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Fix post-render-html.R
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@danielvartan
danielvartan committed Sep 29, 2023
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2 changes: 2 additions & 0 deletions R/_dev.R
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Expand Up @@ -72,3 +72,5 @@
# * Fix relative path for images.
# * Transform BiBTeX keys in LaTeX citations, when rendered with pandoc
# * Add a update function for tags in the latex files (e.g., cover page)
# * Find why the document have to be rendered twice
# * Add stop list em transforming titles in setence case
5 changes: 3 additions & 2 deletions R/quarto-post-render-html.R
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Expand Up @@ -20,14 +20,15 @@ project_name <- here::here() |> basename() # rstudioapi::getActiveProject()

output_dir_html <- here::here(quarto_yml_html_vars$project$`output-dir`)
output_dir_pdf <- here::here(quarto_yml_pdf_vars$project$`output-dir`)
pdf_dir <- here::here("pdf")

for (i in c(output_dir_html, output_dir_pdf)) {
for (i in c(output_dir_html, output_dir_pdf, pdf_dir)) {
if (!checkmate::test_directory_exists(i)) dir.create(i) |> invisible()
}

# Copy PDF (if exists) to `docs` folder ----------

pdf_file <- list.files(pdf, full.names = TRUE, pattern = ".pdf$")
pdf_file <- list.files(pdf_dir, full.names = TRUE, pattern = ".pdf$")

if (length(pdf_file) == 1) {
rutils:::copy_file(pdf_file, file.path(output_dir_html, "index.pdf"))
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5 changes: 3 additions & 2 deletions R/quarto-post-render-pdf.R
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Expand Up @@ -20,8 +20,9 @@ project_name <- here::here() |> basename() # rstudioapi::getActiveProject()

output_dir_html <- here::here(quarto_yml_html_vars$project$`output-dir`)
output_dir_pdf <- here::here(quarto_yml_pdf_vars$project$`output-dir`)
pdf_dir <- here::here("pdf")

for (i in c(output_dir_html, output_dir_pdf)) {
for (i in c(output_dir_html, output_dir_pdf, pdf_dir)) {
if (!checkmate::test_directory_exists(i)) dir.create(i) |> invisible()
}

Expand All @@ -32,7 +33,7 @@ pdf_file <- list.files(output_dir_pdf, full.names = TRUE, pattern = ".pdf$")
if (length(pdf_file) == 1) {
rutils:::remove_pdf_cover(pdf_file)

rutils:::copy_file(pdf_file, file.path("pdf", "index.pdf"))
rutils:::copy_file(pdf_file, file.path(pdf_dir, "index.pdf"))
rutils:::copy_file(pdf_file, file.path(output_dir_html, "index.pdf"))

list.files(here::here(), full.names = TRUE, pattern = ".tex$") |>
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2 changes: 1 addition & 1 deletion _quarto-html.yml
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Expand Up @@ -40,7 +40,7 @@ book:

citation:
type: thesis
url: https://danielvartan.github.io/mastersthesis/
url: https://danielvartan.github.io/tesesusp/
google-scholar: false

