医学实验班

.github/workflows/install-packages.sh

@@ -14,7 +14,7 @@ REQUIRED_PKGS="$XECJK_PKGS $CTEX_PKGS bibunits bigfoot caption enumitem
     environ etoolbox filehook footmisc notoccite pdfpages threeparttable \
     titlesec trimspaces unicode-math";
 FONT_PKGS="fandol tex-gyre xits";
-EXTRA_PKGS="algorithms apacite $BIBLATEX_PKGS booktabs $HYPERREF_PKGS $NOMENCL_PKGS ntheorem siunitx";
+EXTRA_PKGS="algorithms apacite $BIBLATEX_PKGS booktabs cell $HYPERREF_PKGS $NOMENCL_PKGS ntheorem siunitx";
 MARKDOWN_PKGS="markdown fancyvrb csvsimple gobble"
 DOC_PKGS="hologo hypdoc listings xcolor $MARKDOWN_PKGS";
 EXAMPLE_PKGS="float fp metalogo multirow mwe"

.github/workflows/test.yml

@@ -1,6 +1,9 @@
 name: Test
 
-on: [push, pull_request]
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
 
 jobs:
 
@@ -10,6 +13,8 @@ jobs:
     container: ghcr.io/tuna/thuthesis-test-env
     steps:
     - uses: actions/checkout@v4
+    - name: Install required packages
+      run: bash .github/workflows/install-packages.sh
     - name: Test thesis
       run: make thesis
     - name: Test spine

data/chap02.tex

@@ -13,14 +13,11 @@ \section{插图}
 \begin{figure}
   \centering
   \includegraphics[width=0.5\linewidth]{example-image-a.pdf}
-  \caption*{国外的期刊习惯将图表的标题和说明文字写成一段，需要改写为标题只含图表的名称，其他说明文字以注释方式写在图表下方，或者写在正文中。}
-  \caption{示例图片标题}
+  \caption{Viral load and CD4+T cells changed over time (Zhang, San)}
+  \figurenote{Viral load and CD4+T cells changed though time since HAART initiation in INR group (a) and IR group (b); the increase of naïve CD4+T cell count ($\increment n$) was significantly different between INR group and IR group (c); the increase of memory CD4+T cell count ($\increment n$) was similar in INR and IR groups (d). *, significant difference}
   \label{fig:example}
 \end{figure}
 
-若图或表中有附注，采用英文小写字母顺序编号，附注写在图或表的下方。
-国外的期刊习惯将图表的标题和说明文字写成一段，需要改写为标题只含图表的名称，其他说明文字以注释方式写在图表下方，或者写在正文中。
-
 如果一个图由两个或两个以上分图组成时，各分图分别以 (a)、(b)、(c)...... 作为图序，并须有分图题。
 推荐使用 \pkg{subcaption} 宏包来处理， 比如图~\ref{fig:subfig-a} 和图~\ref{fig:subfig-b}。
 
@@ -43,16 +40,17 @@ \section{表格}
 
 \begin{table}
   \centering
-  \caption{三线表示例}
-  \begin{tabular}{ll}
+  \caption{Antibodies}
+  \begin{tabular}{ccc}
     \toprule
-    文件名          & 描述                         \\
+    Antigen & Clone    & Manufacturer \\
     \midrule
-    thuthesis.dtx   & 模板的源文件，包括文档和注释 \\
-    thuthesis.cls   & 模板文件                     \\
-    thuthesis-*.bst & BibTeX 参考文献表样式文件    \\
+    CD3     & 145-2C11 & eBioscience \\
+    CD4     & GK1.5    & eBioscience \\
+    CD8     & 53-6.7   & eBioscience \\
     \bottomrule
   \end{tabular}
+  \tablenote{\raggedleft(Neefjes et al., 2011)}
   \label{tab:three-line}
 \end{table}
 
@@ -62,21 +60,19 @@ \section{表格}
 \begin{table}
   \centering
   \begin{threeparttable}[c]
-    \caption{带附注的表格示例}
+    \caption{Antibodies}
     \label{tab:three-part-table}
-    \begin{tabular}{ll}
+    \begin{tabular}{ccc}
       \toprule
-      文件名                 & 描述                         \\
+      Antigen & Clone             & Manufacturer \\
       \midrule
-      thuthesis.dtx\tnote{a} & 模板的源文件，包括文档和注释 \\
-      thuthesis.cls\tnote{b} & 模板文件                     \\
-      thuthesis-*.bst        & BibTeX 参考文献表样式文件    \\
+      CD3     & 145-2C11\tnote{a} & eBioscience \\
+      CD4     & GK1.5\tnote{b}    & eBioscience \\
+      CD8     & 53-6.7            & eBioscience \\
       \bottomrule
     \end{tabular}
     \begin{tablenotes}
-      \item [a] 可以通过 xelatex 编译生成模板的使用说明文档；
-        使用 xetex 编译 \file{thuthesis.ins} 时则会从 \file{.dtx} 中去除掉文档和注释，得到精简的 \file{.cls} 文件。
-      \item [b] 更新模板时，一定要记得编译生成 \file{.cls} 文件，否则编译论文时载入的依然是旧版的模板。
+      \item Table note text.
     \end{tablenotes}
   \end{threeparttable}
 \end{table}

