new package nih (29sep06)

git-svn-id: svn://tug.org/texlive/trunk@2230 c570f23f-e606-0410-a88d-b1316a301751

10 files changed, 1150 insertions, 0 deletions

diff --git a/Master/texmf-dist/doc/latex/nih/README b/Master/texmf-dist/doc/latex/nih/README
new file mode 100644
index 00000000000..607d588c29c
--- /dev/null
+++ b/Master/texmf-dist/doc/latex/nih/README
@@ -0,0 +1,14 @@
+nih.cls provides a class for grant applications to NIH, the National
+Institutes of Health, a US government agency.  
+
+The example-* files provide a template for using nih.cls and submitting
+the biographical sketches the NIH wants.  They (potentially) use
+denselists.sty, which just reduces list spacing; this is not part of the
+class proper.
+
+These files were originally created and are still maintained by Bruce
+Donald.  For more information, please see the author's web sites at
+http://www.cs.dartmouth.edu/brd/NIH/tips and http://www.cs.duke.edu/brd.
+
+All of these files are freely redistributable, see each for details.
+(You may freely use, modify and/or distribute this README itself, too.)
diff --git a/Master/texmf-dist/doc/latex/nih/example-biosketch.pdf b/Master/texmf-dist/doc/latex/nih/example-biosketch.pdf
new file mode 100644
index 00000000000..1ebe5214ca9
--- /dev/null
+++ b/Master/texmf-dist/doc/latex/nih/example-biosketch.pdf
diff --git a/Master/texmf-dist/doc/latex/nih/example-biosketch.tex b/Master/texmf-dist/doc/latex/nih/example-biosketch.tex
new file mode 100644
index 00000000000..f001cc4e834
--- /dev/null
+++ b/Master/texmf-dist/doc/latex/nih/example-biosketch.tex
@@ -0,0 +1,698 @@
+% This example file for NIH biographical sketches was originally written
+% by Bruce Donald (http://www.cs.duke.edu/brd/).
+% 
+% You may freely use, modify and/or distribute this file.
+% 
+\documentclass[11pt]{nih}
+%\documentclass[12pt]{nih-times}
+% last revision:
+\def\mydate{2006-09-16 17:10:33 karl}
+%\usepackage[dvips]{graphicx}
+%\usepackage{psfrag}
+\usepackage{color}
+%\usepackage{boxedminipage}
+\usepackage{amsfonts}
+\usepackage{denselists}
+
+\long\def\gobble#1{}
+
+\long\def\MEMS#1{}
+
+%Note from brd
+\long\def\todo#1{}
+\def\ICRA{IEEE International Conference on Robotics and Automation (ICRA)}
+
+\def\cbk#1{[{\em #1}]}
+
+\def\degree{$^\circ$}
+\def\R{\mathbb{R}}
+\def\Fscr{\mathcal{F}}
+\def\set#1{{\{#1\}}}
+\def\edge{\!\rightarrow\!}
+\def\dedge{\!\leftrightarrow\!}
+
+\def\Jigsaw{{\sc Jigsaw}}
+\def\ahelix{\ensuremath{\alpha}-helix}
+\def\ahelices{\ensuremath{\alpha}-helices}
+\def\ahelical{$\alpha$-helical}
+\def\bstrand{\ensuremath{\beta}-strand}
+\def\bstrands{\ensuremath{\beta}-strands}
+\def\bsheet{\ensuremath{\beta}-sheet}
+\def\bsheets{\ensuremath{\beta}-sheets}
+\def\hone{\ensuremath{^1}\rm{H}}
+\def\htwo{$^{2}$H}
+\def\cthir{\ensuremath{^{13}}\rm{C}}
+\def\nfif{\ensuremath{^{15}}\rm{N}}
+\def\hn{\rm{H}\ensuremath{^\mathrm{N}}}
+\def\hnone{\textup{H}\ensuremath{^1_\mathrm{N}}}
+\def\ca{\rm{C}\ensuremath{^\alpha}}
+\def\catwel{\ensuremath{^{12}}\rm{C}\ensuremath{^\alpha}}
+\def\ha{\rm{H}\ensuremath{^\alpha}}
+\def\cb{\rm{C}\ensuremath{^\beta}}
+\def\hb{\rm{H}\ensuremath{^\beta}}
+\def\hg{\rm{H}\ensuremath{^\gamma}}
+\def\dnn{\ensuremath{d_{\mathrm{NN}}}}
+\def\dan{\ensuremath{d_{\alpha \mathrm{N}}}}
+\def\jconst{\ensuremath{^{3}J_{\mathrm{H}^{\mathrm{N}}\mathrm{H}^{\alpha}}}}
+
+\def\cbfb{CBF-$\beta$}
+
+\newtheorem{defn}{Definition}
+\newtheorem{claim}{Claim}
+
+\newenvironment{closeenumerate}{\begin{list}{\arabic{enumi}.}{\topsep=0in\itemsep=0in\parsep=0in\usecounter{enumi}}}{\end{list}}
+\def\CR{\hspace{0pt}}           % ``invisible'' space for line break
+
+%\long\def\efforta mount#1{#1}
+\long\def\effortamount#1{}
+
+\begin{document}
+
+%\setcounter{page}{20} % or whatever
+\setcounter{page}{7} % or whatever
+
+%\newsec{Biographical Sketch: Bruce Randall Donald}
+\def\vp{\vphantom{\Large{O}}}
+\def\Vp{\vphantom{\LARGE{O}}}
+
+
+\subsubsection*{Biographical Sketch}
+
+%\gobble{
+
+\begin{tabular}{|l|l|}
+\hline
+\Vp{\sf Name} & {\sf Position Title}\\
+\hline
+\Vp \ \ {\bf Bruce R.~Donald, Ph.D.} & \ 
+ {\bf   Professor of Computer Science and Biochemistry}\\
+\gobble{{\bf   William and Sue Gross Professor  }\\
+ & \ \ \ \ \ \ {\bf  of Computer Science and Biochemistry (as of 8/1/2006)}\\}
+\hline
+\end{tabular}
+
+%}
+
+\subsubsection*{Education/Training}
+
+\begin{tabular}{|l|c|c|l|}
+\hline
+\Vp{\sf INSTITUTION} & 	{\sf DEGREE} &
+     {\sf YEAR} & {\sf	FIELD OF STUDY}\\
+\hline
+\hline
+\Vp Yale University	& B.A.	& 1980	& \\
+\hline
+\Vp Massachusetts Institute of Technology	& S.M.&	1984 &	Electrical Engineering \& Computer Science\\
+\hline
+\Vp Massachusetts Institute of Technology &	Ph.D.	&1987&
+Computer Science\\
+\hline
+\end{tabular}
+
+\bigskip
+
+\gobble{
+\noindent
+\begin{Description}
+\item[]
+Ph.D.~Advisor: Tom\'as Lozano-P\'erez, MIT Artificial Intelligence
+Laboratory and Department of Electrical Engineering \& Computer Science.
