add sub repository for clinical epidemiology journal

Epidemiology/alzheimer/query

+# query :
+https://trialsearch.who.int/ alzheimer
\ No newline at end of file

Epidemiology/alzheimer/trialsToGargantext.py

+#######
+# trialsToGargantext.py
+# description : turn a trials registry (downloaded as a csv file from https://trialsearch.who.int/) a GarganText corpus
+# licence : AGPL + CECILL v3
+# author : quentin lobbé - qlobbe@iscpif.fr
+#######
+
+# python3 trialsToGargantext.py ./trials.csv
+
+import sys
+import csv
+
+pathTrials = ""
+
+try :
+    pathTrials = sys.argv[1]
+except :
+    print ("! args error\n")
+    sys.exit(0)
+
+def isResults (item) :
+	results = "no"
+	if "Yes" in item or "yes" in item :
+		results = "yes"
+	return results
+
+def toWeight (item) :
+	weight = "1"
+	if item != "" :
+		weight = item
+	return weight
+
+def cleanStr (item) :
+	return item.strip().replace("\n","").replace("\t","").replace('"','').replace('<br>','')
+
+def toAbstract (lst) :
+	abstract = ""
+	for item in lst :
+		if item != "" :
+			abstract += " " + cleanStr(item)
+	return abstract.strip()
+
+output = open("./corpus.csv", "w")
+header = "title\tsource\tpublication_year\tpublication_month\tpublication_day\tabstract\tauthors\tweight\n"
+output.write(header)
+
+# read the raw trials
+
+with open(pathTrials, newline='\n') as file :
+
+	# 0: TrialID; 1: Last Refreshed on; 2: Public title;
+	# 3: Scientific title; 4: Acronym; 5: Primary sponsor;
+	# 6: Date registration; 7: Date registration3; 8: Export date;
+	# 9: Source Register; 10: web address; 11: Recruitment Status;
+	# 12: other records; 13: Inclusion agemin; 14: Inclusion agemax;
+	# 15: Inclusion gender; 16: Date enrollement; 17: Target size;
+	# 18: Study type; 19: Study design; 20: Phase;
+	# 21: Countries; 22: Contact Firstname; 23: Contact Lastname;
+	# 24: Contact Address; 25: Contact Email; 26: Contact Tel;
+	# 27: Contact Affiliation; 28: Inclusion Criteria; 29: Exclusion Criteria;
+	# 30: Condition; 31: Intervention; 32: Primary outcome;
+	# 33: Secondary outcome; 34: results date posted; 35: results date completed;
+	# 36: results url link; 37: Retrospective flag; 38: Bridging flag truefalse;
+	# 39: Bridged type; 40: results yes no
+	
+    rawTrials = csv.reader(file, delimiter=',')
+
+    # skip the header
+    next(rawTrials)
+
+    for row in rawTrials :
+
+    	title = cleanStr(row[2])
+    	source = isResults(row[40])
+    	abstract = toAbstract([row[3],row[4],row[18],row[31]])
+    	weight = toWeight(row[17])
+    	date = row[6].split('/')
+    	author = row[9]
+
+    	output_row = title + "\t" + source + "\t" + date[2] + "\t" + date[1] + "\t" + date[0] + "\t" + abstract + "\t" + author + "\t" + weight + "\n"
+    	output.write(output_row)
\ No newline at end of file