data/chap04.tex

@@ -5,72 +5,5 @@ \chapter{引用文献的标注}
 模板支持 BibTeX 和 BibLaTeX 两种方式处理参考文献。
 下文主要介绍 BibTeX 配合 \pkg{natbib} 宏包的主要使用方法。
 
-
-\section{顺序编码制}
-
-在顺序编码制下，默认的 \cs{cite} 命令同 \cs{citep} 一样，序号置于方括号中，
-引文页码会放在括号外。
-统一处引用的连续序号会自动用短横线连接。
-
-\thusetup{
-  cite-style = super,
-}
-\noindent
-\begin{tabular}{l@{\quad$\Rightarrow$\quad}l}
-  \verb|\cite{zhangkun1994}|               & \cite{zhangkun1994}               \\
-  \verb|\citet{zhangkun1994}|              & \citet{zhangkun1994}              \\
-  \verb|\citep{zhangkun1994}|              & \citep{zhangkun1994}              \\
-  \verb|\cite[42]{zhangkun1994}|           & \cite[42]{zhangkun1994}           \\
-  \verb|\cite{zhangkun1994,zhukezhen1973}| & \cite{zhangkun1994,zhukezhen1973} \\
-\end{tabular}
-
-
-也可以取消上标格式，将数字序号作为文字的一部分。
-建议全文统一使用相同的格式。
-
-\thusetup{
-  cite-style = inline,
-}
-\noindent
-\begin{tabular}{l@{\quad$\Rightarrow$\quad}l}
-  \verb|\cite{zhangkun1994}|               & \cite{zhangkun1994}               \\
-  \verb|\citet{zhangkun1994}|              & \citet{zhangkun1994}              \\
-  \verb|\citep{zhangkun1994}|              & \citep{zhangkun1994}              \\
-  \verb|\cite[42]{zhangkun1994}|           & \cite[42]{zhangkun1994}           \\
-  \verb|\cite{zhangkun1994,zhukezhen1973}| & \cite{zhangkun1994,zhukezhen1973} \\
-\end{tabular}
-
-
-
-\section{著者-出版年制}
-
-著者-出版年制下的 \cs{cite} 跟 \cs{citet} 一样。
-
-\thusetup{
-  cite-style = author-year,
-}
-\noindent
-\begin{tabular}{@{}l@{$\Rightarrow$}l@{}}
-  \verb|\cite{zhangkun1994}|                & \cite{zhangkun1994}                \\
-  \verb|\citet{zhangkun1994}|               & \citet{zhangkun1994}               \\
-  \verb|\citep{zhangkun1994}|               & \citep{zhangkun1994}               \\
-  \verb|\cite[42]{zhangkun1994}|            & \cite[42]{zhangkun1994}            \\
-  \verb|\citep{zhangkun1994,zhukezhen1973}| & \citep{zhangkun1994,zhukezhen1973} \\
-\end{tabular}
-
-\vskip 2ex
-\thusetup{
-  cite-style = super,
-}
 注意，引文参考文献的每条都要在正文中标注
-\cite{zhangkun1994,zhukezhen1973,dupont1974bone,zhengkaiqing1987,%
-  jiangxizhou1980,jianduju1994,merkt1995rotational,mellinger1996laser,%
-  bixon1996dynamics,mahui1995,carlson1981two,taylor1983scanning,%
-  taylor1981study,shimizu1983laser,atkinson1982experimental,%
-  kusch1975perturbations,guangxi1993,huosini1989guwu,wangfuzhi1865songlun,%
-  zhaoyaodong1998xinshidai,biaozhunhua2002tushu,chubanzhuanye2004,%
-  who1970factors,peebles2001probability,baishunong1998zhiwu,%
-  weinstein1974pathogenic,hanjiren1985lun,dizhi1936dizhi,%
-  tushuguan1957tushuguanxue,aaas1883science,fugang2000fengsha,%
-  xiaoyu2001chubanye,oclc2000about,scitor2000project%
-}。
+\cite{cell:1, cell:2, cell:3, cell:4, cell:5}。