+\end{Description}
+}
+
+\subsubsection*{A. Research and Professional Experience}
+
+\underline{Professional Experience}
+
+\def\myitem{\ $\bullet$\ }
+
+ %\def\parens#1{({#1})}
+\def\parens#1{{#1}:}
+
+%\begin{Description}
+{\myitem} \parens{1978-84} Research Analyst,
+Laboratory for Computer Graphics and Spatial
+Analysis, GSD, Harvard University.  
+{\myitem} \parens{1984} Research Staff, Artificial Intelligence Laboratory, MIT.
+{\myitem} \parens{1982-1987} Graduate student, Artificial Intelligence Laboratory and Department of EECS, MIT. 
+{\myitem} \parens{1987-1993} Assistant Professor; 
+\parens{1993-1998} Associate Professor (with tenure), Computer Science Department, Cornell University.
+{\myitem} \parens{1995-1996} Consultant and Contractor, Interval Research Corporation, Palo Alto, CA.
+{\myitem} \parens{1994-1996} Visiting Professor, Computer Science Department,
+Stanford. 
+{\myitem} \parens{1997-1999} Associate Professor (with tenure);
+  \parens{1999-2006} Professor of Computer Science,
+  Dartmouth College.
+\gobble{{\myitem} \parens{1998} Founder, M.D.-Ph.D.~Program in Computational Biology, Dartmouth College and
+Dartmouth Medical School.}
+{\myitem} \parens{1999-2006} M.D.-Ph.D.~Committee, Dartmouth College and
+Dartmouth Medical School.
+{\myitem} \parens{2000} Conference chair, Int'l.~Workshop on Algorithmic
+Foundations of Robotics.
+{\myitem} 11 NSF Advisory Panels (1990-2003).
+{\myitem} \parens{2000-2001} Visiting Scientist, Artificial Intelligence Laboratory and Department of EECS, MIT.
+{\myitem} \parens{2000-2002} Scientific Advisory Board, Carta
+Proteomics, Inc. (now ExSAR). 
+{\myitem} \parens{2000-2006} Member, Dartmouth Center for Structural
+Biology and Computational Chemistry.
+{\myitem} \parens{2000-2006} Adjunct Professor of Chemistry, Dartmouth.
+{\myitem} \parens{2002-2006} Adjunct Professor of Biological Sciences, Dartmouth.
+{\myitem} \parens{2002, 2004, 2005} {\em Ad hoc} Member, NIH Study Sections (BBCA,
+ ALY, ZRG1 CFS).
+{\myitem}  \parens{2003--2006} Joan and Edward Foley Professor, Dartmouth.
+{\myitem}\parens{2006--now} William and Sue Gross Professor of Computer
+Science, Duke University. 
+{\myitem}\parens{2006--now}
+Professor of Biochemistry, School of Medicine, Duke University Medical Center.
+
+%\end{Description}
+
+\noindent\underline{Honors and Awards}
+
+%\begin{Description}
+
+{\myitem} \parens{1979} Phi Beta Kappa; \parens{1980} Distinction in the Major, Yale University.
+{\myitem} \parens{1980} Graduated  {\em Summa Cum Laude,} Yale.
+{\myitem} \parens{1985-1987} NASA/JPL Graduate Student Researcher Fellowship.
+{\myitem} \parens{1989-1994} NSF Presidential Young Investigator.
+{\myitem} \parens{1997-2000} NSF Challenges in Computer and Information Science and Engineering Grant.	
+{\myitem} \parens{2001} Guggenheim Fellow, {\em
+``Algorithms in Structural Proteomics."}
+{\myitem} \parens{2002} Distinguished Lectures, Robert Mueller-Thuns
+(Univ.~Illinois, Urbana-Champaign); Triangle (UNC Chapel Hill, Duke
+\& N.C.~State).
+
+%\end{Description}
+
+\def\mystar{{$\star$}}
+
+%\subsubsection*{Selected Peer-reviewed Publications (from a list of
+%159 total, with 28 in 2003-4). }
+
+\medskip
+
+\noindent{\bf B. Selected Peer-reviewed Publications (from a list of
+176 total, with 19 in 2005--6)}\gobble{\\ {\sf Publications available online at
+  {\tt
+  www.cs.dartmouth.edu/brd/Research/Bio/}} }
+
+\vspace*{-0.1in}
+
+\gobble{{{\mystar} {\em Note: In Computer Science, certain conferences
+(Marked with a $\star$) are are highly selective and rigorously
+refereed, often by 3 reviewers plus the conference chairs. Conference
+papers are published not as one-page abstracts, but as 8-12 page full
+papers (in 10pt double-column format). For this reason, conference
+papers are considered primary publications in the field.  Selectivity
+can be roughly quantitated by the acceptance rate.}}}
+
+\def\Nospacing{\itemsep=0pt\topsep=0pt\partopsep=0pt\parskip=0pt\parsep=0pt}
+
+\makeatletter
+\def\thebibliography#1{\list
+{[\arabic{enumiv}]}{\settowidth\labelwidth{[#1]}\leftmargin\labelwidth
+\advance\leftmargin\labelsep
+\usecounter{enumiv}\Nospacing}
+\def\newblock{\hskip .11em plus .33em minus .07em}
+\sloppy\clubpenalty4000\widowpenalty4000
+\sfcode`\.=1000\relax
+}
+\let\endthebibliography=\endlist
+\makeatother
+
+%%%%%%% begin papers/biblio
+%\begin{thebibliography}{10}
+
+\def\th{$^{\rm{th}}$}
+
+%\def\mybibitem#1#2{\bibitem{#1}{#2}}
+\def\brd{B.~R. Donald}
+%\def\brd{{\bf B.~R. Donald}}
+
+\def\mybibitem#1{\item}
+\begin{Enumerate}
+
+%\input{papers-r01}
+%% %\begin{thebibliography}{10}
+
+%% \def\th{$^{\rm{th}}$}
+
+%% %\def\mybibitem#1#2{\bibitem{#1}{#2}}
+
+%% \def\mybibitem#1{\item}
+%% \begin{Enumerate}
+
+\bibitem{KapurMundyDonald92}
+B.~R. Donald, D.~Kapur, and J.~Mundy.
+\newblock {\em Symbolic and Numerical Computation for Artificial Intelligence}.
+\newblock Academic Press, Harcourt Jovanovich, London, 1992.
+
+\bibitem{CannyDonaldReifXavier93}
+B.~R. Donald, P.~Xavier, J.~Canny, and J.~Reif.
+\newblock Kinodynamic motion planning.
+\newblock {\em Journal of the ACM}, 40(5):1048--1066, 1993.
+
+\bibitem{jcb00-jigsaw}
+C.~Bailey-Kellogg, A.~Widge, J.~J. {Kelley III}, M.~J. Berardi, J.~H.