Epidemiology/cas-sc.cls

+%%
+%% This is file `cas-dc.cls'.
+%%
+%% This file is part of the 'CAS Bundle'.
+%% ......................................
+%% 
+%% It may be distributed under the conditions of the LaTeX Project Public
+%% License, either version 1.2 of this license or (at your option) any
+%% later version.  The latest version of this license is in
+%%    http://www.latex-project.org/lppl.txt
+%% and version 1.2 or later is part of all distributions of LaTeX
+%% version 1999/12/01 or later.
+%% 
+%% The list of all files belonging to the 'CAS Bundle' is
+%% given in the file `manifest.txt'.
+%% 
+
+%% $Id: cas-sc.cls 49 2020-03-14 09:05:10Z rishi $
+
+ \def\RCSfile{cas-sc}%
+ \def\RCSversion{2.1}%
+ \def\RCSdate{2020/03/14}%
+\NeedsTeXFormat{LaTeX2e}[1995/12/01]
+\ProvidesClass{\RCSfile}[\RCSdate, \RCSversion: Formatting class
+   for CAS single column articles]
+%
+\def\ABD{\AtBeginDocument}
+%
+% switches
+% 
+\newif\iflongmktitle    \longmktitlefalse
+\newif\ifdc             \global\dcfalse
+\newif\ifsc             \global\sctrue
+\newif\ifcasreviewlayout  \global\casreviewlayoutfalse
+\newif\ifcasfinallayout   \global\casfinallayoutfalse
+
+\newcounter{blind}
+\setcounter{blind}{0}
+
+\def\blstr#1{\gdef\@blstr{#1}}
+\def\@blstr{1}
+\newdimen\@bls
+\@bls=\baselineskip
+
+\DeclareOption{singleblind}{\setcounter{blind}{1}}
+\DeclareOption{doubleblind}{\setcounter{blind}{2}}
+\DeclareOption{longmktitle}{\global\longmktitletrue}
+\DeclareOption{final}{\global\casfinallayouttrue}
+\DeclareOption{review}{\global\casreviewlayouttrue}
+
+\ExecuteOptions{a4paper,10pt,oneside,fleqn,review}
+\DeclareOption*{\PassOptionsToClass{\CurrentOption}{article}}
+\ProcessOptions
+\LoadClass{article}
+
+\RequirePackage{graphicx}
+\RequirePackage{amsmath,amsfonts,amssymb}
+\allowdisplaybreaks
+
+\RequirePackage{expl3,xparse}
+\@ifundefined{regex_match:nnTF}{\RequirePackage{l3regex}}{}
+\RequirePackage{etoolbox}
+\RequirePackage{booktabs,makecell,multirow,array,colortbl,dcolumn,stfloats}
+\RequirePackage{xspace,xstring,footmisc}
+\RequirePackage[svgnames,dvipsnames]{xcolor}
+
+\RequirePackage[colorlinks]{hyperref}
+\colorlet{scolor}{black}
+\colorlet{hscolor}{DarkSlateGrey}
+\hypersetup{%
+  pdfcreator={LaTeX3; cas-sc.cls; hyperref.sty},
+  pdfproducer={pdfTeX;},
+  linkcolor={hscolor},
+  urlcolor={hscolor},
+  citecolor={hscolor},
+  filecolor={hscolor},
+  menucolor={hscolor},
+}
+% \AtEndDocument{\hypersetup
+%   {pdftitle={\csuse{__short_title:}},
+%   pdfauthor={\csuse{__short_authors:}}}}
+ 
+ \let\comma\@empty
+\let\tnotesep\@empty
+\let\@title\@empty
+%
+% Load Common items
+%
+
+\RequirePackage{cas-common}
+
+%
+% Specific to Single Column
+%
+\ExplSyntaxOn
+
+\RenewDocumentCommand \maketitle {}
+{
+  \ifbool { usecasgrabsbox }
+    { 
+      \setcounter{page}{0}
+      \thispagestyle{empty}
+      \unvbox\casgrabsbox  
+    } { }  
+  \pagebreak  
+  \ifbool { usecashlsbox }
+    { 
+      \setcounter{page}{0}
+      \thispagestyle{empty}
+      \unvbox\casauhlbox
+    } { }    
+  \pagebreak  
+  \thispagestyle{first}
+  \ifbool{longmktitle}
+  {
+    \LongMaketitleBox
+    \ProcessLongTitleBox
+  }
+  {
+    \MaketitleBox
+    \printFirstPageNotes
+  }
+  \normalcolor \normalfont
+  \setcounter{footnote}{\int_use:N \g_stm_fnote_int}
+  \renewcommand\thefootnote{\arabic{footnote}}
+  \gdef\@pdfauthor{\infoauthors}
+  \gdef\@pdfsubject{Complex ~STM ~Content}
+}
+
+%
+% Fonts
+%
+\RequirePackage[T1]{fontenc}
+
+\file_if_exist:nTF { stix.sty }
+{
+  \file_if_exist:nTF { charis.sty }
+  {
+    \RequirePackage[notext]{stix} 
+    \RequirePackage{charis}
+  }
+  { \RequirePackage{stix} }
+}
+{
+  \iow_term:x {  *********************************************************** }
+  \iow_term:x { ~Stix ~ and ~ Charis~ fonts ~ are ~ not ~ available ~ }
+  \iow_term:x { ~ in ~TeX~system.~Hence~CMR~ fonts~ are ~ used. }
+  \iow_term:x {  *********************************************************** }
+}
+
+\file_if_exist:nTF { inconsolata }
+{ \RequirePackage[scaled=.85]{inconsolata} }
+{ \tex_gdef:D \ttdefault { cmtt } }
+
+
+\ExplSyntaxOff
+
+%
+% Page geometry
+%
+
+\usepackage[%
+  paperwidth=192mm,
+  paperheight=262mm,
+%  vmargin={12.4mm,11.5mm},
+  vmargin={19mm,19mm},
+  hmargin={13.7mm,13.7mm},
+  headsep=12pt,
+  footskip=12pt,
+]{geometry}
+
+
+\endinput
+  
+%
+% End of class 'cas-sc'
+%
+

