commonmeta-ruby 3.2.6 → 3.2.8
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- checksums.yaml +4 -4
- data/Gemfile.lock +22 -8
- data/commonmeta.gemspec +1 -0
- data/lib/commonmeta/author_utils.rb +20 -3
- data/lib/commonmeta/cli.rb +2 -2
- data/lib/commonmeta/crossref_utils.rb +27 -19
- data/lib/commonmeta/readers/json_feed_reader.rb +27 -2
- data/lib/commonmeta/utils.rb +13 -1
- data/lib/commonmeta/version.rb +1 -1
- data/resources/crossref/common5.3.1.xsd +43 -35
- data/spec/author_utils_spec.rb +38 -0
- data/spec/cli_spec.rb +5 -5
- data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed_unregistered/blog_post_uuid.yml +49 -0
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/unregistered_posts.yml +215 -0
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/blogger_post.yml +20 -11
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_author_name_suffix.yml +215 -0
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_doi.yml +14 -9
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_without_doi.yml +9 -8
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/jekyll_post.yml +15 -10
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/syldavia_gazette_post_with_references.yml +328 -0
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/upstream_post_with_references.yml +824 -0
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post.yml +14 -9
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post_with_references.yml +390 -0
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/{json_feed_url → json_feed_unregistered_url}/all_posts.yml +11 -11
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/another_schema_org_from_front-matter.yml +103 -105
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/journal_article.yml +5 -5
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/journal_article_from_datacite.yml +4 -4
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_doi.yml +60 -9
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_upstream_blog.yml +55 -7
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_with_references.yml +824 -0
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/posted_content.yml +17 -17
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/schema_org_from_another_science_blog.yml +12 -8
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/schema_org_from_front_matter.yml +178 -181
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/schema_org_from_upstream_blog.yml +104 -92
- data/spec/readers/json_feed_reader_spec.rb +106 -12
- data/spec/utils_spec.rb +23 -5
- data/spec/writers/crossref_xml_writer_spec.rb +31 -3
- metadata +25 -9
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/json_feed_url/front-matter_blog.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_item_from_rogue_scholar_with_doi.yml +0 -163
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_item_from_upstream_blog.yml +0 -243
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_post_from_rogue_scholar_with_doi.yml +0 -210
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_post_from_upstream_blog.yml +0 -290
data/spec/author_utils_spec.rb
CHANGED
@@ -44,10 +44,42 @@ describe Commonmeta::Metadata, vcr: true do
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44
44
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expect(subject.is_personal_name?(name: author['name'])).to be true
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45
45
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end
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46
46
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47
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+
it 'has unknown given name and middle initial' do
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48
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author = { 'name' => 'Tejas S. Sathe' }
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49
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+
expect(subject.is_personal_name?(name: author['name'])).to be true
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50
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end
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51
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+
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47
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it 'has no info' do
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48
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author = { 'name' => 'M Fenner' }
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49
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expect(subject.is_personal_name?(name: author['name'])).to be true
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50
55
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end
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56
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+
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it 'name with title' do
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author = { 'name' => 'Tejas S. Sathe, MD' }
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expect(subject.is_personal_name?(name: author['name'])).to be true
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end
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61
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end
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+
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context 'cleanup_author' do
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it 'Smith J.' do
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author = 'Smith J.'
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expect(subject.cleanup_author(author)).to eq('Smith, J.')
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end
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+
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it 'Smith, John' do
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author = 'Smith, John'
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expect(subject.cleanup_author(author)).to eq('Smith, John')
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end
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it 'John Smith' do
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author = 'John Smith'
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expect(subject.cleanup_author(author)).to eq('John Smith')
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end
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it 'with email' do
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author = 'noreply@blogger.com (Roderic Page)'
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expect(subject.cleanup_author(author)).to eq('Roderic Page')
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end
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end
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context 'get_one_author' do
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@@ -69,6 +101,12 @@ describe Commonmeta::Metadata, vcr: true do
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)
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end
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it 'has name with title' do
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author = { 'name' => "Tejas S. Sathe, MD" }
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response = subject.get_one_author(author)
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expect(response).to eq('givenName' => 'Tejas S.', 'familyName' => 'Sathe', 'type' => 'Person')
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end
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it 'has name in display-order with ORCID' do
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input = 'https://doi.org/10.6084/M9.FIGSHARE.4700788'
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subject = described_class.new(input: input)
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data/spec/cli_spec.rb
CHANGED
@@ -341,9 +341,9 @@ describe Commonmeta::CLI do
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341
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end
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end
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343
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-
describe "
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-
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-
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-
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-
end
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# describe "json_feed_unregistered", vcr: true do
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# it "blog post uuid" do
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# expect { subject.json_feed_unregistered }.to output(/e4872b3e-cd15-407d-8406-33642c1a98b0\n/).to_stdout
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# end
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# end
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end
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@@ -0,0 +1,49 @@
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---
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http_interactions:
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- request:
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method: get
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uri: https://rogue-scholar.org/api/posts/unregistered
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body:
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encoding: UTF-8