+  Bushweller, and {\brd}.
+\newblock The {NOESY} {Jigsaw}: Automated protein secondary structure and
+  main-chain assignment from sparse, unassigned {NMR} data.
+\newblock {\em Jour. Comp. Biol.}, 3-4(7):537--558, 2000.
+
+\bibitem{jcb00-sar}
+C.~Bailey-Kellogg, J.~J. {Kelley III}, C.~Stein, and {\brd}.
+\newblock Reducing mass degeneracy in {SAR} by {MS} by stable isotopic
+  labeling.
+\newblock {\em Jour. Comp. Biol.}, 8(1):19--36, 2001.
+
+\gobble{
+\bibitem{icra01}
+C.~Bailey-Kellogg, J.~J. {Kelley III}, R.~Lilien, and {\brd}.
+\newblock Physical geometric algorithms for structural molecular biology.
+\newblock In {\em the Special Session on Computational Biology \& Chemistry,
+  {\it Proc.~{IEEE} Int'l Conf. on Robotics and Automation
+  ({ICRA})}}, pp.~940--947, May 2001.
+}
+
+\bibitem{recomb01}
+C.~Langmead and {\brd}.
+\newblock Extracting structural information using time-frequency analysis of
+  protein {NMR} data.
+\newblock In {\em Proc.~5{\th}  Int'l.~Conf.~on
+  Research in Computational Molecular Biology (RECOMB)}, pp.~164--175. ACM
+  Press, April 2001.
+
+\gobble{
+\bibitem{csb02}
+C.~Langmead, C.~R. McClung, and {\brd}.
+\newblock A maximum entropy algorithm for rhythmic analysis of genome-wide
+  expression patterns.
+\newblock In {\em Proc.~IEEE Computer Society Bioinformatics
+  Conference (IEEE CSB)}, pp.~237--245, August 2002.
+}
+
+\bibitem{jcb-rage}
+C.~Langmead, A.~Yan, C.~R. McClung, and {\brd}.
+\newblock Phase-independent rhythmic analysis of genome-wide expression
+  patterns.
+\newblock {\em Journal of Computational Biology}, 10(3-4):521--536, 2003.
+
+\bibitem{jcb-fld03}
+R.~Lilien, H.~Farid, and {\brd}.
+\newblock Probabilistic disease classification of expression-dependent
+  proteomic data from mass spectrometry of human serum.
+\newblock {\em Journal of Computational Biology}, 10(6):925--946, 2003.
+
+\bibitem{recomb03}
+C.~Langmead, A.~Yan, R.~Lilien, L.~Wang, and {\brd}.
+\newblock A polynomial-time nuclear vector replacement algorithm for automated
+  {NMR} resonance assignments.
+\newblock In {\em Proc.~7{\th} Int'l.~Conf.~on
+  Research in Computational Molecuar Biology (RECOMB)}, pp.~176--187,
+  Berlin, Germany, April 2003. ACM Press.
+
+\bibitem{ieeecsb-langmead03}
+C.~Langmead and {\brd}.
+\newblock 3{D} structural homology detection via unassigned residual dipolar
+  couplings.
+\newblock In {\em Proc.~{IEEE} Computer Society Bioinformatics
+  Conference ({CSB})}, pp.~209--217, Stanford, Aug.~2003.
+
+\bibitem{oneil-jbc03}
+R.~O'Neil, R.~Lilien, {\brd}, R.~Stroud, and A.~Anderson.
+\newblock Phylogenetic classification of protozoa based on the structure of the
+  linker domain in the bifunctional enzyme, dihydrofolate reductase-thymidylate
+  synthase.
+\newblock {\em Jour. Biol. Chem.}, 278(52):52980--52987, 2003.
+
+\bibitem{oneil-jem03}
+R.~O'Neil, R.~Lilien, {\brd}, R.~Stroud, and A.~Anderson.
+\newblock The crystal structure of dihydrofolate reductase-thymidylate synthase
+  from {{\em Cryptosporidium hominis}} reveals a novel architecture for the
+  bifunctional enzyme.
+\newblock {\em Jour. Eukaryotic Microbiology}, 50(6):555--556, 2003.
+
+\gobble{
+\bibitem{ieeecsb03-wang}
+L.~Wang, R.~Mettu, R.~Lilien, and {\brd}.
+\newblock An exact algorithm for determining protein backbone structure from
+  {NH} residual dipolar couplings.
+\newblock In {\em Proc.~{IEEE} Computer Society Bioinformatics
+  Conference ({CSB})}, pp.~611--612, Stanford, August 2003.
+}
+
+\bibitem{langmead-jbnmr04}
+C.~Langmead and {\brd}.
+\newblock An expectation/maximization nuclear vector replacement algorithm for
+  automated {NMR} resonance assignments.
+\newblock {\em Jour. Biomolecular {NMR}}, 29(2):111--138, 2004.
+
+\bibitem{wang-jbnmr03}
+L.~Wang and {\brd}.
+\newblock Exact solutions for internuclear vectors and backbone dihedral angles
+  from {NH} residual dipolar couplings in two media, and their application in a
+  systematic search algorithm for determining protein backbone structure.
+\newblock {\em Jour. Biomolecular {NMR}}, 29(3):223--242, 2004.
+
+\bibitem{langmead-jcb04}
+C.~Langmead, A.~Yan, R.~Lilien, L.~Wang, and {\brd}.
+\newblock A polynomial-time nuclear vector replacement algorithm for automated
+  {NMR} resonance assignments.
+\newblock {\em Jour. Comp. Biol.}, 11(2-3):277--298, 2004.
+
+\bibitem{recomb-04}
+R.~Lilien, B.~Stevens, A.~Anderson, and {\brd}.
+\newblock A novel ensemble-based scoring and search algorithm for protein
+  redesign, and its application to modify the substrate specificity of the
+  gramicidin synthetase {A} phenylalanine adenylation enzyme.
+\newblock In {\em Proc.~Eighth Annual International Conference on
+  Research in Computational Molecular Biology ({RECOMB})}, pp.~46--57, San
+  Diego, March 2004.
+
+\bibitem{lilien-acd04}
+R.~Lilien, C.~Bailey-Kellogg, A.~Anderson, and {\brd}.
+\newblock {A subgroup algorithm to identify cross-rotation peaks consistent
+  with non-crystallographic symmetry}.
+\newblock {\em Acta Crystallographica Section D: Biological Crystallography},
+  60(6):1057--1067, Jun 2004.
+
+\bibitem{LangmeadDonald-csb04}
+C.~Langmead and {\brd}.
+\newblock High-throughput 3{D} structural homology detection via {NMR}
+  resonance assignment.
+\newblock In {\em Proc.~{IEEE} Computational Systems
+  Bioinformatics Conference ({CSB})}, pp.~278--289, Stanford, CA, August
+  2004.