data/clinical-research.tex

@@ -0,0 +1,65 @@
+\bibliographyunit[\chapter]
+
+\renewcommand{\chaptermark}[1]{\markboth{#1}{}}
+\chapter*{\mdseries 因素A对因素B的影响}
+
+\addcontentsline{toc}{chapter}{临床研究}
+\markboth{临床研究}{}
+
+\newcommand{\chineseHead}[1]{{\heiti #1}}
+\newcommand{\englishTitle}[1]{{\sffamily\centering\Large #1\par}}
+
+% \vspace{24pt}
+% \chineseTitle{粮食安全对早期肺功能异常的影响}
+% \vspace{24pt} % Space before abstract
+
+% Chinese abstract
+\noindent\chineseHead{【摘要】}
+黑体，小四号字，左右实心凸形括号。摘要内容书写，宋体， 小四号，两端对齐，字符间距为 常规（标准） 。行距为固定值20磅，段前空0磅， 段后空0磅。
+\\ \hspace*{\fill} \\
+\noindent\chineseHead{【关键词】}
+因素A；因素B；关系C
+
+\vspace{18pt} % Space after Chinese part
+
+\englishTitle{Impact of factor A to factor B}
+\vspace{24pt} % Space before abstract
+
+\noindent\textbf{Abstract:} Factor A is xxx
+\\ \hspace*{\fill} \\
+\noindent\textbf{Keywords:} factorA, factorB, relationC
+English abstract
+
+
+\renewcommand{\thesection}{\arabic{section}}
+\setcounter{section}{0}
+\newpage
+\section{Introduction}
+
+Factor A is a xxx
+
+\section{Method}
+
+We used xxx
+
+\section{Results}
+
+We found...
+
+\begin{figure}
+    \centering
+    \includegraphics[width=1\linewidth]{example-image-a.pdf}
+    \caption{Title and Number of figure in Arial}
+    \caption*{This legend is in Times Roman}
+  \end{figure}
+
+\section{Discussion}
+
+In this research xxx
+
+In summary xxx
+
+\section*{参考文献}
+{\renewcommand{\bibsection}{}
+\putbib
+}

data/comments.tex

@@ -1,10 +1,17 @@
 % !TeX root = ../thuthesis-example.tex
 
-\begin{comments}
-% \begin{comments}[name = {指导小组评语}]
+% \begin{comments}
+\begin{comments}[name = {基础导师学术评语}]
 % \begin{comments}[name = {Comments from Thesis Supervisor}]
 % \begin{comments}[name = {Comments from Thesis Supervision Committee}]
 
   论文提出了……
 
 \end{comments}
+
+
+\begin{comments}[name = {临床导师学术评语}]
+
+  论文提出了……
+
+\end{comments}

data/committee.tex

@@ -1,20 +1,9 @@
 % !TeX root = ../thuthesis-example.tex
 
-\begin{committee}[name={学位论文指导小组、公开评阅人和答辩委员会名单}]
+\begin{committee}[name={毕业论文公开评阅人和答辩委员会名单}]
 
   \newcolumntype{C}[1]{@{}>{\centering\arraybackslash}p{#1}}
 
-  \section*{指导小组名单}
-
-  \begin{center}
-    \begin{tabular}{C{3cm}C{3cm}C{9cm}@{}}
-      李XX & 教授     & 清华大学 \\
-      王XX & 副教授   & 清华大学 \\
-      张XX & 助理教授 & 清华大学 \\
-    \end{tabular}
-  \end{center}
-
-
   \section*{公开评阅人名单}
 
   \begin{center}

data/letter-of-authorization.tex

@@ -0,0 +1,5 @@
+% !TeX root = ../thuthesis-example.tex
+
+\chapter{Letter of Authorization}
+
+I, Xinghua Lu, hereby certify that the contents of research work described in the attached thesis were accomplished by Tsinghua scholar Qiao Jin, and I authorize the scholar to use the contents of this research work in his thesis to partially fulfill the requirements of a Doctor of Medicine (M.D.) degree at Tsinghua University School of Medicine.

data/resume.tex

@@ -13,7 +13,7 @@
 
   \section*{在学期间完成的相关学术成果}
 
-  \subsection*{学术论文}
+  \subsection{学术论文}
 
   \begin{achievements}
     \item Yang Y, Ren T L, Zhang L T, et al. Miniature microphone with silicon-based ferroelectric thin films[J]. Integrated Ferroelectrics, 2003, 52:229-235.
@@ -23,7 +23,14 @@
   \end{achievements}
 