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string: ''
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headers:
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Connection:
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- close
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Host:
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- rogue-scholar.org
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User-Agent:
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- http.rb/5.1.1
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response:
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status:
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code: 200
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message: OK
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headers:
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Age:
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- '0'
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Cache-Control:
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- public, max-age=0, must-revalidate
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Content-Length:
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- '2'
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Content-Type:
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- application/json; charset=utf-8
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Date:
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- Sat, 10 Jun 2023 08:41:01 GMT
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Etag:
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- '"38jmpejbxv2"'
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Server:
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- Vercel
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Strict-Transport-Security:
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- max-age=63072000
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X-Matched-Path:
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- "/api/posts/unregistered"
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X-Vercel-Cache:
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- MISS
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X-Vercel-Id:
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- fra1::iad1::zmnzt-1686386457205-d9f9a0745c33
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Connection:
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- close
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body:
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encoding: UTF-8
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string: "[]"
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recorded_at: Sat, 10 Jun 2023 08:41:01 GMT
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recorded_with: VCR 6.1.0
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@@ -0,0 +1,215 @@
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---
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http_interactions:
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- request:
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method: get
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uri: https://rogue-scholar.org/api/posts/unregistered
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body:
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encoding: UTF-8
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string: ''
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headers:
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Connection:
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- close
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Host:
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- rogue-scholar.org
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User-Agent:
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- http.rb/5.1.1
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response:
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status:
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code: 200
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message: OK
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headers:
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Age:
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- '0'
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Cache-Control:
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- public, max-age=0, must-revalidate
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Content-Length:
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- '16766'
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Content-Type:
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- application/json; charset=utf-8
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Date:
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- Sun, 11 Jun 2023 15:55:11 GMT
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Etag:
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- '"ojfwmyfwfacxk"'
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Server:
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- Vercel
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Strict-Transport-Security:
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- max-age=63072000
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X-Matched-Path:
|
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- "/api/posts/unregistered"
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X-Vercel-Cache:
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- MISS
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X-Vercel-Id:
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- fra1::iad1::tfxzn-1686498910666-ea864f114549
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Connection:
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- close
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body:
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encoding: UTF-8
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string: '[{"id":"https://svpow.com/2023/06/09/three-presentations-today-at-mte14-and-the-papers-that-go-with-them/","uuid":"ca2a7df4-f3b9-487c-82e9-27f54de75ea8","url":"https://svpow.com/2023/06/09/three-presentations-today-at-mte14-and-the-papers-that-go-with-them/","title":"Three
|
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+
presentations today at MTE14, and the papers that go with them","summary":"BIG
|
49
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+
day today. The 14th Symposium on Mesozoic Terrestrial Ecosystems and Biota
|
50
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+
(MTE14) is taking place in Salt Lake City this week. Normally I’d be there
|
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in a heartbeat, but my son is graduating from high...","date_published":"2023-06-09T13:02:26Z","date_modified":"2023-06-09T13:02:26Z","authors":[{"url":null,"name":"Matt
|
52
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+
Wedel"}],"image":null,"content_html":"<p><a href=\"https://svpow.files.wordpress.com/2023/06/ripple-rock-in-the-oklahoma-morrison.jpg\"><img
|
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+
loading=\"lazy\" data-attachment-id=\"21001\" data-permalink=\"https://svpow.com/2023/06/09/three-presentations-today-at-mte14-and-the-papers-that-go-with-them/ripple-rock-in-the-oklahoma-morrison/\"
|
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data-orig-file=\"https://svpow.files.wordpress.com/2023/06/ripple-rock-in-the-oklahoma-morrison.jpg\"
|
55
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+
data-orig-size=\"2000,2000\" data-comments-opened=\"1\" data-image-meta=\"{\"aperture\":\"1.8\",\"credit\":\"\",\"camera\":\"iPhone
|
56
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+
7\",\"caption\":\"\",\"created_timestamp\":\"1530009833\",\"copyright\":\"\",\"focal_length\":\"3.99\",\"iso\":\"20\",\"shutter_speed\":\"0.00051203277009729\",\"title\":\"\",\"orientation\":\"1\"}\"
|
57
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+
data-image-title=\"Ripple rock in the Oklahoma Morrison\" data-image-description=\"\"
|
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+
data-image-caption=\"\" data-medium-file=\"https://svpow.files.wordpress.com/2023/06/ripple-rock-in-the-oklahoma-morrison.jpg?w=300\"
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data-large-file=\"https://svpow.files.wordpress.com/2023/06/ripple-rock-in-the-oklahoma-morrison.jpg?w=480\"
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class=\"size-large wp-image-21001 aligncenter\" src=\"https://svpow.files.wordpress.com/2023/06/ripple-rock-in-the-oklahoma-morrison.jpg?w=480\"
|
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alt=\"\" width=\"480\" height=\"480\" srcset=\"https://svpow.files.wordpress.com/2023/06/ripple-rock-in-the-oklahoma-morrison.jpg?w=480
|
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480w, https://svpow.files.wordpress.com/2023/06/ripple-rock-in-the-oklahoma-morrison.jpg?w=960
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960w, https://svpow.files.wordpress.com/2023/06/ripple-rock-in-the-oklahoma-morrison.jpg?w=150
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150w, https://svpow.files.wordpress.com/2023/06/ripple-rock-in-the-oklahoma-morrison.jpg?w=300
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300w, https://svpow.files.wordpress.com/2023/06/ripple-rock-in-the-oklahoma-morrison.jpg?w=768
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768w\" sizes=\"(max-width: 480px) 100vw, 480px\" /></a></p>\n<p>BIG day today.