+
+\gobble{
+\bibitem{Dartmouth:TR2004-492}
+R.~Lilien, M.~Sridharan, and {\brd}.
+\newblock {Identification of Novel Small Molecule Inhibitors of Core-Binding
+  Factor Dimerization by Computational Screening against NMR Molecular
+  Ensembles}.
+\newblock Technical Report TR2004-492, Dartmouth College, Computer Science,
+  Hanover, NH, March 2004.
+}
+
+\bibitem{WangDonald-csb04}
+L.~Wang and {\brd}.
+\newblock Analysis of a systematic search-based algorithm for determining
+  protein backbone structure from a minimal number of residual dipolar
+  couplings.
+\newblock In {\em Proc.~{IEEE} Computational Systems
+  Bioinformatics Conference ({CSB})}, pp.~319--330, Stanford, CA, August
+  2004.
+
+\bibitem{ismb05}
+R.~Mettu, R.~Lilien, and B.~R. Donald.
+\newblock High-throughput inference of protein-protein interfaces from
+  unassigned {NMR} data.
+\newblock {\em Bioinformatics}, 2005; {\bf{21}}(Suppl.~1):i292--i301.   
+\gobble{special issue from papers presented at the 2005 Int'l.~Conf.~on
+Intelligent Systems for Molecular Biology, Detroit, MI) }
+
+\mybibitem{jcb04-NRPS}
+R.~Lilien, B.~Stevens, A.~Anderson, and {\brd}.
+\newblock A novel ensemble-based scoring and search algorithm for protein
+  redesign, and its application to modify the substrate specificity of the
+  gramicidin synthetase {A} phenylalanine adenylation enzyme.
+\newblock {\em Journal of Computational Biology} 2005; {\bf{12}}(6-7):740--761.
+
+\mybibitem{csb05-noe}
+L.~Wang and B.~R. Donald.
+\newblock An efficient and accurate algorithm for assigning nuclear
+  {Overhauser} effect restraints using a rotamer library ensemble and residual
+  dipolar couplings.
+\newblock In {\em Proceedings of the {IEEE} Computational Systems
+  Bioinformatics Conference ({CSB})}, pp.~189--202,
+Stanford, CA, August 2005.
+
+\mybibitem{csb05-poly}
+L.~Wang, R.~Mettu, and B.~R. Donald.
+\newblock An algebraic geometry approach to protein backbone structure
+  determination from {NMR} data.
+\newblock In {\em Proceedings of the {IEEE} Computational Systems
+  Bioinformatics Conference ({CSB})}, pp.~235--246, Stanford, CA,
+August 2005.
+
+\gobble{
+\mybibitem{recomb-06}
+I.~Georgiev, R.~Lilien, and B.~R. Donald.
+\newblock A novel minimized dead-end elimination criterion and its application
+  to protein redesign in a hybrid scoring and search algorithm for computing
+  partition functions over molecular ensembles.
+\newblock In {\em Proc.~Tenth Ann.~Intl.~Conf.~on
+  Research in Computational Molecular Biology (RECOMB)}, pp. 530--545,
+  Venice, Italy, April 2006. Springer Berlin, Lecture Notes in
+  Computer Science, LNBI 3909.
+}
+
+\bibitem{ismb06}
+I.~Georgiev, R.~Lilien, and B.~R. Donald.
+\newblock Improved pruning algorithms and divide-and-conquer strategies for
+  dead-end elimination, with application to protein design.
+\newblock {\em Bioinformatics} 2006; {\bf{22}}(14):e174--183.
+\newblock Special issue on papers from the Int'l Conf. on Intelligent
+  Sys. for Mol. Biol. ({ISMB 2006}), Fortaleza, Brazil.
+
+\bibitem{csb06}
+L.~Wang and B.~R. Donald.
+\newblock A data-driven, systematic search algorithm for structure
+  determination of denatured or disordered proteins.
+\newblock In {\em Proceedings of the LSS Computational Systems Bioinformatics
+  Conference ({CSB})}, Stanford, CA, August 2006.
+ Pages 67-78. ISBN 1-86094-700-X.
+
+\bibitem{jcb-poly06}
+L.~Wang, R.~Mettu, and B.~R. Donald.
+\newblock A polynomial-time algorithm for {\em de novo} protein backbone
+  structure determination from {NMR} data.
+\newblock {\em Journal of Computational Biology}, 2006.
+\newblock In press.
+
+\bibitem{proteins06}
+S.~Potluri, A.~Yan, B.~R. Donald, and C.~Bailey-Kellogg.
+\newblock Structure determination of symmetric homo-oligomers by a complete
+  search of symmetry configuration space using {NMR} restraints and van der
+  {Waals} packing.
+\newblock {\em Proteins: Structure, Function and Bioinformatics},
+  2006; 65(1):203--219.
+
+%\end{Enumerate}
+
+%\end{thebibliography}
+
+\end{Enumerate}
+
+%\end{thebibliography}
+%%%%%%% endpapers/biblio
+
+
+%\input{papers}
+%\input{papers2}
+
+\MEMS{Change URL}
+
+\gobble{
+\begin{center}
+{\sf Publications available online at {\tt www.cs.dartmouth.edu/\lower1.50ex\hbox{\LARGE{\~{}}}brd/Research/Bio/}}
+\end{center}
+}
+
+%\newpage
+%\setcounter{page}{1} % or whatever
+
+\subsection*{C. Research Projects and Funding}
+
+\subsection*{CURRENT SUPPORT}
+
+\def\myhrule{\smallskip\hrule\smallskip}
+
+\myhrule 
+\noindent \begin{tabular}{ll}
+DONALD, BRUCE R.	&		ONGOING\\
+	(PI: Donald)	&	2002-2007	\\
+	NIH/NIGMS & R01 GM-65982\\
+{\em Automated NMR Assignment and Protein Structure}\\
+\effortamount{\$150,000 &\\}
+\end{tabular}
+
+The long-term objective of this project is the development of new
+computational methods for biomolecular NMR, to be applied in
+structural genomics. Two main foci are novel algorithms for automated
+assignments, and algorithms for automated structure determination from
+solution-state protein NMR.
+
+\myhrule 
+\noindent \begin{tabular}{ll}
+DONALD, BRUCE R.&			ONGOING \\
+(PI: A. Anderson,     Co-investigator: B. Donald) & 2003-2008\\
+NIH (NIGMS \& NIAID) &
+R01 GM-067542   \\
+{\em Design of C.~parvum and T.~gondii DHFR-TS Inhibitors}\\
+\effortamount{\$150,000 {(total); Donald sub only: \$11,000.} & \\}
+\end{tabular}
+
+The major goal of this project is to design selective and potent
+inhibitors against the dihydrofolate reductase (DHFR) domain of
+dihydrofolate reductase-thymidylate synthase (DHFR-TS) from
+{\em Cryptosporidium hominis} and {\em Toxoplasma gondii.  }
+
+\myhrule 
+
+\subsection*{Completed Research Support}
+ 
+\myhrule
+\noindent
+\begin{tabular}{ll}
+DONALD, BRUCE R.	&		COMPLETED\\
+	(PI: Donald)	&	2003-2005 \\
+	NSF	& EIA-0305444\\
+{\em Algorithmic Challenges in Computational Biology}\\
+\effortamount{        \$37,500 &\\}
+\end{tabular}
+
+This grant supported computational research in functional genomics and
+computational methods in NMR structural biology.