Epidemiology/doc_data.txt

+InfoBegin
+InfoKey: Creator
+InfoValue: Microsoft® Word 2010
+InfoBegin
+InfoKey: ModDate
+InfoValue: D:20180118085247+11'00'
+InfoBegin
+InfoKey: CreationDate
+InfoValue: D:20180112162105Z
+InfoBegin
+InfoKey: Producer
+InfoValue: Microsoft® Word 2010
+InfoBegin
+InfoKey: Author
+InfoValue: Windows User
+InfoBegin
+InfoKey: PXCViewerInfo
+InfoValue: PDF-XChange Viewer;2.5.322.7;Aug 11 2017;07:10:51;D:20180118085247+11'00'
+PdfID0: 744871e5bb29fb49abee27650943d691
+PdfID1: 0123456789abcdeffedcba9876543210
+NumberOfPages: 4
+PageMediaBegin
+PageMediaNumber: 1
+PageMediaRotation: 0
+PageMediaRect: 0 0 594.96 841.92
+PageMediaDimensions: 594.96 841.92
+PageMediaBegin
+PageMediaNumber: 2
+PageMediaRotation: 0
+PageMediaRect: 0 0 594.96 841.92
+PageMediaDimensions: 594.96 841.92
+PageMediaBegin
+PageMediaNumber: 3
+PageMediaRotation: 0
+PageMediaRect: 0 0 594.96 841.92
+PageMediaDimensions: 594.96 841.92
+PageMediaBegin
+PageMediaNumber: 4
+PageMediaRotation: 0
+PageMediaRect: 0 0 594.96 841.92
+PageMediaDimensions: 594.96 841.92

Epidemiology/els-cas-templates/README

+cas-sc.cls and cas-dc.cls are the two new class files created
+for typesetting Elsevier's journal articles which go through
+Complex Article Service (CAS) workflow. These are now accepted for
+submitting articles, both in Elsevier's electronic submission system
+and elsewhere.
+
+Bugs and problems with elsarticle.cls may be reported to the
+developers of the class via elsarticle@stmdocs.in.
+
+The file manifest.txt provides a list of the files in the
+elsarticle-cas bundle.  The following are the main files available:
+
+- cas-sc-template.tex, template file for single column journals
+- cas-dc-template.tex, template file for double column journals
+- cas-sc-template.pdf, PDF of the cas-sc-template.tex 
+- cas-dc-template.pdf, PDF of the cas-ddc-template.tex
+- cas-common.sty, additional macro package for formatting
+  model2-names.bst, BibTeX style file
+- cas-twitter.jpeg, cas-linkedin.jpeg, cas-url.jpeg, cas-gplus.jpeg, 
+  cas-facebook.jpeg, cas-email.jpeg - thumbnail images of social 
+  networking sites
+
+The documentation file is elsdoc-cas.tex in the doc directory.  To
+compile it:
+
+1. pdflatex elsdoc-cas
+2. pdflatex elsdoc-cas
+3. pdflatex elsdoc-cas
+
+or
+
+use the makefile. Use the target `all' (eg: make all) in doc
+directory.
+
+The above procedure will create a print version, namely elsdoc-cas.pdf.
+
+Copyright 2019-2020, Elsevier. Bugs, feature requests, suggestions and
+comments may be mailed to elsarticle@stmdocs.in. cas-sc.cls, cas-dc.cls
+related documentations and supporting packages are released under the
+LATEX Project Public Licence, either version 1.2 or any later
+version. This work has the LPPL maintenance status
+'author-maintained'.

Epidemiology/els-cas-templates/cas-dc-template.abs

+This template helps you to create a properly formatted \LaTeX\ manuscript.
+
+\noindent\texttt{\textbackslash begin{abstract}} \dots
+\texttt{\textbackslash end{abstract}} and
+\verb+\begin{keyword}+ \verb+...+ \verb+\end{keyword}+
+which
+contain the abstract and keywords respectively.
+
+\noindent Each keyword shall be separated by a \verb+\sep+ command.

