pnaslatex

Unofficial LaTeX class and LyX layout files for PNAS article submissions.

Introduction

PNAS accepts LaTeX submissions and provides a LaTeX class and style file for this purpose. Unfortunately, it is very hard to use these to produce decent output, with features such as side captions and modern LaTeX features available through Xe-/Lua-LaTeX being unsupported. After quite a bit of hacking, James Manton in the lab gave up on trying to use them and re-engineered an alternative version from scratch to give a much more satisfactory output.

It is important to remember that these files are unofficial and include a few hacks to produce output that is similar to, but not exactly identical, to that produced by the official files. In fact, these files produce output that is closer in appearance to that of a final, PNAS-published article than either of the PNAS-provided LaTeX files or the PNAS online manuscript length checking service.

An example document, based on the official PNAS LaTeX example, is included in the examples directory, along with full LaTeX source. This has a number of advantages over the PNAS-provided example, such as Unicode suppport for both text and mathematics, the ability to use side captions for figures and tables, proper bibliography support (i.e. BibTeX, biblatex, etc. can be used instead of lists of \bibitems) and easier customisation.

These files were originally designed for, and successfully used in, the submission of the manuscript for:

Kohl J, et al. (2014) Ultrafast tissue staining with chemical tags. Proc Natl Acad Sci USA. doi: 10.1073/pnas.1411087111

If you use these files in a submission to PNAS I would appreciate an email to ajd.manton <at> googlemail <dot> com so I can maintain a rough idea of how useful these files are. If you try and use these files and instead resort to using the official PNAS files or submitting a Word document I would very much appreciate an email detailing why, so that I can try and improve the files/support.

Advantages over the official PNAS files

These include:

• Side captions for figures and tables, just like in actual PNAS articles

• Full support for Unicode, so you can write:

  \frac{\Dif{θ}}{\Dif{t}} = \frac{∂θ}{∂t} + u · ∇θ = 0
  

  rather than:

  \frac{\Dif{\theta}}{\Dif{t}} = \frac{\partial \theta}{\partial t} + u \cdot \nabla \theta = 0
  

• Sensible bibliography handling, via BibTeX, BibLaTeX, etc., such that instead of:

  \bibitem{BN}
      M.~Belkin and P.~Niyogi, {\em Using manifold structure for partially labelled classification}, Advances in NIPS, 15 (2003).
  \bibitem{BBG:EmbeddingRiemannianManifoldHeatKernel}
      P.~B\'erard, G.~Besson, and S.~Gallot, {\em Embedding {R}iemannian manifolds by their heat kernel}, Geom. and Fun. Anal., 4 (1994), pp.~374--398.
  

  you can just write:

  \bibliography{mybibfile}
  

  and use your favourite reference manager to organise the references, with BibLaTeX/BibTeX handling the formatting for you.

• Easy font configuration, with PNAS-like fonts used by default out-of-the-box without any need to specify Karl Berry names, etc. as with the official files

• Well-documented, simple code, in fewer than 200 lines (cf. > 3300 lines in the official class file)

LaTeX

A small number of common packages are required for full functionality:

• geometry – specifies paper size
• fontspec — specifies fonts
• titlesec – formats section headers
• lettrine — used for initial dropcap at start of article
• fancyhdr — specifies the headers and footers
• ifthen — ensures the right footer appears on the right pages
• lastpage — allows the footer to contain the total number of pages
• caption — handles table and figure captions
• sidecap — provides the ability to use side captions
• titling – used for article title
• ftnright — necessary for the Significance Statement and Publication Footnotes
• calc — ensures Significance Statement and Publication Footnotes use the right amount of space

By default, the Myriad Pro and TeX Gyre Termes font families are used for sans-serif and serif text, respectively.

LyX

The simplest approach is to put

• pnas.cls
• pnas.layout
• pnas2011.bst (optional, but recommended)

next to your LyX file. You can try this out with the example2.lyx LyX file kindly provided by @tommy-engels.

Installation

For regular use, it is recommended to install the LyX file, pnas.layout, copy it to the layouts folder of your user directory and then reconfigure LyX using Tools > Reconfigure. After restarting LyX, a new PNAS document class should be selectable.

Usage