+
+%\myhrule
+
+%\newpage
+
+\myhrule
+
+\noindent
+\begin{tabular}{ll}
+DONALD, BRUCE R.	&		COMPLETED\\
+	(co-PI: B.~Donald)	&	1998-2003 \\
+	NSF	& NSF 98-02068 \\
+\end{tabular}
+
+{\em Systems Science for Physical Geometric Algorithms}
+
+
+NSF research infrastructure grant. The major goals of this project
+were to provide research infrastructure for computational science and
+computational biology in the Computer Science Department.  This
+includes workstations, supercomputing facilities, networking, etc.
+
+\myhrule
+
+\newpage
+
+\myhrule
+
+\noindent
+\begin{tabular}{ll}
+DONALD, BRUCE R.	&		COMPLETED\\
+	(PI: Donald)	&	2001-2003 \\
+	NSF	& EIA-0102710\\
+\end{tabular}
+
+{\em Physical Geometric Algorithms and Systems for
+        High-Throughput NMR Structural Biology}
+
+  The major goals of this project were to
+develop novel computational methods for biomolecular NMR.
+
+\myhrule
+
+
+\noindent
+\begin{tabular}{ll}
+DONALD, BRUCE R.	&		COMPLETED\\
+	(PI: Donald)	&	2001-2003 \\
+	NSF	& EIA-0102712\\
+\end{tabular}
+
+{\em Physical Geometric Algorithms and Systems for
+        Structural Biology using Mass Spectrometry}
+
+The major goals of this project were to
+develop novel computational methods for structural mass
+spectrometry and proteomics.
+
+\myhrule
+
+\noindent
+\begin{tabular}{ll}
+DONALD, BRUCE R.	&		COMPLETED\\
+	(PI: Donald)	&	2000-2006 \\
+	DHS/ODP	& 2000-DT-CX-K001
+\end{tabular}
+
+{\em Microelectromechanical Systems for Infosecurity}
+
+
+The major goal of this project was the development of novel
+microelectromechanical systems ("MEMS") to be useful in micro- and
+nano-technology applications for homeland security, in particular,
+information security and micro robotics.
+
+\myhrule
+
+
+
+\subsection*{PENDING SUPPORT}
+
+
+\myhrule 
+\noindent \begin{tabular}{ll} DONALD, BRUCE R.& PENDING \\
+ (PI: D. Madden, Co-investigator: B. Donald) & 2007-2012\\
+Submitted to NIH (NIDDK) & R01 Application \\
+ {\em Keeping CFTR in its
+Place: An Integrated Small-Molecule Approach}\\
+\end{tabular}
+
+The major goal of this project is to develop an integrated
+experimental and theoretical approach to identifying small-molecule
+inhibitors selective for the CAL PDZ domain (a molecular scaffolding
+protein), which interacts with the cytoplasmic C-terminus of the
+cystic fibrosis transmembrane conductance regulator protein (CFTR).
+ 
+
+\myhrule 
+\noindent \begin{tabular}{ll} DONALD, BRUCE R.& PENDING \\
+ (PI: J. Hoch, Co-PIs: B. Donald, G. Wagner, A. Alexandrescu,
+ P. Bolton) & 2006-2008\\ 
+Submitted to NSF & MRI application \\
+{\em	Acquisition of a High Perfomance Computational
+Resource for NMR Structural Biology}.&\\
+\end{tabular}
+
+The major goal of this project is the acquisition of a supercomputer
+that will be attached to a high field NMR spectrometer in order to
+facilitate the development of data-directed high-throughput
+computational protocols for NMR data processing, automated assignment,
+and structure determination.
+
+\myhrule 
+
+\noindent \begin{tabular}{ll} DONALD, BRUCE R.& PENDING \\
+ (PI: B. Donald) & 2007-2012\\
+Submitted to NIH (NIGMS) & R01 Application \\
+ {\em Computational Active-Site Redesign and Binding Prediction via Molecular Ensembles}\\
+\end{tabular}
+
+The major goal of this project is to develop novel algorithms to plan
+structure-based site-directed mutations to a protein's active site in
+order to modify its function.  The new algorithms will make progress
+towards the long-term objective of reprogramming the specificity of
+non-ribosomal peptide synthetase domains, whose products include
+natural antibiotics, antifungals, antivirals, immunosuppressants, and
+antineoplastics.
+
+
+\myhrule 
+
+ 
+\end{document}
+
+%%% Local Variables:
+%%% write-file-hooks:   (time-stamp)
+%%% time-stamp-active:  t
+%%% time-stamp-start:   "\\\\def\\\\mydate{"
+%%% time-stamp-end:     "}"
+%%% time-stamp-line-limit: 20
+%%% End:
diff --git a/Master/texmf-dist/doc/latex/nih/example-nih-cls.pdf b/Master/texmf-dist/doc/latex/nih/example-nih-cls.pdf
new file mode 100644
index 00000000000..7e96b4778da
--- /dev/null
+++ b/Master/texmf-dist/doc/latex/nih/example-nih-cls.pdf
diff --git a/Master/texmf-dist/doc/latex/nih/example-nih-cls.tex b/Master/texmf-dist/doc/latex/nih/example-nih-cls.tex
new file mode 100644
index 00000000000..d17a4bb807a
--- /dev/null
+++ b/Master/texmf-dist/doc/latex/nih/example-nih-cls.tex
@@ -0,0 +1,243 @@
+% This example file for NIH submissions was originally written
+% by Bruce Donald (http://www.cs.duke.edu/brd/).
+% 
+% You may freely use, modify and/or distribute this file.