|
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+
The 14th Symposium on Mesozoic Terrestrial Ecosystems and Biota (MTE14) is
|
68
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+
taking place in Salt Lake City this week. Normally I’d be there in a
|
69
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+
heartbeat, but my son is graduating from high school next week and I’m
|
70
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+
far too busy to get away. Still, I’m an author on one poster and two
|
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+
talks that are running today, along with the three associated short papers
|
72
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+
that are published in the conference volume in The Anatomical Record. </p>\n<p>I
|
73
|
+
will be blogging about these things, and shortly, but for now here are Wedel-related
|
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+
presentations and links to the papers, in chronological order. (The whole
|
75
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+
conference volume is available <a href=\"https://anatomypubs.onlinelibrary.wiley.com/doi/full/10.1002/ar.25219\">here</a>,
|
76
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+
I just extracted the papers I’m on as separate PDFs to post in the links
|
77
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+
below.)</p>\n<p>1. Wedel and Atterholt on expanded neurocentral joints in
|
78
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+
sauropods — Jessie is presenting our poster, which should be up for
|
79
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most of the day. Citation and link to paper:</p>\n<p style=\"padding-left:
|
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+
40px\"><a href=\"https://sauroposeidon.files.wordpress.com/2010/04/wedel-and-atterholt-2023-expanded-neurocentral-joints-in-sauropods.pdf\">Wedel,
|
81
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+
M.J., and Atterholt, J. 2023. Expanded neurocentral joints in the vertebrae
|
82
|
+
of sauropod dinosaurs. In Hunt-Foster, R.K., Kirkland, J.I., and Loewen, M.A.
|
83
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+
(eds), 14th Symposium on Mesozoic Terrestrial Ecosystems and Biota. The Anatomical
|
84
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+
Record 306(S1):256-257.</a></p>\n<p>2. Curtice et al. on the first material
|
85
|
+
of <em>Haplocanthosaurus</em> from Dry Mesa — I believe Brian Curtice
|
86
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+
and Colin Boisvert are tag-teaming this talk at 2:00 pm MDT. </p>\n<p style=\"padding-left:
|
87
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+
40px\"><a href=\"https://sauroposeidon.files.wordpress.com/2010/04/curtice-et-al-2023-haplocanthosaurus-from-dry-mesa.pdf\">Curtice,
|
88
|
+
B., Wedel, M.J., Wilhite, D.R., and Boisvert, C. 2023. New material of <em>Haplocanthosaurus</em>
|
89
|
+
(Hatcher 1903) from the Dry Mesa Dinosaur Quarry and a comment on sauropod
|
90
|
+
diversity. In Hunt-Foster, R.K., Kirkland, J.I., and Loewen, M.A. (eds), 14th
|
91
|
+
Symposium on Mesozoic Terrestrial Ecosystems and Biota. The Anatomical Record
|
92
|
+
306(S1):79-81.</a></p>\n<p>3. Weil et al. on Morrison microvertebrates from
|
93
|
+
the Oklahoma panhandle — Anne Weil is giving this talk at 2:15 pm MDT.</p>\n<p
|
94
|
+
style=\"padding-left: 40px\"><a href=\"https://sauroposeidon.files.wordpress.com/2010/04/weil-et-al-2023-oklahoma-morrison-microvertebrates.pdf\">Weil,
|
95
|
+
A., Hall, L., and Wedel, M.J. 2023. Microvertebrate expansion of known fauna
|
96
|
+
of the Morrison Formation of Oklahoma will enable more meaningful comparisons
|
97
|
+
with other regions. In Hunt-Foster, R.K., Kirkland, J.I., and Loewen, M.A.
|
98
|
+
(eds), 14th Symposium on Mesozoic Terrestrial Ecosystems and Biota. The Anatomical
|
99
|
+
Record 306(S1):257-258.</a></p>\n<p>Stand by for more info on all this stuff.