# See <https://quarto.org/docs/output-formats/html-themes.html>.
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2 changes: 1 addition & 1 deletion _variables.yml
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@@ -1 +1 @@
format: pdf
format: html
11 changes: 1 addition & 10 deletions docs/index.html
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Expand Up @@ -301,7 +301,7 @@ <h1 class="title">{tesesusp}: a Quarto format for USP theses and dissertations</
</div>
</div>
<p>You are seeing the web version of this thesis.</p>
<p>The analyses contained in this document are 100% reproducible. They were performed using the <a href="https://www.r-project.org/">R programming language</a> and the <a href="https://quarto.org/">Quarto</a> publishing system (an evolution of <a href="https://rmarkdown.rstudio.com/">R Markdown</a>). Click on the GitHub icon in the menu to access the thesis code repository.</p>
<p>The analyses contained in this document are 100% reproducible. They were performed using the <a href="https://www.r-project.org/">R programming language</a> and the <a href="https://quarto.org/">Quarto</a> publishing system (an evolution of <a href="https://rmarkdown.rstudio.com/">R Markdown</a>). Click on the GitHub icon in the menu to access the thesis research compendium.</p>
<section id="citation" class="level2"><h2 class="anchored" data-anchor-id="citation">Citation</h2>
<p>For attribution, please cite this work as:</p>
<p>[SURNAME], [INITIALS]. ([YEAR]). <em>[TITLE]</em> [[TYPE OF THESIS]]. [SCHOOL/DEPARTMENT], University of São Paulo, São Paulo. [THESIS’S URL]</p>
Expand All @@ -325,12 +325,6 @@ <h1 class="title">{tesesusp}: a Quarto format for USP theses and dissertations</
<div id="ref-assis2014" class="csl-entry" role="listitem">
Assis, Machado de. 2014. <em>Memórias póstumas de Brás Cubas</em>. São Paulo: Companhia das Letras.
</div>
<div id="ref-bertalanffy1968" class="csl-entry" role="listitem">
Bertalanffy, Ludwig von. 1968. <em>General System Theory: Foundations, Development, Applications</em>. New York, NY: George Braziller.
</div>
<div id="ref-cambridgeuniversitypress" class="csl-entry" role="listitem">
Cambridge University Press. n.d. <span>“Cambridge Dictionary.”</span> Accessed September 21, 2023. <a href="https://dictionary.cambridge.org/">https://dictionary.cambridge.org/</a>.
</div>
<div id="ref-ehret1974" class="csl-entry" role="listitem">
Ehret, Charles F. 1974. <span>“The Sense of Time: Evidence for Its Molecular Basis in the Eukaryotic Gene-Action System.”</span> In <em>Advances in Biological and Medical Physics</em>, 15:47–77. Elsevier. <a href="https://doi.org/10.1016/B978-0-12-005215-8.50009-7">https://doi.org/10.1016/B978-0-12-005215-8.50009-7</a>.
</div>
Expand All @@ -343,9 +337,6 @@ <h1 class="title">{tesesusp}: a Quarto format for USP theses and dissertations</
<div id="ref-latinitium" class="csl-entry" role="listitem">
Latinitium. n.d. <span>“Latin Dictionaries.”</span> Latinitium. Accessed September 21, 2023. <a href="https://latinitium.com/latin-dictionaries/">https://latinitium.com/latin-dictionaries/</a>.
</div>
<div id="ref-levins1998" class="csl-entry" role="listitem">
Levins, Richard. 1998. <span>“Dialectics and Systems Theory.”</span> <em>Science &amp; Society</em> 62 (3): 375–99. <a href="https://www.jstor.org/stable/40403729">https://www.jstor.org/stable/40403729</a>.
</div>
<div id="ref-marques2012" class="csl-entry" role="listitem">
Marques, Mirian David, and Gisele Oda. 2012. <span>“Glossário.”</span> <em>Revista da Biologia</em> 9 (3). <a href="https://www.revistas.usp.br/revbiologia/article/view/114816">https://www.revistas.usp.br/revbiologia/article/view/114816</a>.
</div>
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9 changes: 0 additions & 9 deletions docs/qmd/acknowledgments.html