+% 
+\documentclass[11pt]{nih}
+%\documentclass{article}
+%\documentclass[12pt]{article}%
+% last revision:
+\def\mydate{2005-06-09 13:58:03 brd}
+
+
+%%%%%%% Two column control
+\newif\ifdotwocol
+\dotwocoltrue   % two col
+%\dotwocolfalse   % one col
+\long\def\twocol#1#2{\ifdotwocol{#1}\else{#2}\fi}
+%%%%%%%
+
+\def\mybeforeequation{\footnotesize}
+%\def\mybeforeequation{\small}
+%\def\mybeforeequation{}
+
+\def\myafterequation{\renewcommand\baselinestretch{1.1}}
+%\def\myafterequation{}
+
+%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%
+
+\def\citeusmark{$^{\textstyle \star}$}
+\def\citeus#1#2{\cite{#1}}
+
+\def\crow#1#2{#2}
+
+%\usepackage{denselists}
+%\usepackage{scaledfullpage}
+\usepackage[dvips]{graphicx}
+\usepackage{color}
+\usepackage{boxedminipage}
+\usepackage{amsfonts}
+\usepackage{amsmath}
+\usepackage{url}
+%\usepackage{times}
+%\usepackage{nih}		% PHS 398 Forms
+%\usepackage{nihblank}		% For printing on Blank PHS 398 Forms
+%\usepackage{confidential}
+
+\def\Paper{grant application}
+\def\paper{application}
+\def\refappendix{Sec.}
+
+\def\poster{(Poster)}
+
+%Note from brd
+\long\def\todo#1{{\bf{To do:}} #1}
+%\long\def\todo#1{}
+\def\ICRA{IEEE International Conference on Robotics and Automation (ICRA)}
+
+\long\def\squeezable#1{#1}
+
+%\def\a5{$\alpha_{_5}$
+
+\def\a5{5}
+
+%\def\mycaptionsize{\normalsize}
+%\def\mycaptionsize{\small}
+%\def\mycaptionsize{\small}
+\def\mycaptionsize{\footnotesize}
+\def\mycodesize{\footnotesize}
+\def\myeqnsize{\small}
+
+\def\sheading#1{{\bf #1:}\ }
+\def\sheading#1{\subsubsection{#1}}
+%\def\sheading#1{\bigskip {\bf #1.}}
+
+\def\ssheading#1{\noindent {\bf #1.}\ } 
+
+\newtheorem{hypothesis}{Hypothesis}
+\long\def\hyp#1{\begin{hypothesis} #1 \end{hypothesis}}
+
+\def\cbk#1{[{\em #1}]}
+
+\def\R{\mathbb{R}}
+\def\midv{\mathop{\,|\,}}
+\def\Fscr{\mathcal{F}}
+\def\Gscr{\mathcal{G}}
+\def\Sscr{\mathcal{S}}
+\def\set#1{{\{#1\}}}
+\def\edge{\!\rightarrow\!}
+\def\dedge{\!\leftrightarrow\!}
+\newcommand{\EOP}{\nolinebreak[1]~~~\hspace*{\fill} $\Box$\vspace*{\parskip}\vspace*{1ex}}
+%my way of doing starred references
+\newcommand{\mybibitem}[1]{\bibitem{#1} 
+\label{mybiblabel:#1}}
+\newcommand{\BC}{[}
+\newcommand{\EC}{]}
+\newcommand{\mycite}[1]{\ref{mybiblabel:#1}\nocite{#1}}
+\newcommand{\starcite}[1]{\ref{mybiblabel:#1}\citeusmark\nocite{#1}}
+
+
+\def\degree{$^\circ$}
+\def\R{\mathbb{R}}
+\def\Fscr{\mathcal{F}}
+\def\set#1{{\{#1\}}}
+\def\edge{\!\rightarrow\!}
+\def\dedge{\!\leftrightarrow\!}
+
+\long\def\gobble#1{}
+\def\Jigsaw{{\sc Jigsaw}}
+\def\ahelix{\ensuremath{\alpha}-helix}
+\def\ahelices{\ensuremath{\alpha}-helices}
+\def\ahelical{$\alpha$-helical}
+\def\bstrand{\ensuremath{\beta}-strand}
+\def\bstrands{\ensuremath{\beta}-strands}
+\def\bsheet{\ensuremath{\beta}-sheet}
+\def\bsheets{\ensuremath{\beta}-sheets}
+\def\hone{{\ensuremath{^1}\rm{H}}}
+\def\htwo{{$^{2}$H}}
+\def\cthir{{\ensuremath{^{13}}\rm{C}}}
+\def\nfif{{\ensuremath{^{15}}\rm{N}}}
+\def\hn{{\rm{H}\ensuremath{^\mathrm{N}}}}
+\def\hnone{{\textup{H}\ensuremath{^1_\mathrm{N}}}}
+\def\ca{{\rm{C}\ensuremath{^\alpha}}}
+\def\catwel{{\ensuremath{^{12}}\rm{C}\ensuremath{^\alpha}}}
+\def\ha{{\rm{H}\ensuremath{^\alpha}}}
+\def\cb{{\rm{C}\ensuremath{^\beta}}}
+\def\hb{{\rm{H}\ensuremath{^\beta}}}
+\def\hg{{\rm{H}\ensuremath{^\gamma}}}
+\def\dnn{{\ensuremath{d_{\mathrm{NN}}}}}
+\def\dan{{\ensuremath{d_{\alpha \mathrm{N}}}}}
+\def\jconst{{\ensuremath{^{3}\mathrm{J}_{\mathrm{H}^{\mathrm{N}}\mathrm{H}^{\alpha}}}} }
+\def\cbfb{{CBF-$\beta$}}
+
+\newtheorem{defn}{Definition}
+\newtheorem{claim}{Claim}
+
+    \gobble{
+    \psfrag{CO}[][]{\colorbox{white}{C}}
+    \psfrag{OO}[][]{\colorbox{white}{O}}
+    \psfrag{CA}[][]{\colorbox{white}{\ca}}
+    \psfrag{HA}[][]{\colorbox{white}{\ha}}
+    \psfrag{CB}[][]{\colorbox{white}{\cb}}
+    \psfrag{HB}[][]{\colorbox{white}{\hb}}
+    \psfrag{HN}[][]{\colorbox{white}{\hn}}
+    \psfrag{N15}[][]{\colorbox{white}{\nfif}}
+    \psfrag{dnn}[][]{\dnn}
+    \psfrag{dan}[][]{\dan}
+    \psfrag{phi}[][]{$\phi$}
+    }
+
+\newenvironment{closeenumerate}{\begin{list}{\arabic{enumi}.}{\topsep=0in\itemsep=0in\parsep=0in\usecounter{enumi}}}{\end{list}}
+\def\CR{\hspace{0pt}}           % ``invisible'' space for line break
+
+
+
+\newif\ifdbspacing
+%\dbspacingtrue  % For double spacing
+\dbspacingfalse  % For normal spacing
+
+\ifdbspacing
+ \doublespacing
+ \newcommand{\capspacing}{\doublespace\mycaptionsize}
+\else
+ \newcommand{\capspacing}{\mycaptionsize}
+\fi
+
+\def\rulefigure{\smallskip\hrule}
+
+% \def\codesize{\normalsize}
+\def\codesize{\small}
+
+% Can use macros \be, \ee, \en as shortcuts
+%  for \begin{enumerate}, \end{enumerate}, \item
+%  respectively.