|
100
|
+
And if you’re attending MTE14, go catch these presentations and say
|
101
|
+
hi to all these excellent human beings!</p>\n","tags":["#MTE14","conferences","navel
|
102
|
+
blogging","timely"],"language":"en","blog_id":"dkvra02","blog":{"id":"dkvra02","title":"Sauropod
|
103
|
+
Vertebra Picture of the Week","description":"SV-POW! ... All sauropod vertebrae,
|
104
|
+
except when we're talking about Open Access","language":"en","favicon":null,"feed_url":"https://svpow.com/feed/atom/","home_page_url":"https://svpow.com","user_id":"8498eaf6-8c58-4b58-bc15-27eda292b1aa","created_at":"2023-05-31T14:28:02+00:00","indexed_at":"2023-02-01","feed_format":"application/atom+xml","license":"https://creativecommons.org/licenses/by/4.0/legalcode","generator":"WordPress
|
105
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+
(.com)","category":"Natural Sciences","prefix":"10.59350","modified_at":"2023-05-27T00:26:38+00:00","version":"https://jsonfeed.org/version/1.1","backlog":true}},{"id":"http://bjoern.brembs.net/2023/06/the-beginning-of-the-end-for-academic-publishers/","uuid":"c0ebaf2d-8e50-404c-8db7-4fd04e56aded","url":"http://bjoern.brembs.net/2023/06/the-beginning-of-the-end-for-academic-publishers/","title":"The
|
106
|
+
beginning of the end for academic publishers?","summary":"On May 23, the Council
|
107
|
+
of the EU adopted a set of conclusions on scholarly publishing that, if followed
|
108
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+
through, would spell the end for academic publishers and scholarly journals
|
109
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as we know them. On the same...","date_published":"2023-06-02T07:01:14Z","date_modified":"2023-06-02T07:01:15Z","authors":[{"url":null,"name":"Björn
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Brembs"}],"image":null,"content_html":"<img src=\"http://bjoern.brembs.net/wp//wp-content/uploads/2013/05/politics.gif\"
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width=\"50\" height=\"50\" alt=\"science politics\" title=\"science politics\"
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/><br/>\n<p>On May 23, the <a href=\"https://en.wikipedia.org/wiki/Council_of_the_European_Union\">Council
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of the EU</a> adopted a <a href=\"https://www.consilium.europa.eu/en/press/press-releases/2023/05/23/council-calls-for-transparent-equitable-and-open-access-to-scholarly-publications/\">set
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of conclusions</a> on scholarly publishing that, if followed through, would
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spell the end for academic publishers and scholarly journals as we know them.
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On the same day, the adoption was followed by a <a href=\"https://www.coalition-s.org/open-science-stakeholders-welcome-european-efforts-towards-publicly-owned-and-not-for-profit-scholarly-communication/\">joint
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statement</a> of support by the largest and most influential research organizations
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in Europe. At the heart of the goals spelled out in the conclusions and the
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statement of support is the creation of a “publicly owned and not-for-profit”
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infrastructure for scholarly publications.</p>\n\n\n\n<p>Specifically, the
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Council </p>\n\n\n\n<blockquote class=\"wp-block-quote\">\n<p>ENCOURAGES Member
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States and the Commission to invest in and foster interoperable, not-for-profit
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infrastructures for publishing based on open source software and open standards,
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in order to avoid the lock-in of services as well as proprietary systems,
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and to connect these infrastructures to the EOSC</p>\n</blockquote>\n\n\n\n<p>This
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echos almost verbatim our proposal from 2021 where we outline a <a href=\"https://doi.org/10.5281/zenodo.5526634\">replacement
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for academic journals</a>. In this post, we detail the reasons behind this
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seemingly radical proposal:</p>\n\n\n\n<figure class=\"wp-block-image size-large
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is-resized\"><a href=\"http://bjoern.brembs.net/wp/wp-content/uploads/2023/06/FIG_circular_v1.5.png\"><img
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decoding=\"async\" src=\"http://bjoern.brembs.net/wp/wp-content/uploads/2023/06/FIG_circular_v1.5-1024x863.png\"
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alt=\"Three major scholarly crises in a vicious cycle\" class=\"wp-image-2571\"
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width=\"512\" height=\"432\" srcset=\"http://bjoern.brembs.net/wp/wp-content/uploads/2023/06/FIG_circular_v1.5-1024x863.png
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1024w, http://bjoern.brembs.net/wp/wp-content/uploads/2023/06/FIG_circular_v1.5-300x253.png
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300w, http://bjoern.brembs.net/wp/wp-content/uploads/2023/06/FIG_circular_v1.5-768x647.png
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768w, http://bjoern.brembs.net/wp/wp-content/uploads/2023/06/FIG_circular_v1.5-50x42.png
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50w, http://bjoern.brembs.net/wp/wp-content/uploads/2023/06/FIG_circular_v1.5.png
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1175w\" sizes=\"(max-width: 512px) 100vw, 512px\" /></a><figcaption class=\"wp-element-caption\"><em>A
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vicious cycle of three crises</em>.<br />With their supra-inflationary price
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increases, profit-maximizing journals overcharge (via subscriptions or article
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processing charges) institutions by a factor of up to tenfold, extracting
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library budgets with little if anything left for infrastructural development.
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The resulting lack of infrastructure funds is a crisis of affordability: institutions
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cannot afford to invest in technology and human support for relieving researchers
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of menial tasks such as manuscript submission, data deposition, code publication,
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etc. This results in a functionality crisis that entails researchers lacking
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time, functionalities and human support both for efficient scrutiny during
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the review process as well as for making their own research open and reproducible.
