelps","year":"2016","journal-title":"eLife"},{"key":"bib139","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1038\/nature10661","article-title":"A
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microRNA regulon that mediates endothelial recruitment and metastasis by cancer
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inhibitors transactivate RAF dimers and ERK signalling in cells with wild-type
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carcinoma","volume":"5","author":"Repass","year":"2016","journal-title":"eLife"},{"key":"bib154","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.25801","article-title":"Replication
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of transparency indicators across the biomedical literature: How open is open","volume":"19","author":"Serghiou","year":"2021","journal-title":"PLOS
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for MLL-fusion leukaemia","volume":"6","author":"Shan","year":"2017","journal-title":"eLife"},{"key":"bib163","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1016\/j.cell.2010.02.027","article-title":"A
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chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations","volume":"141","author":"Sharma","year":"2010","journal-title":"Cell"},{"key":"bib164","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.11566","article-title":"Registered
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favors tumor invasion and metastasis","volume":"8","author":"Sheen","year":"2019","journal-title":"eLife"},{"key":"bib167","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.26030","article-title":"Replication
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a neomorphic enzyme activity converting alpha-ketoglutarate to 2-hydroxyglutarate","volume":"6","author":"Showalter","year":"2017","journal-title":"eLife"},{"key":"bib168","doi-asserted-by":"publisher","first-page":"1359","DOI":"10.1177\/0956797611417632","article-title":"False-positive
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recently, but less flagrantly questionable research practices may be more
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prevalent and, ultimately, more damaging to the academic enterprise. Using
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an anonymous elicitation format supplemented by incentives for honest reporting,
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we surveyed over 2,000 psychologists about their involvement in questionable
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research practices. The impact of truth-telling incentives on self-admissions
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3156
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of questionable research practices was positive, and this impact was greater
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for practices that respondents judged to be less defensible. Combining three
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Vocational Behavior, 29(3)."},{"key":"p_7_7","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1093\/bjps\/38.4.533","volume":"38","author":"Brink
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Minnesota Press."},{"key":"p_24_24","unstructured":"Feyerabend, P. (1970).
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Against method. In M. Radner & S. Winokur (Eds.), Minnesota studies in thephilosophy
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of science: Vol. IV. Analyses of theories and methods of physics andpsychology
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the history of the psycho-analytic movement. In J. Strachey (Ed. &Trans.),
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R. M. (1987). Judgment andchoice: Thepsychology ofdecision. New York: Wiley."},{"key":"p_43_43","unstructured":"Hull,
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C. L. (1943). Principles of behavior. New York: Appleton-Century-Crofts."},{"key":"p_44_44","unstructured":"Hunter,
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across studies. Beverly Hills, CA: Sage."},{"key":"p_45_45","doi-asserted-by":"crossref","unstructured":"Kahneman,
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D., Slovic, P. & Tversky, A. (Eds.). (1982). Judgments under uncertainty:
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Heuristics and biases. Cambridge, England: Cambridge University Press.","DOI":"10.1017\/CBO9780511809477"},{"key":"p_46_46","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1177\/030631283013001003","volume":"13","author":"Kern
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T. S. (1970). The structure of scientific revolutions (2nd ed.; Vol. 2, No.
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2 of International Encyclopedia of Unzjied Science). Chicago: University of
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of the Aristotelian Society"},{"key":"p_49_49","unstructured":"Lakatos, I.
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(1 970). Falsification and the methodology of scientific research programmes.
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In I. Lakatos & A. Musgrave (Eds.), Criticism and the growth of knowledge
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(pp. 91-195). Cambridge, England: Cambridge University Press. (Reprinted in
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+
J. Worrall & G. Currie [Eds.], Imre Lakatos: Philosophical papers. Vol. I:
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The methodology of scientific research programmes [pp. 8- 1011. New York:
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Cambridge University Press, 1978)"},{"key":"p_50_50","doi-asserted-by":"crossref","unstructured":"Lakatos,
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& R. S. Cohen (Eds.), P. S. A. (1970 Boston Studies in the Philosophy of Science,
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Vol. 8, pp. 91-135). Dordrecht, Netherlands: Reidel. (Reprinted in J. Worrall
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& G. Currie [Eds.], Imre Lakatos: Philosophical papers. Vol. I: The methodology
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in social psychology \u2013 a discussion and suggested template","volume":"67","author":"van
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the prevalence of questionable research practices with incentives for truth
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claims and low levels of reproducibility are commonplace in psychology and
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cognitive neuroscience, due to an incentive structure that demands \u201cnewsworthy\u201d
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results. My overall argument here is that in addition to methodological reform,
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greater modesty is required across all levels - from individual researchers
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hiring committees) - to redirect expectations regarding what psychological
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and brain science can effectively deliver. Empirical work and the reform agenda
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should pivot away from making big claims on narrow evidence bases or single
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tools and focus on the limitations of our individual efforts, as well as how
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we can work together to build ways of thinking that enable integration and
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why modesty matters for science including the reform agenda, provide some
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practical steps that we can take to embrace modesty, rebut common misconceptions
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of what modesty means for science, and present some limitations of the approach.
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whilst placing work within a wider context that respects the complexity of
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the human brain, we will bolster the fidelity of scientific inference and
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thus help in a small way to generate a firmer footing upon which to build
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