Epidemiology/els-cas-templates/cas-dc-template.aux

+\relax 
+\providecommand\hyper@newdestlabel[2]{}
+\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
+\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
+\global\let\oldcontentsline\contentsline
+\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
+\global\let\oldnewlabel\newlabel
+\gdef\newlabel#1#2{\newlabelxx{#1}#2}
+\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
+\AtEndDocument{\ifx\hyper@anchor\@undefined
+\let\contentsline\oldcontentsline
+\let\newlabel\oldnewlabel
+\fi}
+\fi}
+\global\let\hyper@last\relax 
+\gdef\HyperFirstAtBeginDocument#1{#1}
+\providecommand\HyField@AuxAddToFields[1]{}
+\providecommand\HyField@AuxAddToCoFields[2]{}
+\csgdef{mark@title}{1,2}
+\orcidauthor{0000-0001-7511-2910}{CV Radhakrishnan}
+\csgdef{mark@corau1}{1}
+\csgdef{mark@fnau1}{1}
+\emailauthor{cvr_1@tug.org.in}{CV Radhakrishnan}
+\urlauthor{www.cvr.cc, cvr@sayahna.org}{CV Radhakrishnan}
+\creditauthor{Conceptualization of this study, Methodology, Software}{CV Radhakrishnan}
+\csgdef{mark@fnau3}{2}
+\emailauthor{cvr3@sayahna.org}{CV Rajagopal}
+\urlauthor{www.sayahna.org}{CV Rajagopal}
+\creditauthor{Data curation, Writing - Original draft preparation}{CV Rajagopal}
+\csgdef{mark@corau4}{2}
+\csgdef{mark@fnau4}{1,3}
+\emailauthor{rishi@stmdocs.in}{Rishi T.}
+\urlauthor{www.stmdocs.in}{Rishi T.}
+\NewLabel{cor1}{1}
+\NewLabel{cor2}{2}
+\NewLabel{fn1}{1}
+\NewLabel{fn2}{2}
+\citation{Fortunato2010}
+\citation{Fortunato2010,NewmanGirvan2004}
+\citation{Fortunato2010,Vehlowetal2013}
+\@writefile{toc}{\contentsline {section}{\numberline {1}Introduction}{1}{section.1}\protected@file@percent }
+\@writefile{toc}{\contentsline {section}{\numberline {2}Installation}{1}{section.2}\protected@file@percent }
+\@writefile{toc}{\contentsline {section}{\numberline {3}Front matter}{1}{section.3}\protected@file@percent }
+\@writefile{toc}{\contentsline {section}{\numberline {4}Bibliography styles}{1}{section.4}\protected@file@percent }
+\@writefile{toc}{\contentsline {section}{\numberline {5}Floats}{1}{section.5}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces The evanescent light - $1S$ quadrupole coupling ($g_{1,l}$) scaled to the bulk exciton-photon coupling ($g_{1,2}$). The size parameter $kr_{0}$ is denoted as $x$ and the \textsc  {\lowercase {PMS}}\xspace  is placed directly on the cuprous oxide sample ($\delta r=0$, See also Table \ref {tbl1}).}}{2}{figure.1}\protected@file@percent }
+\newlabel{FIG:1}{{1}{2}{The evanescent light - $1S$ quadrupole coupling ($g_{1,l}$) scaled to the bulk exciton-photon coupling ($g_{1,2}$). The size parameter $kr_{0}$ is denoted as $x$ and the \PMS is placed directly on the cuprous oxide sample ($\delta r=0$, See also Table \protect \ref {tbl1})}{figure.1}{}}
+\@writefile{lot}{\contentsline {table}{\numberline {1}{\ignorespaces This is a test caption. This is a test caption. This is a test caption. This is a test caption.}}{2}{table.1}\protected@file@percent }
+\newlabel{tbl1}{{1}{2}{This is a test caption. This is a test caption. This is a test caption. This is a test caption}{table.1}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {6}Theorem and ...}{2}{section.6}\protected@file@percent }
+\newlabel{10}{{1}{2}{Theorem and ..}{equation.6.1}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {7}Enumerated ...}{2}{section.7}\protected@file@percent }
+\bibstyle{cas-model2-names}
+\bibdata{cas-refs}
+\bibcite{Fortunato2010}{{1}{2010}{{Fortunato}}{{}}}
+\bibcite{NewmanGirvan2004}{{2}{2004}{{Newman and Girvan}}{{}}}
+\bibcite{Vehlowetal2013}{{3}{2013}{{Vehlow et~al.}}{{Vehlow, Reinhardt and Weiskopf}}}
+\csgdef{cabio1lines}{14}
+\csgdef{cabio2lines}{8}
+\csxdef{lastpage}{3}
+\@writefile{toc}{\contentsline {section}{\numberline {8}Cross-references}{3}{section.8}\protected@file@percent }
+\@writefile{toc}{\contentsline {section}{\numberline {9}Bibliography}{3}{section.9}\protected@file@percent }
+\@writefile{toc}{\contentsline {section}{\numberline {A}My Appendix}{3}{appendix.A}\protected@file@percent }

Epidemiology/els-cas-templates/cas-dc-template.bbl

+\begin{thebibliography}{3}
+\expandafter\ifx\csname natexlab\endcsname\relax\def\natexlab#1{#1}\fi
+\providecommand{\url}[1]{\texttt{#1}}
+\providecommand{\href}[2]{#2}
+\providecommand{\path}[1]{#1}
+\providecommand{\DOIprefix}{doi:}
+\providecommand{\ArXivprefix}{arXiv:}
+\providecommand{\URLprefix}{URL: }
+\providecommand{\Pubmedprefix}{pmid:}
+\providecommand{\doi}[1]{\href{http://dx.doi.org/#1}{\path{#1}}}
+\providecommand{\Pubmed}[1]{\href{pmid:#1}{\path{#1}}}
+\providecommand{\bibinfo}[2]{#2}
+\ifx\xfnm\relax \def\xfnm[#1]{\unskip,\space#1}\fi
+%Type = Article
+\bibitem[{Fortunato(2010)}]{Fortunato2010}
+\bibinfo{author}{Fortunato, S.}, \bibinfo{year}{2010}.
+\newblock \bibinfo{title}{Community detection in graphs}.
+\newblock \bibinfo{journal}{Phys. Rep.-Rev. Sec. Phys. Lett.}
+  \bibinfo{volume}{486}, \bibinfo{pages}{75--174}.
+%Type = Article
+\bibitem[{Newman and Girvan(2004)}]{NewmanGirvan2004}
+\bibinfo{author}{Newman, M.E.J.}, \bibinfo{author}{Girvan, M.},
+  \bibinfo{year}{2004}.
+\newblock \bibinfo{title}{Finding and evaluating community structure in
+  networks}.
+\newblock \bibinfo{journal}{Phys. Rev. E.} \bibinfo{volume}{69},
+  \bibinfo{pages}{026113}.
+%Type = Article
+\bibitem[{Vehlow et~al.(2013)Vehlow, Reinhardt and Weiskopf}]{Vehlowetal2013}
+\bibinfo{author}{Vehlow, C.}, \bibinfo{author}{Reinhardt, T.},
+  \bibinfo{author}{Weiskopf, D.}, \bibinfo{year}{2013}.
+\newblock \bibinfo{title}{Visualizing fuzzy overlapping communities in
+  networks}.
+\newblock \bibinfo{journal}{IEEE Trans. Vis. Comput. Graph.}
+  \bibinfo{volume}{19}, \bibinfo{pages}{2486--2495}.
+
+\end{thebibliography}