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Not shown: Journals have apparently not invested their surplus into reviewer
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support, resulting in little improvement over the last decades, such that
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researchers are still lacking basic functionalities such as, e.g., comments
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via authoring system, direct author communication, AI-assisted error and fraud
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detection, efficient manuscript submission, etc., contributing to the functionality
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crisis. As the journals keep increasing their prices without a concomitant
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rise in investments, they fuel the replicability crisis.</figcaption></figure>\n\n\n\n<p>This
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vicious cycle has been allowed to go on for so long, that more and more experts
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are now calling for precisely such a disruptive break. The time for small,
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evolutionary steps has passed and the parasitic publishing corporations have
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shown little willingness over the last decades even to just mitigate, let
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alone solve the problems caused by their extractive business models. For more
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than a decade, an ever-growing group of researchers have called to <a href=\"http://bjoern.brembs.net/2013/06/cut-out-the-parasitic-middlemen/\">cut
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out these parasitic middle-men</a>. It now finally seems as if our arguments
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have been convincing. Everything in the Council’s conclusions reiterates
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what the open science community has been fighting for in all this time: vendor
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lock-in needs to be broken, scholarly governance established and fragmenting
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silos replaced with interoperable, federated infrastructure.</p>\n\n\n\n<p>The
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technical solutions needed for this modernization from 17th century journals
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to 21 century digital technology are plenty and readily available off the
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shelf. Scholarship has the choice of either picking pre-existing solutions
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such as <a href=\"https://core.ac.uk/\">CORE</a> or <a href=\"https://openresearchcentral.org/\">ORC</a>,
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or design a new network. In either case, the general structural design of
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such a network may look something like this:</p>\n\n\n\n<figure class=\"wp-block-image
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size-large is-resized\"><a href=\"http://bjoern.brembs.net/wp/wp-content/uploads/2023/06/FIG_openscience_platform_v1.6.png\"><img
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decoding=\"async\" loading=\"lazy\" src=\"http://bjoern.brembs.net/wp/wp-content/uploads/2023/06/FIG_openscience_platform_v1.6-1024x623.png\"
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alt=\"\" class=\"wp-image-2572\" width=\"512\" height=\"312\" srcset=\"http://bjoern.brembs.net/wp/wp-content/uploads/2023/06/FIG_openscience_platform_v1.6-1024x623.png
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768w, http://bjoern.brembs.net/wp/wp-content/uploads/2023/06/FIG_openscience_platform_v1.6-1536x934.png
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2048w, http://bjoern.brembs.net/wp/wp-content/uploads/2023/06/FIG_openscience_platform_v1.6-50x30.png
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50w\" sizes=\"(max-width: 512px) 100vw, 512px\" /></a><figcaption class=\"wp-element-caption\"><em>Concept
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for a federated scholarly information network</em>.<br />A federated network
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of institutional repositories constitutes the underlying infrastructure. Ideally,
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this infrastructure is designed redundantly, such that large fractions of
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nodes may go offline and the remaining nodes still provide 100% of the content.
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Users only directly interact with the output and narrative layers. The output
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layer contains all research objects, text, data and code. The narrative layer
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combines research objects in various forms, including research articles. The
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community layer encompasses standard social technologies such as likes, follows
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+
and other network tools (see also “<a href=\"https://doi.org/10.5281/zenodo.7643817\">Mastodon
|
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over Mammon</a>“). Modified from <a href=\"https://blogs.lse.ac.uk/impactofsocialsciences/2017/04/10/rather-than-simply-moving-from-paying-to-read-to-paying-to-publish-its-time-for-a-european-open-access-platform\">LSE</a>.</figcaption></figure>\n\n\n\n<p>Picking
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an existing solution such as CORE or ORC comes with the advantage that little
|
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new development has to be done and that it is obviously very cheap: everything
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is already in place and only needs to be expanded. The downsides are that
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the existing solutions have been designed in the current ecosystem and that
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may have entailed some historical baggage one would need to identify and fix.
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Conversely, picking off-the-shelf components to build a replacement from scratch
|
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+
costs more, but has the advantage to be able to build a state-of.the-art system
|
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with all the bells and whistles from the ground up. It’s a bit like
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the choice between buying a used or new car or house.</p>\n\n\n\n<p>Obviously,
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right after the declaration came out, the corporate misinformation machine
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sprang into high gear. I won’t repeat the misleading, false or sometimes
|
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just comically desperate attempts at smearing an obviously well thought-through,
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sound and logical solution that has been decades in the making. Suffice it
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to say, there are plenty of reasons why the plans outlined by the Council
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have drawn such widespread support from all corners of the research community,
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while the only resistance comes from the monopolistic corporations. This declaration
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tackles the root of the replicability, affordability and functionality crises.