 
-  \subsection*{专利}
+  \subsection{专利}
+
+  \begin{achievements}
+    \item 任天令, 杨轶, 朱一平, 等. 硅基铁电微声学传感器畴极化区域控制和电极连接的方法: 中国, CN1602118A[P]. 2005-03-30.
+    \item Ren T L, Yang Y, Zhu Y P, et al. Piezoelectric micro acoustic sensor based on ferroelectric materials: USA, No.11/215, 102[P]. (美国发明专利申请号.)
+  \end{achievements}
+
+  \subsection*{3  奖项}
 
   \begin{achievements}
     \item 任天令, 杨轶, 朱一平, 等. 硅基铁电微声学传感器畴极化区域控制和电极连接的方法: 中国, CN1602118A[P]. 2005-03-30.

ref/refs-cell.bib

@@ -0,0 +1,72 @@
+@article{cell:1,
+  title = {Rnq1: An Epigenetic Modifier of Protein Function in Yeast},
+  shorttitle = {Rnq1},
+  author = {Sondheimer, Neal and Lindquist, Susan},
+  year = {2000},
+  month = jan,
+  journal = {Molecular Cell},
+  volume = {5},
+  number = {1},
+  pages = {163--172},
+  publisher = {{Elsevier}},
+  issn = {1097-2765},
+  doi = {10.1016/S1097-2765(00)80412-8},
+  url = {https://www.cell.com/molecular-cell/abstract/S1097-2765(00)80412-8},
+  urldate = {2024-01-27},
+  langid = {american},
+  pmid = {10678178}
+}
+
+@preprint{cell:2,
+  title = {Spatially Distinct Pools of {{TORC1}} Balance Protein Homeostasis},
+  author = {De Virgilio, Claudio and Hatakeyama, Riko and {P{\'e}li-Gulli}, Marie-Pierre and Hu, Zehan and Jaquenoud, Malika and Osuna, Guillermo Miguel Garcia and Sardu, Alessandro and Dengjel, J{\"o}rn},
+  year = {2018},
+  month = dec,
+  publisher = {{Mendeley Data}},
+  doi = {10.17632/m9s42s94fc.1},
+  archiveprefix = {Mendeley Data},
+  langid = {american}
+}
+
+@incollection{cell:3,
+  title = {Dynein Motors: Structure, Mechanochemistry and Regulation},
+  shorttitle = {Dynein {{Motors}}},
+  booktitle = {Molecular Motors},
+  author = {King, Stephen M.},
+  editor = {Schliwa, Manfred},
+  year = {2002},
+  pages = {45--78},
+  publisher = {{Wiley-VCH Verlag GmbH}},
+  doi = {10.1002/3527601503.ch2},
+  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/3527601503.ch2},
+  urldate = {2024-01-27},
+  abstract = {This chapter contains sections titled: Introduction Structural Organization of the Motor, Cargo-binding and Regulatory Components Heavy Chains Intermediate Chains Light Intermediate Chains The LC8 Light Chain Class The Tctex1/Tctex2 Light Chain Class The LC7/roadblock Light Chain Class Heavy Chain-associated Regulatory Light Chains Light Chains Associated with Inner Arms I2/3 Mechanochemistry and Motility Dynein Deficiencies and Disease Conclusions},
+  copyright = {Copyright {\textcopyright} 2003 Wiley-VCH Verlag GmbH \& Co. KGaA},
+  isbn = {978-3-527-60150-9},
+  langid = {american}
+}
+
+@book{cell:4,
+  title = {Molecular and Cellular Approaches to Neural Development},
+  editor = {Cowan, W. Maxwell and Jessell, Thomas M. and {S. Lawrence Zipursky}},
+  year = {1998},
+  month = apr,
+  publisher = {{Oxford University Press}},
+  doi = {10.1093/acprof:oso/9780195111668.001.0001},
+  url = {https://academic.oup.com/book/2106},
+  urldate = {2024-01-27},
+  abstract = {Abstract. Although the major features of neural development have been known for nearly a century, it is only relatively recently that the underlying molecular a},
+  isbn = {978-0-19-986583-3},
+  langid = {american}
+}
+
+@misc{cell:5,
+  title = {Goal 7: {{Ensure}} Access to Affordable, Reliable, Sustainable and Modern Energy for All},
+  year = 2024,
+  author = {{United Nations}},
+  journal = {United Nations Sustainable Development},
+  url = {https://www.un.org/sustainabledevelopment/energy/},
+  urldate = {2024-01-27},
+  abstract = {United Nations Sustainable Development Goals - Time for Global Action for People and Planet},
+  langid = {american}
+}