+
+\def\be{\begin{enumerate}}   % Begin Enumerate
+\def\ee{\end{enumerate}}     % End Enumerate
+\def\en{\item}               % ENtry (item)
+\def\bi{\begin{itemize}}     % Begin Itemize
+\def\ei{\end{itemize}}       % End Itemize
+\def\bv{\begin{verbatim}}    % Begin Verbatim
+\def\ev{\end{verbatim}}      % End Verbatim
+
+\def\matlab{{\sc matlab} }
+\def\amber{{\sc amber} }
+\def\KS{{$K^*$}}
+\def\KSM{{K^*}} % K-Star Math
+\def\KSTM{{\tilde{K}^*}}  % K-Star Tilde Math (appx K*)
+\def\KOP{{$K^{\dagger}_{o}$}}  % K-Star Optimal partial
+\def\KOPM{{K^{\dagger}_{o}}}  % K-Star Optimal partial Math
+\def\KP{{$K^{\dagger}$}}  % K-Star partial
+\def\KPM{{K^{\dagger}}}  % K-Star partial Math
+\def\KTPM{{\tilde{K}^{\dagger}}}  % K-Star Tilde partial Math
+\def\KD{{$K_{_D}$}}
+\def\KA{{$K_{_A}$}}
+\def\qpM{{q_{_P}}}
+\def\qlM{{q_{_L}}}
+\def\qplM{{q_{_{PL}}}}
+\def\qSplM{{q^*_{_{PL}}}}
+\def\KSO{{$K^*_{o}$}} % K-Star Optimal
+\def\KSOM{{K^*_{o}}}  % K-Star Optimal Math
+\def\CBFB{{CBF-$\beta$}}   % Core binding factor beta
+\def\argmin{\mathop{\mathrm{argmin}}}
+\def\rhl#1{{\em \underline{RYAN}: *\{{#1}\}*}}
+\def\set#1{{\left\{ #1 \right\}}}
+\def\Escr{{\mathcal{E}}}
+\def\Jscr{{\mathcal{J}}}
+\def\Kscr{{\mathcal{K}}}
+\def\th{{$^{{\mathrm{th}}}$}}
+
+\newtheorem{proposition}{Proposition}
+\newtheorem{lemma}{Lemma}
+
+
+
+\begin{document}
+
+\bigskip
+
+\appendix 
+
+%\mydate
+
+\setcounter{page}{20} % or whatever
+
+%\noindent{\Large\bf Research Plan}
+
+\section{Specific Aims}
+
+\noindent Realization of novel molecular function requires the ability
+to alter molecular complex formation. Enzymatic function can be
+altered by changing enzyme-substrate interactions via modification of
+an enzyme's active site. A redesigned enzyme may either perform a
+novel reaction on its native substrates or its native reaction on
+novel substrates.  We propose a novel algorithm for protein redesign,
+which searches over possible active site mutations and combines a
+statistical mechanics-derived ensemble-based approach to computing the
+binding constant with the speed and completeness of a branch-and-bound
+pruning algorithm. We will develop an efficient$\ldots$
+
+\end{document}
+
+
diff --git a/Master/texmf-dist/tex/latex/nih/denselists.sty b/Master/texmf-dist/tex/latex/nih/denselists.sty
new file mode 100644
index 00000000000..d8188083d48
--- /dev/null
+++ b/Master/texmf-dist/tex/latex/nih/denselists.sty
@@ -0,0 +1,18 @@
+% These definitions for minimizing list spacing come from Michel Goossens,
+% as put together by Bruce Donald (http://www.cs.duke.edu/brd/).
+% 
+% You may freely use, modify and/or distribute this file.
+% 
+% Prevent infinite loops
+\typeout{Style New lists - dense lists}
+
+\let\Otemize =\itemize
+\let\Onumerate =\enumerate
+\let\Oescription =\description
+% Zero the vertical spacing parameters
+\def\Nospacing{\itemsep=0pt\topsep=0pt\partopsep=0pt\parskip=0pt\parsep=0pt}
+% Redefine the environments in terms of the original values
+\newenvironment{Itemize}{\Otemize\Nospacing}{\endlist}
+\newenvironment{Enumerate}{\Onumerate\Nospacing}{\endlist}
+\newenvironment{Description}{\Oescription\Nospacing}{\endlist}
+
diff --git a/Master/texmf-dist/tex/latex/nih/nih.cls b/Master/texmf-dist/tex/latex/nih/nih.cls
new file mode 100644
index 00000000000..835118db2a5
--- /dev/null
+++ b/Master/texmf-dist/tex/latex/nih/nih.cls
@@ -0,0 +1,136 @@
+% vim:tabstop=4 expandtab syntax=tex:
+%
+% nih.cls - class for preparing NIH (US National Institutes of Health)
+% grant applications.
+% 
+% Copyright (C) 2003, 2004, 2005, 2006 Bruce Donald.
+% 
+% This work may be distributed and/or modified under the
+% conditions of the LaTeX Project Public License, either version 1.3c
+% 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 1.3 or later is part of all distributions of LaTeX
+% version 2003/12/01 or later.
+%
+% This work has the LPPL maintenance status "author-maintained".
+% 
+% The Current Maintainer of this work is Bruce Donald
+% (http://www.cs.duke.edu/brd/).
+%
+% This work consists of only this one file, nih.cls.
+% Accompanying example files are not under the LPPL.
+%
+% last changed by Bruce Donald in 2005
+% to mimic the two PHS forms.
+%
+% Previous modified by Alan Shields, May 2003
+% email: Alan-Shields2omrf.ouhsc.edu
+% Heavily based upon (read: copied almost exactly from)
+%    nih.sty by Bruce R. Donald and Matthew L. Fidler
+%
+\NeedsTeXFormat{LaTeX2e}
+%\ProvidesClass{nih}[2005 NIH PHS 398 as of June 2005]
+\ProvidesClass{nih}[2005/06/01 NIH PHS 398 as of June 2005]
+
+% includes needed for preliminary code
+\RequirePackage{ifthen}
+
+% Preliminary code
+\newcommand{\nih@kk}{~}
+
+\newboolean{nih@blank}
+\setboolean{nih@blank}{false}% not strictly necessary, but let's be clear about it
+
+% Options
+%%%% Changed by M A Lewis, Ph.D. (mal11 at alumni.cwru.edu)
+%%%% NIH suggests Helvetica or Arial 12pt. Use Helvetica Postscript fonts for 12pt also.