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It aims to treat the disease, not the symptoms and has the potential to develop
|
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into an effective vaccine against parasitic businesses striving to leech the
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public purse. Little wonder these businesses fear it so much.</p>\n","tags":["science
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politics","Council of the EU","infrastructure","publishers"],"language":"en","blog_id":"8q8xh52","blog":{"id":"8q8xh52","title":"bjoern.brembs.blog","description":"The
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blog of neurobiologist Björn Brembs","language":"en","favicon":null,"feed_url":"http://bjoern.brembs.net/feed/atom/","home_page_url":"http://bjoern.brembs.net","user_id":"8498eaf6-8c58-4b58-bc15-27eda292b1aa","created_at":"2023-05-31T08:09:10+00:00","indexed_at":"2023-04-04","feed_format":"application/atom+xml","license":"https://creativecommons.org/licenses/by/4.0/legalcode","generator":"WordPress","category":"Natural
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Sciences","prefix":"10.59350","modified_at":"2023-03-14T14:13:30+00:00","version":"https://jsonfeed.org/version/1.1","backlog":true}}]'
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years and a million links","summary":"As trailed on a Twitter thread last
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names to their original descriptions in the taxonomic literature. Putting
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together a manuscript on linking taxonomic names to the primary literature,
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basically “um, what, exactly, have you been doing all these years?”. TL;DR
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Across fungi, plants, and animals approx 1.3 million names have been linked
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to a persistent identifier for a publication.— Roderic Page (@rdmpage) May
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(Roderic Page)"}],"image":null,"content_html":"<p>As trailed on a Twitter
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to map taxonomic names to their original descriptions in the taxonomic literature.</p>\n<blockquote
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class=\"twitter-tweet\"><p lang=\"en\" dir=\"ltr\">Putting together a manuscript
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exactly, have you been doing all these years?”. TL;DR Across fungi, plants,
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is also a simple app to demonstrate these links, see <a href=\"https://species-cite.herokuapp.com\">https://species-cite.herokuapp.com</a>.\n\n\n\n<blockquote>\n<p>Written
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raves (and occasionally considered opinions) on phyloinformatics, taxonomy,
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and biodiversity informatics. For more ranty and less considered opinions,
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see my <a href=\"https://twitter.com/rdmpage\">Twitter feed</a>.<br>ISSN 2051-8188.
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Written content on this site is licensed under a <a href=\"https://creativecommons.org/licenses/by/4.0/\">Creative
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to Build an Academic Powerhouse: Let''s Study Who''s Doing it","summary":"A
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Data Exploration with Public Data from the Academic Surgical Congress","date_published":"2023-06-03T04:54:30Z","date_modified":null,"authors":[{"url":null,"name":"Tejas
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S. Sathe, MD"}],"image":null,"content_html":"<p>Students and residents aspiring
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for a career in academic surgery are looking for training programs that will
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help jumpstart their careers by exposing them to mentorship and opportunities
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to conduct research. While the gold standard of academic productivity (for
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the time being) remains peer-reviewed publications, conference presentations
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are an important secondary metric. In addition to feeding eventual papers,
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conference talks allow trainees to practice presentation skills, build their
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networks, and learn about the work being done at peer institutions and the
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field more broadly. Residents pursuing professional development are encouraged
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+
to apply to and attend conferences, though in the post COVID era the cost
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of conference attendance and travel are being re-evaluated. Even moreso than
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publications, conference presentations are typically led by students and residents.
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For now, academic conference participation can serve as an important albeit
|
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limited metric to evaluate an overall institution''s research power –
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especially as it relates to trainees.</p><p>In order to understand how to
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build a successful research program, we wanted to understand who had already
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done so. Conceivably, by finding successful examples, we can conduct interviews
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+
and focus groups among key stakeholders at these programs to understand what
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they did, and how these actions can be replicated. We were particularly interested
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in seeing which programs demonstrated a high number of accepted abstracts
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and which programs were able to improve their abstract performance from year
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to year. </p><p>The <a href=\"https://www.academicsurgicalcongress.org/?ref=ideasurg.pub\">Academic
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Surgical Congress</a> (ASC) is a joint surgical meeting co-hosted by the <a
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href=\"https://www.aasurg.org/?ref=ideasurg.pub\">Association for Academic
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Surgery</a> (AAS) and the <a href=\"https://www.susweb.org/?ref=ideasurg.pub\">Society
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for University Surgeons</a> (SUS) and held annually in February. Anecdotally,
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it is a popular conference for students and residents to attend. The ASC maintains
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a public archive of all abstracts dating from 2015-2020. We obtained a machine
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readable version of this public database through the webmaster (this version
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of the data spans 2016 to 2023).</p><p>For each abstract, we looked at the
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year and primary institution at which the work was conducted. In order to
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intuit the primary institution, we searched the institution block string for
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the first presence of \"university\", \"hospital\", \"institute\", or \"medical
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center\" or the first expression to occur before a comma. This method was
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chosen as institutions’ names are written variably (Department of Surgery,
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University Hospital, New York, NY vs. University Hospital, Division of Colorectal
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Surgery, Department of Surgery, New York, NY). Unfortunately, our code is
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unable to merge slight variations in the resultant institution name (University
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of Michigan vs. University of Michigan Ann Arbor). </p><p>In order to do a
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primary survey of institutional trends in this dataset, we conducted the following
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analyses. First, we measured the number of abstracts accepted each year from
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2016 to 2023. Second, we looked at the number of accepted abstracts by institution
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over the entire study period. Then, we looked at the number of abstract institutions
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by institution and year to study changes in institutional trends over time.