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Expand Up @@ -275,12 +275,6 @@ <h1 class="title">Acknowledgments</h1>
<div id="ref-assis2014" class="csl-entry" role="listitem">
Assis, Machado de. 2014. <em>Memórias póstumas de Brás Cubas</em>. São Paulo: Companhia das Letras.
</div>
<div id="ref-bertalanffy1968" class="csl-entry" role="listitem">
Bertalanffy, Ludwig von. 1968. <em>General System Theory: Foundations, Development, Applications</em>. New York, NY: George Braziller.
</div>
<div id="ref-cambridgeuniversitypress" class="csl-entry" role="listitem">
Cambridge University Press. n.d. <span>“Cambridge Dictionary.”</span> Accessed September 21, 2023. <a href="https://dictionary.cambridge.org/">https://dictionary.cambridge.org/</a>.
</div>
<div id="ref-ehret1974" class="csl-entry" role="listitem">
Ehret, Charles F. 1974. <span>“The Sense of Time: Evidence for Its Molecular Basis in the Eukaryotic Gene-Action System.”</span> In <em>Advances in Biological and Medical Physics</em>, 15:47–77. Elsevier. <a href="https://doi.org/10.1016/B978-0-12-005215-8.50009-7">https://doi.org/10.1016/B978-0-12-005215-8.50009-7</a>.
</div>
Expand All @@ -293,9 +287,6 @@ <h1 class="title">Acknowledgments</h1>
<div id="ref-latinitium" class="csl-entry" role="listitem">
Latinitium. n.d. <span>“Latin Dictionaries.”</span> Latinitium. Accessed September 21, 2023. <a href="https://latinitium.com/latin-dictionaries/">https://latinitium.com/latin-dictionaries/</a>.
</div>
<div id="ref-levins1998" class="csl-entry" role="listitem">
Levins, Richard. 1998. <span>“Dialectics and Systems Theory.”</span> <em>Science &amp; Society</em> 62 (3): 375–99. <a href="https://www.jstor.org/stable/40403729">https://www.jstor.org/stable/40403729</a>.
</div>
<div id="ref-marques2012" class="csl-entry" role="listitem">
Marques, Mirian David, and Gisele Oda. 2012. <span>“Glossário.”</span> <em>Revista da Biologia</em> 9 (3). <a href="https://www.revistas.usp.br/revbiologia/article/view/114816">https://www.revistas.usp.br/revbiologia/article/view/114816</a>.
</div>
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9 changes: 0 additions & 9 deletions docs/qmd/appendice-1.html
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Expand Up @@ -293,12 +293,6 @@ <h1 class="title">Appendix A — Appendix 1</h1>
<div id="ref-assis2014" class="csl-entry" role="listitem">
Assis, Machado de. 2014. <em>Memórias póstumas de Brás Cubas</em>. São Paulo: Companhia das Letras.
</div>
<div id="ref-bertalanffy1968" class="csl-entry" role="listitem">
Bertalanffy, Ludwig von. 1968. <em>General System Theory: Foundations, Development, Applications</em>. New York, NY: George Braziller.
</div>
<div id="ref-cambridgeuniversitypress" class="csl-entry" role="listitem">
Cambridge University Press. n.d. <span>“Cambridge Dictionary.”</span> Accessed September 21, 2023. <a href="https://dictionary.cambridge.org/">https://dictionary.cambridge.org/</a>.
</div>
<div id="ref-ehret1974" class="csl-entry" role="listitem">
Ehret, Charles F. 1974. <span>“The Sense of Time: Evidence for Its Molecular Basis in the Eukaryotic Gene-Action System.”</span> In <em>Advances in Biological and Medical Physics</em>, 15:47–77. Elsevier. <a href="https://doi.org/10.1016/B978-0-12-005215-8.50009-7">https://doi.org/10.1016/B978-0-12-005215-8.50009-7</a>.
</div>
Expand All @@ -311,9 +305,6 @@ <h1 class="title">Appendix A — Appendix 1</h1>
<div id="ref-latinitium" class="csl-entry" role="listitem">
Latinitium. n.d. <span>“Latin Dictionaries.”</span> Latinitium. Accessed September 21, 2023. <a href="https://latinitium.com/latin-dictionaries/">https://latinitium.com/latin-dictionaries/</a>.
</div>
<div id="ref-levins1998" class="csl-entry" role="listitem">