+\DeclareOption{12pt}{\AtEndOfClass{\RequirePackage{helvet}\renewcommand{\familydefault}{\sfdefault}}}
+%\DeclareOption{12pt}{\AtEndOfClass{\RequirePackage{times}}}
+%\DeclareOption{12pt}{\AtEndOfClass{\RequirePackage{arial}}}
+\DeclareOption{11pt}{\AtEndOfClass{\RequirePackage{helvet}\renewcommand{\familydefault}{\sfdefault}}}
+\DeclareOption{nihblank}{\setboolean{nih@blank}{true}}
+\DeclareOption{kk}{\renewcommand{\nih@kk}{\small KK}}
+\DeclareOption*{\PassOptionsToClass{\CurrentOption}{article}}
+\ProcessOptions\relax
+
+% The class we're overwriting
+\LoadClassWithOptions{article}
+
+
+% Begin Requirements
+%%%% Changed by M A Lewis, Ph.D. (mal11 at alumni.cwru.edu)
+%%%% PHS 398 allows 0.5in magins everywhere. Simplify page layout using geometry package.
+%\RequirePackage{fullpage}
+\RequirePackage[letterpaper,margin=0.5in,includeheadfoot]{geometry}
+\RequirePackage{fancyhdr}
+\RequirePackage{amsmath}
+
+
+
+%%%% More code
+% preamble stuff
+\newcommand{\nih@PIname}{Donald, Bruce R.}
+\newcommand{\piname}[1]{\renewcommand{\nih@PIname}{#1}}
+
+% constants
+\newcommand{\nih@sillysize}{\scriptsize}
+
+% set the page style
+\pagestyle{fancy}
+\chead{\fancyplain{}{%
+        \ifthenelse{\boolean{nih@blank}}%
+            {}% fi
+            {%
+                {{\sf\scriptsize Principal Investigator/Program Director%
+                    (Last, First, Middle):}}%
+            }% esle
+    }
+}
+\rhead{\fancyplain{}{%
+        \ifthenelse{\boolean{nih@blank}}%
+            {\ \ \ {\nih@PIname}\ \ \ \ \ }% fi
+            {%
+                \underline{\ \ \ {\nih@PIname}\ \ \ \ \ }%
+            }% esle
+    }
+}
+\lhead{\fancyplain{}{\nih@kk}}
+\lfoot{\fancyplain{}{%
+        \ifthenelse{\boolean{nih@blank}}%
+            {}% fi
+            {\sf\footnotesize PHS 398/2590 (Rev.~09/04)\\}% esle
+    }
+}
+\cfoot{\ifthenelse{\boolean{nih@blank}}%
+        {\thepage}% fi
+        {\sf\footnotesize{Page}}% esle
+    \ \underline{\ \ \ {\sf\thepage}\ \ \ }%
+}
+\rfoot{\fancyplain{}%
+    {\sf\footnotesize{\textbf{Continuation Format Page}}}%
+}
+
+\renewcommand{\headrulewidth}{0pt}
+\renewcommand{\footrulewidth}{0.75pt}
+
+%%%% Changed by M A Lewis, Ph.D. (mal11 at alumni.cwru.edu)
+%%%% Simplify page layout by using geometry package above.
+% page dimensions (note: assumes 8.5x11)
+%\setlength{\oddsidemargin}{31pt}
+%\setlength{\textwidth}{8.5in}
+%\addtolength{\textheight}{0in} % 0.5in margins on both sides
+%\addtolength{\textwidth}{-1.1in}
+%\setlength{\oddsidemargin}{-1in}
+%\addtolength{\oddsidemargin}{0.505in}
+%\setlength{\evensidemargin}{\oddsidemargin}
+%\addtolength{\textheight}{0.2in}
+%\addtolength{\topmargin}{-0.2in}
+%\renewcommand{\baselinestretch}{.9}
+%\headwidth=\textwidth
+
+\addtolength{\headheight}{2.5pt}
+
+% rename the bibliography section
+\AtBeginDocument{\renewcommand{\refname}{Literature~Cited}}
+%FIXME: something is going on with the bibliography style. Dunno what.
diff --git a/Master/texmf-dist/tpm/nih.tpm b/Master/texmf-dist/tpm/nih.tpm
new file mode 100644
index 00000000000..8212f679ff2
--- /dev/null
+++ b/Master/texmf-dist/tpm/nih.tpm
@@ -0,0 +1,29 @@
+<!DOCTYPE rdf:RDF SYSTEM "../../support/tpm.dtd">
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:TPM="http://texlive.dante.de/">
+  <rdf:Description about="http://texlive.dante.de/texlive/Package/nih.zip">
+    <TPM:Name>nih</TPM:Name>
+    <TPM:Type>Package</TPM:Type>
+    <TPM:Date>2006/09/29 13:55:00</TPM:Date>
+    <TPM:Version></TPM:Version>
+    <TPM:Creator>karl</TPM:Creator>
+    <TPM:Title>The nih package.</TPM:Title>
+    <TPM:Description></TPM:Description>
+    <TPM:Author></TPM:Author>
+    <TPM:Size>67287</TPM:Size>
+    <TPM:Build/>
+    <TPM:RunFiles size="6197">
+texmf-dist/tex/latex/nih/denselists.sty
+texmf-dist/tex/latex/nih/nih.cls
+texmf-dist/tpm/nih.tpm
+    </TPM:RunFiles>
+    <TPM:DocFiles size="62124">
+texmf-dist/doc/latex/nih/README
+texmf-dist/doc/latex/nih/example-biosketch.pdf
+texmf-dist/doc/latex/nih/example-biosketch.tex
+texmf-dist/doc/latex/nih/example-nih-cls.pdf
+texmf-dist/doc/latex/nih/example-nih-cls.tex
+    </TPM:DocFiles>
+    <TPM:Provides>Package/nih</TPM:Provides>
+  </rdf:Description>
+</rdf:RDF>
+
diff --git a/Master/texmf/lists/nih b/Master/texmf/lists/nih
new file mode 100644
index 00000000000..25acc513e03
--- /dev/null
+++ b/Master/texmf/lists/nih
@@ -0,0 +1,11 @@
+texmf-dist/doc/latex/nih/README
+texmf-dist/doc/latex/nih/example-biosketch.pdf
+texmf-dist/doc/latex/nih/example-biosketch.tex
+texmf-dist/doc/latex/nih/example-nih-cls.pdf
+texmf-dist/doc/latex/nih/example-nih-cls.tex
+
+texmf-dist/tex/latex/nih/denselists.sty
+texmf-dist/tex/latex/nih/nih.cls
+texmf-dist/tpm/nih.tpm
+
+texmf/lists/nih
diff --git a/Master/texmf/tpm/collection-publishers.tpm b/Master/texmf/tpm/collection-publishers.tpm
index 57aa56e1ddb..49755884a94 100644
--- a/Master/texmf/tpm/collection-publishers.tpm
+++ b/Master/texmf/tpm/collection-publishers.tpm
@@ -42,6 +42,7 @@
       <TPM:Package name="mnras"/>
       <TPM:Package name="muthesis"/>
       <TPM:Package name="nature"/>
+      <TPM:Package name="nih"/>
       <TPM:Package name="nrc"/>
       <TPM:Package name="osa"/>
       <TPM:Package name="pracjourn"/>