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Finally, we did a subset analysis on post-COVID data (2021 to 2023) to look
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at absolute and per cent year-over-year changes in accepted abstracts to see
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which institutions were able to significantly increase their abstract performance
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in one year. </p><h3 id=\"accepted-abstracts-are-increasing-but-down-from-peak\">Accepted
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Abstracts are increasing but down from peak</h3><p>We plotted the total number
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of abstracts accepted by year. The number of accepted abstracts increased
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from 1125 in 2016 to an all-time high of 1742 in 2020 before declining to
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922 and 848 in 2021 and 2022, respectively. Accepted abstracts have since
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rebounded to 1469 in 2023, or roughly 84% of the maximum amount. Of note,
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the 2021 and 2022 meetings were held virtually due to the COVID-19 pandemic.
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Conversely the 2020 meeting was held immediately prior to the institution
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of lockdowns and other social distancing policies.</p><figure class=\"kg-card
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kg-image-card kg-width-wide\"><img src=\"https://www.ideasurg.pub/content/images/2023/06/newplot--1-.png\"
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class=\"kg-image\" alt loading=\"lazy\" width=\"1400\" height=\"800\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/newplot--1-.png
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600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/newplot--1-.png
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1000w, https://www.ideasurg.pub/content/images/2023/06/newplot--1-.png 1400w\"
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sizes=\"(min-width: 1200px) 1200px\"></figure><h3 id=\"alabama-michigan-lead-abstract-acceptances-during-study-period\">Alabama,
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Michigan lead abstract acceptances during study period</h3><p>Next, we plotted
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the total number of accepted abstracts by institution. The graph shows data
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for the twenty leading institutions. The University of Alabama and the University
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of Michigan lead in abstract acceptances during the study period (477 and
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348, respectively). Given an eight year time-range, the top twenty institutions
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reflect an average annual abstract acceptance ranging from roughly thirteen
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to 60.</p><figure class=\"kg-card kg-image-card kg-width-wide\"><img src=\"https://www.ideasurg.pub/content/images/2023/06/newplot--2-.png\"
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class=\"kg-image\" alt loading=\"lazy\" width=\"1400\" height=\"800\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/newplot--2-.png
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600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/newplot--2-.png
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1000w, https://www.ideasurg.pub/content/images/2023/06/newplot--2-.png 1400w\"
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sizes=\"(min-width: 1200px) 1200px\"></figure><p>We also plotted the number
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of accepted abstracts by year using a separate line plot for each individual.
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While Michigan has maintained between 30 and 60 abstracts for each year, Alabama
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went from 6 to 48 abstracts between 2016 and 2017 and has maintained greater
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than 60 accepted abstracts each year. There is a notable dip in the number
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of accepted abstracts from 2021 to 2022, consistent with a similar trend in
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the total yearly acceptance data. </p><figure class=\"kg-card kg-image-card
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kg-width-wide\"><img src=\"https://www.ideasurg.pub/content/images/2023/06/newplot--8-.png\"
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class=\"kg-image\" alt loading=\"lazy\" width=\"1400\" height=\"800\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/newplot--8-.png
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600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/newplot--8-.png
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1000w, https://www.ideasurg.pub/content/images/2023/06/newplot--8-.png 1400w\"
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sizes=\"(min-width: 1200px) 1200px\"></figure><p>Overall, there appears to
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be a general clustering of the other eighteen institutions in the top twenty,
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a trend seen in both the aggregate and the year-to-year data.</p><h3 id=\"mgh-brigham-lead-absolute-and-per-cent-increase-in-abstracts-in-2023\">MGH,
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Brigham lead absolute and per cent increase in abstracts in 2023</h3><p>Next,
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we measured the absolute and percent change between accepted abstracts in
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consecutive years for the top twenty institutions. We restricted our analysis
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to 2021, 2022, and 2023. The greatest absolute increases in accepted abstracts
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came from Massachusetts General Hospital in 2023 (27), Brigham and Women''s
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Hospital in 2023 (16), and UCLA in 2022 (16). The greatest percentage increases
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in accepted abstracts came from Brigham and Women''s Hospital in 2023 (800%),
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Johns Hopkins in 2023 (500%), and Massachusetts General Hospital in 2023 (386%).