Epidemiology/els-cas-templates/cas-dc-template.blg

+This is BibTeX, Version 0.99d (TeX Live 2019/Debian)
+Capacity: max_strings=100000, hash_size=100000, hash_prime=85009
+The top-level auxiliary file: cas-dc-template.aux
+The style file: cas-model2-names.bst
+Database file #1: cas-refs.bib
+Reallocated singl_function (elt_size=4) to 100 items from 50.
+You've used 3 entries,
+            2990 wiz_defined-function locations,
+            757 strings with 6701 characters,
+and the built_in function-call counts, 1896 in all, are:
+= -- 143
+> -- 54
+< -- 2
++ -- 21
+- -- 18
+* -- 195
+:= -- 279
+add.period$ -- 9
+call.type$ -- 3
+change.case$ -- 21
+chr.to.int$ -- 3
+cite$ -- 3
+duplicate$ -- 145
+empty$ -- 151
+format.name$ -- 27
+if$ -- 352
+int.to.chr$ -- 1
+int.to.str$ -- 1
+missing$ -- 27
+newline$ -- 30
+num.names$ -- 12
+pop$ -- 49
+preamble$ -- 1
+purify$ -- 18
+quote$ -- 0
+skip$ -- 41
+stack$ -- 0
+substring$ -- 96
+swap$ -- 99
+text.length$ -- 0
+text.prefix$ -- 0
+top$ -- 0
+type$ -- 27
+warning$ -- 0
+while$ -- 12
+width$ -- 0
+write$ -- 56