Levins, Richard. 1998. <span>“Dialectics and Systems Theory.”</span> <em>Science &amp; Society</em> 62 (3): 375–99. <a href="https://www.jstor.org/stable/40403729">https://www.jstor.org/stable/40403729</a>.
</div>
<div id="ref-marques2012" class="csl-entry" role="listitem">
Marques, Mirian David, and Gisele Oda. 2012. <span>“Glossário.”</span> <em>Revista da Biologia</em> 9 (3). <a href="https://www.revistas.usp.br/revbiologia/article/view/114816">https://www.revistas.usp.br/revbiologia/article/view/114816</a>.
</div>
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9 changes: 0 additions & 9 deletions docs/qmd/conclusion.html
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Expand Up @@ -296,12 +296,6 @@ <h1 class="title">
<div id="ref-assis2014" class="csl-entry" role="listitem">
Assis, Machado de. 2014. <em>Memórias póstumas de Brás Cubas</em>. São Paulo: Companhia das Letras.
</div>
<div id="ref-bertalanffy1968" class="csl-entry" role="listitem">
Bertalanffy, Ludwig von. 1968. <em>General System Theory: Foundations, Development, Applications</em>. New York, NY: George Braziller.
</div>
<div id="ref-cambridgeuniversitypress" class="csl-entry" role="listitem">
Cambridge University Press. n.d. <span>“Cambridge Dictionary.”</span> Accessed September 21, 2023. <a href="https://dictionary.cambridge.org/">https://dictionary.cambridge.org/</a>.
</div>
<div id="ref-ehret1974" class="csl-entry" role="listitem">
Ehret, Charles F. 1974. <span>“The Sense of Time: Evidence for Its Molecular Basis in the Eukaryotic Gene-Action System.”</span> In <em>Advances in Biological and Medical Physics</em>, 15:47–77. Elsevier. <a href="https://doi.org/10.1016/B978-0-12-005215-8.50009-7">https://doi.org/10.1016/B978-0-12-005215-8.50009-7</a>.
</div>
Expand All @@ -314,9 +308,6 @@ <h1 class="title">
<div id="ref-latinitium" class="csl-entry" role="listitem">
Latinitium. n.d. <span>“Latin Dictionaries.”</span> Latinitium. Accessed September 21, 2023. <a href="https://latinitium.com/latin-dictionaries/">https://latinitium.com/latin-dictionaries/</a>.
</div>
<div id="ref-levins1998" class="csl-entry" role="listitem">
Levins, Richard. 1998. <span>“Dialectics and Systems Theory.”</span> <em>Science &amp; Society</em> 62 (3): 375–99. <a href="https://www.jstor.org/stable/40403729">https://www.jstor.org/stable/40403729</a>.
</div>
<div id="ref-marques2012" class="csl-entry" role="listitem">
Marques, Mirian David, and Gisele Oda. 2012. <span>“Glossário.”</span> <em>Revista da Biologia</em> 9 (3). <a href="https://www.revistas.usp.br/revbiologia/article/view/114816">https://www.revistas.usp.br/revbiologia/article/view/114816</a>.
</div>
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9 changes: 0 additions & 9 deletions docs/qmd/development.html
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Expand Up @@ -296,12 +296,6 @@ <h1 class="title">
<div id="ref-assis2014" class="csl-entry" role="listitem">
Assis, Machado de. 2014. <em>Memórias póstumas de Brás Cubas</em>. São Paulo: Companhia das Letras.
</div>
<div id="ref-bertalanffy1968" class="csl-entry" role="listitem">
Bertalanffy, Ludwig von. 1968. <em>General System Theory: Foundations, Development, Applications</em>. New York, NY: George Braziller.
</div>
<div id="ref-cambridgeuniversitypress" class="csl-entry" role="listitem">
Cambridge University Press. n.d. <span>“Cambridge Dictionary.”</span> Accessed September 21, 2023. <a href="https://dictionary.cambridge.org/">https://dictionary.cambridge.org/</a>.
</div>
<div id="ref-ehret1974" class="csl-entry" role="listitem">
Ehret, Charles F. 1974. <span>“The Sense of Time: Evidence for Its Molecular Basis in the Eukaryotic Gene-Action System.”</span> In <em>Advances in Biological and Medical Physics</em>, 15:47–77. Elsevier. <a href="https://doi.org/10.1016/B978-0-12-005215-8.50009-7">https://doi.org/10.1016/B978-0-12-005215-8.50009-7</a>.