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Of note, Johns Hopkins and Brigham and Women''s Hospital also had the largest
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absolute and percentage decrease in accepted abstracts in 2022. Interestingly,
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University of Alabama (+4 in 2022, +3 in 2023) and University of Michigan
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(+11 in 2023)  - which rank at the top in all time and yearly abstracts
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- experienced less extreme swings during the 2021-2023 time period.</p><figure
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class=\"kg-card kg-image-card kg-width-wide\"><img src=\"https://www.ideasurg.pub/content/images/2023/06/newplot--7-.png\"
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class=\"kg-image\" alt loading=\"lazy\" width=\"1400\" height=\"800\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/newplot--7-.png
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600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/newplot--7-.png
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1000w, https://www.ideasurg.pub/content/images/2023/06/newplot--7-.png 1400w\"
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sizes=\"(min-width: 1200px) 1200px\"></figure><figure class=\"kg-card kg-image-card
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kg-width-wide\"><img src=\"https://www.ideasurg.pub/content/images/2023/06/newplot--4-.png\"
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class=\"kg-image\" alt loading=\"lazy\" width=\"1400\" height=\"800\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/newplot--4-.png
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600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/newplot--4-.png
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1000w, https://www.ideasurg.pub/content/images/2023/06/newplot--4-.png 1400w\"
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sizes=\"(min-width: 1200px) 1200px\"></figure><h3 id=\"conclusions\">Conclusions</h3><p>In
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this data exploration, we analyzed abstract acceptance data for the Academic
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Surgical Congress between 2016 and 2023. We showed that the number of abstracts
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increased from 2016 to 2020, dipped in 2021 and 2022, and is recovering in
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2023 - likely reflecting the variability forced by COVID19 and the transition
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to virtual conferences in 2021 and 2022. We also showed that the University
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of Alabama and the University of Michigan have significantly led accepted
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abstracts throughout the study period with University of Alabama maintaining
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a top position following an impressive 700 percent increase in abstracts between
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2016 and 2017. In 2023, Massachusetts General Hospital and Brigham and Women''s
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Hospital have led absolute and percent increases in abstract submissions,
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though this may reflect some degree of reversion following drops in abstract
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acceptances in 2022.</p><h3 id=\"limitations-and-future-directions\">Limitations
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and Future Directions</h3><p>This data exploration has several limitations.
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First, our study is limited to one conference and conferences themselves are
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only a limited component of academic productivity. However, the Academic Surgical
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Congress is an international meeting that is well regarded, popular among
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trainees, and has consistent multi-year data. Another limitation of our study
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is our assumption that the first institution listed in the author block is
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the primary institution–a method which does not take into account multi-institutional
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abstracts. However, we suspect this reflects the minority of the abstracts.
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Finally, we have not fully optimized name-matching to correctly combine terms
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like \"University of Michigan\" and \"University of Michigan Ann Arbor\".
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However, given that most of the data currently is only for the top 20 institutions,
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we believe the overall trends will be preserved.</p><p>In the future, we can
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attempt to obtain more granular data on authors and institutions and optimize
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the capture of this data for aggregated analysis. We are also researching
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different techniques to perform string matching to fix the institution name
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issue. We can improve the generalizability of our findings by bringing in
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similar data from other large meetings – such as the American College
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of Surgeons Clinical Congress and the Society of American Gastrointestinal
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and Endoscopic Surgeons (SAGES). We can also use the PubMed API to perform
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similar analyses in top surgical journals such as JAMA Surgery or the Annals
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of Surgery.</p><p>With regards to the data we have obtained, we can conduct
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survey-based studies or focus groups with key stakeholders from institutions
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that have demonstrated strong abstract performance during the study period
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as well as those who have shown significant improvement. By talking to department
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chairs, program directors, and research and education leaders we can understand
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what steps each institution took to improve abstract acceptance (e.g. hiring
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a new research faculty, creating a mentorship program, providing administrative
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support for IRBs/stats etc.). Following this, we can map individual interventions
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to improvements to understand the contribution that each can have on increased
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academic productivity.</p><p>We have also not yet mined the abstract body
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for themes. Using natural language processing, we can understand how themes
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and trends of emergent research change from year to year, and even develop
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models to predict which topics will be of interest in future works. This will
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likely be the subject of a future data exploration.</p><p>Overall, we hope
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to demonstrate that abstract acceptance data from a single international meeting
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can provide interesting, meaningful data on which programs have strong research
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infrastructure and which programs are making strides to achieve it. By studying
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this data and improving the inputs, we can better understand whose example
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to follow and ultimately develop a playbook that all institutions can employ
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to maximize the academic opportunities of students and trainees.</p><h3 id=\"see-the-data\">See
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the Data</h3><p>You can see the raw data as well as all of our code here,
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and use this for your own studies with appropriate attribution.</p><p><a href=\"https://deepnote.com/@tejas-sathe-a73f/ASC-Data-Exploration-948ca211-bfc7-459b-9d6d-ef952a5baf32?ref=ideasurg.pub\">https://deepnote.com/@tejas-sathe-a73f/ASC-Data-Exploration-948ca211-bfc7-459b-9d6d-ef952a5baf32</a></p>","tags":["Pre-Print"],"language":"en","references":[],"blog_id":"3cxcm20","blog":{"id":"3cxcm20","title":"I.D.E.A.S.","description":"Innovation
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and Design Experiments in Academic Surgery (I.D.E.A.S.)","language":"en","favicon":"https://www.ideasurg.pub/favicon.png","feed_url":"https://www.ideasurg.pub/rss/","home_page_url":"https://www.ideasurg.pub/","user_id":"8498eaf6-8c58-4b58-bc15-27eda292b1aa","created_at":"2023-05-31T13:44:29+00:00","indexed_at":"2023-01-04","feed_format":"application/rss+xml","license":"https://creativecommons.org/licenses/by/4.0/legalcode","generator":"Ghost
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5.51","category":"Medical and Health Sciences","prefix":"10.59350","modified_at":"2023-06-03T04:54:30+00:00","version":"https://jsonfeed.org/version/1.1","backlog":false}}'
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recorded_at: Thu, 15 Jun 2023 05:34:55 GMT
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recorded_with: VCR 6.1.0
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