Epidemiology/els-cas-templates/cas-dc.cls

+%%
+%% This is file `cas-sc.cls'.
+%%
+%% This file is part of the 'CAS Bundle'.
+%% ......................................
+%% 
+%% It may be distributed under the conditions of the LaTeX Project Public
+%% License, either version 1.2 of this license or (at your option) any
+%% later version.  The latest version of this license is in
+%%    http://www.latex-project.org/lppl.txt
+%% and version 1.2 or later is part of all distributions of LaTeX
+%% version 1999/12/01 or later.
+%% 
+%% The list of all files belonging to the 'CAS Bundle' is
+%% given in the file `manifest.txt'.
+%% 
+
+%% $Id: cas-dc.cls 49 2020-03-14 09:05:10Z rishi $
+
+ \def\RCSfile{cas-dc}%
+ \def\RCSversion{2.1}%
+ \def\RCSdate{2020/03/14}%
+\NeedsTeXFormat{LaTeX2e}[1995/12/01]
+\ProvidesClass{\RCSfile}[\RCSdate, \RCSversion: Formatting class
+   for CAS double column articles]
+%
+\def\ABD{\AtBeginDocument}
+%
+% switches
+% 
+\newif\iflongmktitle    \longmktitlefalse
+\newif\ifdc             \global\dctrue
+\newif\ifsc             \global\scfalse
+\newif\ifcasreviewlayout  \global\casreviewlayoutfalse
+\newif\ifcasfinallayout   \global\casfinallayoutfalse
+
+\newcounter{blind}
+\setcounter{blind}{0}
+
+\def\blstr#1{\gdef\@blstr{#1}}
+\def\@blstr{1}
+\newdimen\@bls
+\@bls=\baselineskip
+
+\DeclareOption{singleblind}{\setcounter{blind}{1}}
+\DeclareOption{doubleblind}{\setcounter{blind}{2}}
+\DeclareOption{longmktitle}{\global\longmktitletrue}
+\DeclareOption{final}{\global\casfinallayouttrue}
+\DeclareOption{review}{\global\casreviewlayouttrue}
+
+\ExecuteOptions{a4paper,10pt,oneside,fleqn,review}
+\DeclareOption*{\PassOptionsToClass{\CurrentOption}{article}}
+\ProcessOptions
+\LoadClass{article}
+
+\RequirePackage{graphicx}
+\RequirePackage{amsmath,amsfonts,amssymb}
+\allowdisplaybreaks
+
+\RequirePackage{expl3,xparse}
+\@ifundefined{regex_match:nnTF}{\RequirePackage{l3regex}}{}
+\RequirePackage{etoolbox,balance}
+\RequirePackage{booktabs,makecell,multirow,array,colortbl,dcolumn,stfloats}
+\RequirePackage{xspace,xstring,footmisc}
+\RequirePackage[svgnames,dvipsnames]{xcolor}
+
+\RequirePackage[colorlinks]{hyperref}
+\colorlet{scolor}{black}
+\colorlet{hscolor}{DarkSlateGrey}
+\hypersetup{%
+  pdftitle={\csuse{__short_title:}},
+  pdfauthor={\csuse{__short_authors:}},
+  pdfcreator={LaTeX3; cas-sc.cls; hyperref.sty},
+  pdfproducer={pdfTeX;},
+  linkcolor={hscolor},
+  urlcolor={hscolor},
+  citecolor={hscolor},
+  filecolor={hscolor},
+  menucolor={hscolor},
+ }
+
+ \let\comma\@empty
+\let\tnotesep\@empty
+\let\@title\@empty
+%
+% Load Common items
+%
+
+\RequirePackage{cas-common}
+
+%
+% Specific to Single Column
+%
+\ExplSyntaxOn
+
+\RenewDocumentCommand \maketitle { }
+{
+  \ifbool { usecasgrabsbox }
+    { 
+      \setcounter{page}{0}
+      \thispagestyle{empty}
+      \unvbox\casgrabsbox  
+    } { }  
+  \pagebreak  
+  \ifbool { usecashlsbox }
+    { 
+      \setcounter{page}{0}
+      \thispagestyle{empty}
+      \unvbox\casauhlbox
+    } { }    
+  \pagebreak
+  \thispagestyle{first}    
+  \ifbool{longmktitle}
+  {
+    \LongMaketitleBox
+    \ProcessLongTitleBox
+  }
+  {
+    \twocolumn[\MaketitleBox]  
+    \printFirstPageNotes
+  }
+  \setcounter{footnote}{\int_use:N \g_stm_fnote_int}
+  \renewcommand\thefootnote{\arabic{footnote}}
+  \gdef\@pdfauthor{\infoauthors}
+  \gdef\@pdfsubject{Complex ~STM ~Content}
+}
+
+%
+% Fonts
+%
+\RequirePackage[T1]{fontenc}
+
+\file_if_exist:nTF { stix.sty }
+{
+  \file_if_exist:nTF { charis.sty }
+  {
+    \RequirePackage[notext]{stix} 
+    \RequirePackage{charis}
+  }
+  { \RequirePackage{stix} }
+}
+{
+  \iow_term:x {  *********************************************************** }
+  \iow_term:x { ~Stix ~ and ~ Charis~ fonts ~ are ~ not ~ available ~ }
+  \iow_term:x { ~ in ~TeX~system.~Hence~CMR~ fonts~ are ~ used. }
+  \iow_term:x {  *********************************************************** }
+}
+
+\file_if_exist:nTF { inconsolata.sty }
+{ \RequirePackage[scaled=.85]{inconsolata} }
+{ \tex_gdef:D \ttdefault { cmtt } }
+
+
+\ExplSyntaxOff
+
+%
+% Page geometry
+%
+\usepackage[%
+   paperwidth=210mm,
+   paperheight=280mm,
+   vmargin={19.5mm,18.2mm},
+   hmargin={18.1mm,18.1mm},
+   headsep=12pt,
+   footskip=12pt,
+   columnsep=18pt
+]{geometry}
+
+
+\endinput
+  
+%
+% End of class 'cas-sc'
+%
+

Epidemiology/els-cas-templates/cas-sc-template.abs

+This template helps you to create a properly formatted \LaTeX\ manuscript.
+
+\noindent\texttt{\textbackslash begin{abstract}} \dots
+\texttt{\textbackslash end{abstract}} and
+\verb+\begin{keyword}+ \verb+...+ \verb+\end{keyword}+
+which
+contain the abstract and keywords respectively.
+Each keyword shall be separated by a \verb+\sep+ command.