</div>
Expand All @@ -314,9 +308,6 @@ <h1 class="title">
<div id="ref-latinitium" class="csl-entry" role="listitem">
Latinitium. n.d. <span>“Latin Dictionaries.”</span> Latinitium. Accessed September 21, 2023. <a href="https://latinitium.com/latin-dictionaries/">https://latinitium.com/latin-dictionaries/</a>.
</div>
<div id="ref-levins1998" class="csl-entry" role="listitem">
Levins, Richard. 1998. <span>“Dialectics and Systems Theory.”</span> <em>Science &amp; Society</em> 62 (3): 375–99. <a href="https://www.jstor.org/stable/40403729">https://www.jstor.org/stable/40403729</a>.
</div>
<div id="ref-marques2012" class="csl-entry" role="listitem">
Marques, Mirian David, and Gisele Oda. 2012. <span>“Glossário.”</span> <em>Revista da Biologia</em> 9 (3). <a href="https://www.revistas.usp.br/revbiologia/article/view/114816">https://www.revistas.usp.br/revbiologia/article/view/114816</a>.
</div>
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9 changes: 0 additions & 9 deletions docs/qmd/epigraph.html
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Expand Up @@ -279,12 +279,6 @@ <h1 class="title">Epigraph</h1>
<div id="ref-assis2014" class="csl-entry" role="listitem">
Assis, Machado de. 2014. <em>Memórias póstumas de Brás Cubas</em>. São Paulo: Companhia das Letras.
</div>
<div id="ref-bertalanffy1968" class="csl-entry" role="listitem">
Bertalanffy, Ludwig von. 1968. <em>General System Theory: Foundations, Development, Applications</em>. New York, NY: George Braziller.
</div>
<div id="ref-cambridgeuniversitypress" class="csl-entry" role="listitem">
Cambridge University Press. n.d. <span>“Cambridge Dictionary.”</span> Accessed September 21, 2023. <a href="https://dictionary.cambridge.org/">https://dictionary.cambridge.org/</a>.
</div>
<div id="ref-ehret1974" class="csl-entry" role="listitem">
Ehret, Charles F. 1974. <span>“The Sense of Time: Evidence for Its Molecular Basis in the Eukaryotic Gene-Action System.”</span> In <em>Advances in Biological and Medical Physics</em>, 15:47–77. Elsevier. <a href="https://doi.org/10.1016/B978-0-12-005215-8.50009-7">https://doi.org/10.1016/B978-0-12-005215-8.50009-7</a>.
</div>
Expand All @@ -297,9 +291,6 @@ <h1 class="title">Epigraph</h1>
<div id="ref-latinitium" class="csl-entry" role="listitem">
Latinitium. n.d. <span>“Latin Dictionaries.”</span> Latinitium. Accessed September 21, 2023. <a href="https://latinitium.com/latin-dictionaries/">https://latinitium.com/latin-dictionaries/</a>.
</div>
<div id="ref-levins1998" class="csl-entry" role="listitem">
Levins, Richard. 1998. <span>“Dialectics and Systems Theory.”</span> <em>Science &amp; Society</em> 62 (3): 375–99. <a href="https://www.jstor.org/stable/40403729">https://www.jstor.org/stable/40403729</a>.
</div>
<div id="ref-marques2012" class="csl-entry" role="listitem">
Marques, Mirian David, and Gisele Oda. 2012. <span>“Glossário.”</span> <em>Revista da Biologia</em> 9 (3). <a href="https://www.revistas.usp.br/revbiologia/article/view/114816">https://www.revistas.usp.br/revbiologia/article/view/114816</a>.
</div>
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9 changes: 0 additions & 9 deletions docs/qmd/errata.html
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Expand Up @@ -275,12 +275,6 @@ <h1 class="title">Errata</h1>
<div id="ref-assis2014" class="csl-entry" role="listitem">
Assis, Machado de. 2014. <em>Memórias póstumas de Brás Cubas</em>. São Paulo: Companhia das Letras.
</div>
<div id="ref-bertalanffy1968" class="csl-entry" role="listitem">
Bertalanffy, Ludwig von. 1968. <em>General System Theory: Foundations, Development, Applications</em>. New York, NY: George Braziller.
</div>
<div id="ref-cambridgeuniversitypress" class="csl-entry" role="listitem">
Cambridge University Press. n.d. <span>“Cambridge Dictionary.”</span> Accessed September 21, 2023. <a href="https://dictionary.cambridge.org/">https://dictionary.cambridge.org/</a>.
</div>
<div id="ref-ehret1974" class="csl-entry" role="listitem">
Ehret, Charles F. 1974. <span>“The Sense of Time: Evidence for Its Molecular Basis in the Eukaryotic Gene-Action System.”</span> In <em>Advances in Biological and Medical Physics</em>, 15:47–77. Elsevier. <a href="https://doi.org/10.1016/B978-0-12-005215-8.50009-7">https://doi.org/10.1016/B978-0-12-005215-8.50009-7</a>.
</div>
Expand All @@ -293,9 +287,6 @@ <h1 class="title">Errata</h1>
<div id="ref-latinitium" class="csl-entry" role="listitem">
Latinitium. n.d. <span>“Latin Dictionaries.”</span> Latinitium. Accessed September 21, 2023. <a href="https://latinitium.com/latin-dictionaries/">https://latinitium.com/latin-dictionaries/</a>.
</div>
<div id="ref-levins1998" class="csl-entry" role="listitem">
Levins, Richard. 1998. <span>“Dialectics and Systems Theory.”</span> <em>Science &amp; Society</em> 62 (3): 375–99. <a href="https://www.jstor.org/stable/40403729">https://www.jstor.org/stable/40403729</a>.
</div>
<div id="ref-marques2012" class="csl-entry" role="listitem">
Marques, Mirian David, and Gisele Oda. 2012. <span>“Glossário.”</span> <em>Revista da Biologia</em> 9 (3). <a href="https://www.revistas.usp.br/revbiologia/article/view/114816">https://www.revistas.usp.br/revbiologia/article/view/114816</a>.
</div>
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9 changes: 0 additions & 9 deletions docs/qmd/foreign-abstract.html
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Expand Up @@ -277,12 +277,6 @@ <h1 class="title">Resumo</h1>
<div id="ref-assis2014" class="csl-entry" role="listitem">
Assis, Machado de. 2014. <em>Memórias póstumas de Brás Cubas</em>. São Paulo: Companhia das Letras.
</div>
<div id="ref-bertalanffy1968" class="csl-entry" role="listitem">
Bertalanffy, Ludwig von. 1968. <em>General System Theory: Foundations, Development, Applications</em>. New York, NY: George Braziller.
</div>
<div id="ref-cambridgeuniversitypress" class="csl-entry" role="listitem">
Cambridge University Press. n.d. <span>“Cambridge Dictionary.”</span> Accessed September 21, 2023. <a href="https://dictionary.cambridge.org/">https://dictionary.cambridge.org/</a>.
</div>
<div id="ref-ehret1974" class="csl-entry" role="listitem">
Ehret, Charles F. 1974. <span>“The Sense of Time: Evidence for Its Molecular Basis in the Eukaryotic Gene-Action System.”</span> In <em>Advances in Biological and Medical Physics</em>, 15:47–77. Elsevier. <a href="https://doi.org/10.1016/B978-0-12-005215-8.50009-7">https://doi.org/10.1016/B978-0-12-005215-8.50009-7</a>.
</div>
Expand All @@ -295,9 +289,6 @@ <h1 class="title">Resumo</h1>
<div id="ref-latinitium" class="csl-entry" role="listitem">
Latinitium. n.d. <span>“Latin Dictionaries.”</span> Latinitium. Accessed September 21, 2023. <a href="https://latinitium.com/latin-dictionaries/">https://latinitium.com/latin-dictionaries/</a>.
</div>
<div id="ref-levins1998" class="csl-entry" role="listitem">
Levins, Richard. 1998. <span>“Dialectics and Systems Theory.”</span> <em>Science &amp; Society</em> 62 (3): 375–99. <a href="https://www.jstor.org/stable/40403729">https://www.jstor.org/stable/40403729</a>.
</div>
<div id="ref-marques2012" class="csl-entry" role="listitem">
Marques, Mirian David, and Gisele Oda. 2012. <span>“Glossário.”</span> <em>Revista da Biologia</em> 9 (3). <a href="https://www.revistas.usp.br/revbiologia/article/view/114816">https://www.revistas.usp.br/revbiologia/article/view/114816</a>.
</div>
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