Epidemiology/els-cas-templates/cas-sc-template.aux

+\relax 
+\providecommand\hyper@newdestlabel[2]{}
+\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
+\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
+\global\let\oldcontentsline\contentsline
+\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
+\global\let\oldnewlabel\newlabel
+\gdef\newlabel#1#2{\newlabelxx{#1}#2}
+\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
+\AtEndDocument{\ifx\hyper@anchor\@undefined
+\let\contentsline\oldcontentsline
+\let\newlabel\oldnewlabel
+\fi}
+\fi}
+\global\let\hyper@last\relax 
+\gdef\HyperFirstAtBeginDocument#1{#1}
+\providecommand\HyField@AuxAddToFields[1]{}
+\providecommand\HyField@AuxAddToCoFields[2]{}
+\csgdef{mark@title}{1,2}
+\orcidauthor{0000-0001-7511-2910}{CV Radhakrishnan}
+\csgdef{mark@corau1}{1}
+\csgdef{mark@fnau1}{1}
+\emailauthor{cvr_1@tug.org.in}{CV Radhakrishnan}
+\urlauthor{www.cvr.cc, cvr@sayahna.org}{CV Radhakrishnan}
+\creditauthor{Conceptualization of this study, Methodology, Software}{CV Radhakrishnan}
+\csgdef{mark@fnau3}{2}
+\emailauthor{cvr3@sayahna.org}{CV Rajagopal}
+\urlauthor{www.sayahna.org}{CV Rajagopal}
+\creditauthor{Data curation, Writing - Original draft preparation}{CV Rajagopal}
+\csgdef{mark@corau4}{2}
+\csgdef{mark@fnau4}{1,3}
+\emailauthor{rishi@stmdocs.in}{Rishi T.}
+\urlauthor{www.stmdocs.in}{Rishi T.}
+\NewLabel{cor1}{1}
+\NewLabel{cor2}{2}
+\NewLabel{fn1}{1}
+\NewLabel{fn2}{2}
+\@writefile{toc}{\contentsline {section}{\numberline {1}Introduction}{1}{section.1}\protected@file@percent }
+\citation{Fortunato2010}
+\citation{Fortunato2010,NewmanGirvan2004}
+\citation{Fortunato2010,Vehlowetal2013}
+\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces The evanescent light - $1S$ quadrupole coupling ($g_{1,l}$) scaled to the bulk exciton-photon coupling ($g_{1,2}$). The size parameter $kr_{0}$ is denoted as $x$ and the \textsc  {\lowercase {PMS}}\xspace  is placed directly on the cuprous oxide sample ($\delta r=0$, See also Table \ref {tbl1}).}}{2}{figure.1}\protected@file@percent }
+\newlabel{FIG:1}{{1}{2}{The evanescent light - $1S$ quadrupole coupling ($g_{1,l}$) scaled to the bulk exciton-photon coupling ($g_{1,2}$). The size parameter $kr_{0}$ is denoted as $x$ and the \PMS is placed directly on the cuprous oxide sample ($\delta r=0$, See also Table \protect \ref {tbl1})}{figure.1}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {2}Installation}{2}{section.2}\protected@file@percent }
+\@writefile{toc}{\contentsline {section}{\numberline {3}Front matter}{2}{section.3}\protected@file@percent }
+\@writefile{toc}{\contentsline {section}{\numberline {4}Bibliography styles}{2}{section.4}\protected@file@percent }
+\@writefile{toc}{\contentsline {section}{\numberline {5}Floats}{2}{section.5}\protected@file@percent }
+\@writefile{lot}{\contentsline {table}{\numberline {1}{\ignorespaces This is a test caption. This is a test caption. This is a test caption. This is a test caption.}}{3}{table.1}\protected@file@percent }
+\newlabel{tbl1}{{1}{3}{This is a test caption. This is a test caption. This is a test caption. This is a test caption}{table.1}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {6}Theorem and ...}{3}{section.6}\protected@file@percent }
+\newlabel{10}{{1}{3}{Theorem and ..}{equation.6.1}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {7}Enumerated ...}{3}{section.7}\protected@file@percent }
+\bibstyle{cas-model2-names}
+\bibdata{cas-refs}
+\bibcite{Fortunato2010}{{1}{2010}{{Fortunato}}{{}}}
+\@writefile{toc}{\contentsline {section}{\numberline {8}Cross-references}{4}{section.8}\protected@file@percent }
+\@writefile{toc}{\contentsline {section}{\numberline {9}Bibliography}{4}{section.9}\protected@file@percent }
+\@writefile{toc}{\contentsline {section}{\numberline {A}My Appendix}{4}{appendix.A}\protected@file@percent }
+\bibcite{NewmanGirvan2004}{{2}{2004}{{Newman and Girvan}}{{}}}
+\bibcite{Vehlowetal2013}{{3}{2013}{{Vehlow et~al.}}{{Vehlow, Reinhardt and Weiskopf}}}
+\csgdef{cabio1lines}{7}
+\csgdef{cabio2lines}{5}
+\csxdef{lastpage}{5}

Epidemiology/els-cas-templates/cas-sc-template.bbl

+\begin{thebibliography}{3}
+\expandafter\ifx\csname natexlab\endcsname\relax\def\natexlab#1{#1}\fi
+\providecommand{\url}[1]{\texttt{#1}}
+\providecommand{\href}[2]{#2}
+\providecommand{\path}[1]{#1}
+\providecommand{\DOIprefix}{doi:}
+\providecommand{\ArXivprefix}{arXiv:}
+\providecommand{\URLprefix}{URL: }
+\providecommand{\Pubmedprefix}{pmid:}
+\providecommand{\doi}[1]{\href{http://dx.doi.org/#1}{\path{#1}}}
+\providecommand{\Pubmed}[1]{\href{pmid:#1}{\path{#1}}}
+\providecommand{\bibinfo}[2]{#2}
+\ifx\xfnm\relax \def\xfnm[#1]{\unskip,\space#1}\fi
+%Type = Article
+\bibitem[{Fortunato(2010)}]{Fortunato2010}
+\bibinfo{author}{Fortunato, S.}, \bibinfo{year}{2010}.
+\newblock \bibinfo{title}{Community detection in graphs}.
+\newblock \bibinfo{journal}{Phys. Rep.-Rev. Sec. Phys. Lett.}
+  \bibinfo{volume}{486}, \bibinfo{pages}{75--174}.
+%Type = Article
+\bibitem[{Newman and Girvan(2004)}]{NewmanGirvan2004}
+\bibinfo{author}{Newman, M.E.J.}, \bibinfo{author}{Girvan, M.},
+  \bibinfo{year}{2004}.
+\newblock \bibinfo{title}{Finding and evaluating community structure in
+  networks}.
+\newblock \bibinfo{journal}{Phys. Rev. E.} \bibinfo{volume}{69},
+  \bibinfo{pages}{026113}.
+%Type = Article
+\bibitem[{Vehlow et~al.(2013)Vehlow, Reinhardt and Weiskopf}]{Vehlowetal2013}
+\bibinfo{author}{Vehlow, C.}, \bibinfo{author}{Reinhardt, T.},
+  \bibinfo{author}{Weiskopf, D.}, \bibinfo{year}{2013}.
+\newblock \bibinfo{title}{Visualizing fuzzy overlapping communities in
+  networks}.
+\newblock \bibinfo{journal}{IEEE Trans. Vis. Comput. Graph.}
+  \bibinfo{volume}{19}, \bibinfo{pages}{2486--2495}.
+
+\end{thebibliography}

Epidemiology/els-cas-templates/cas-sc-template.blg

+This is BibTeX, Version 0.99d (TeX Live 2019/Debian)
+Capacity: max_strings=100000, hash_size=100000, hash_prime=85009
+The top-level auxiliary file: cas-sc-template.aux
+The style file: cas-model2-names.bst
+Database file #1: cas-refs.bib
+Reallocated singl_function (elt_size=4) to 100 items from 50.
+You've used 3 entries,
+            2990 wiz_defined-function locations,
+            757 strings with 6701 characters,
+and the built_in function-call counts, 1896 in all, are:
+= -- 143
+> -- 54
+< -- 2
++ -- 21
+- -- 18
+* -- 195
+:= -- 279
+add.period$ -- 9
+call.type$ -- 3
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+chr.to.int$ -- 3
+cite$ -- 3
+duplicate$ -- 145
+empty$ -- 151
+format.name$ -- 27
+if$ -- 352
+int.to.chr$ -- 1
+int.to.str$ -- 1
+missing$ -- 27
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+num.names$ -- 12
+pop$ -- 49
+preamble$ -- 1
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+text.length$ -- 0
+text.prefix$ -- 0
+top$ -- 0
+type$ -- 27
+warning$ -- 0
+while$ -- 12
+width$ -- 0
+write$ -- 56

Epidemiology/els-cas-templates/doc/makefile

+# $Id: makefile 37 2020-02-25 09:06:02Z rishi $
+
+file=elsdoc-cas
+
+
+all: pdf out 
+	make pdf
+	make pdf
+
+out:
+	if  [ -f $(file).out ] ; then cp $(file).out tmp.out; fi ;
+	sed 's/BOOKMARK/dtxmark/g;' tmp.out > x.out; mv x.out tmp.out ;
+
+pdf:
+	pdflatex $(file).tex
+
+index:
+	makeindex -s gind.ist -o $(file).ind $(file).idx 
+
+changes:
+	makeindex -s gglo.ist -o $(file).gls $(file).glo
+
+xview:
+	xpdf -z 200 $(file).pdf &>/dev/null
+
+view:
+	open -a 'Adobe Reader.app' $(file).pdf
+
+ins:
+	latex $(file).ins 
+
+diff:
+	diff $(file).sty ../$(file).sty |less
+
+copy:
+	cp $(file).sty ../

Epidemiology/toward.abs

+This paper aims at reconstructing the evolution of all the available COVID-19 vaccines trials extracted from the \textit{COVID-NMA database} by applying the \textit{phylomemy reconstruction process}. We visualize the textual contents of 1,794 trials descriptions and explore their collective structure along with their semantic dynamics. We map the continuous progress of the main COVID-19 vaccine platforms from their early-stage trials in February 2020 to their most recent combinations driven by the rise of variants of concern, third dose issues and heterologous vaccinations. This paper brings insights for the global coordination between research teams especially in crisis situations such as the COVID-19 pandemic.

Epidemiology/toward.blg

+This is BibTeX, Version 0.99d (TeX Live 2019/Debian)
+Capacity: max_strings=200000, hash_size=200000, hash_prime=170003
+The top-level auxiliary file: toward.aux
+The style file: cas-model2-names.bst
+Database file #1: references.bib
+Reallocated singl_function (elt_size=4) to 100 items from 50.
+Warning--empty note in delanoe_mining_2021
+Warning--empty pages in uno2004lcm
+You've used 10 entries,
+            2990 wiz_defined-function locations,
+            806 strings with 11711 characters,
+and the built_in function-call counts, 17293 in all, are:
+= -- 900
+> -- 1708
+< -- 3
++ -- 643
+- -- 633
+* -- 2559
+:= -- 2623
+add.period$ -- 29
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+change.case$ -- 261
+chr.to.int$ -- 10
+cite$ -- 12
+duplicate$ -- 863
+empty$ -- 672
+format.name$ -- 667
+if$ -- 2896
+int.to.chr$ -- 1
+int.to.str$ -- 1
+missing$ -- 273
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+pop$ -- 358
+preamble$ -- 1
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+skip$ -- 153
+stack$ -- 0
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+warning$ -- 2
+while$ -- 41
+width$ -- 0
+write$ -- 156
+(There were 2 warnings)