Converting a scientific manuscript from LaTeX to MS Word

I like to write my manuscripts in LaTex — focus on the text and no worries about figure and table numbers, their formatting… have me sold. But sadly, not all journals accept LaTeX source files, some even require the us of MS Word. So, here is, what I have done to get a manuscript ready for submission on a Mac .

My manuscript contained

  • Tables (including “sidewaystable”)
  • Figures
  • Bibliography generated with natbib

I needed

  • MacTeX 2016
  • Preview
  • MS Word
  • SimpleTeX4ht

What I did

  • Copy/paste the manuscript in PDF format from Apple Preview into MS Word (looks surprisingly good). This makes sure to bring the references properly along
  • Clean up the text, replacing e.g., words breaking in the middle of the line (from the PDF line wraps); can be mostly done using find/replace
  • Reapply bold and italics text not carried over from copy/paste
  • Use SimpleTeX4ht to export an HTML file and copy/pasting the tables to the MS Word file, where it is reformatted properly. Not as tedious as it sounds.
  • Figures are copied/pasted from the PDF, but they need to be resized.

Open issues

  • Super- and sub-scripts are not properly copied over; they look fine in MS Word, but do not correspond to a true MS Work sub/superscript. Cannot be fixed using MS Word’s find/replace function either since it is a formatting issue. Needs to be changed manually (… or ask the copy editor nicely, if s/he could do it).

Here is to Reviewer 2!

In a recent manuscript, now under revision, Reviewer 2 suggested to provide more detail on the already published and cited reference method used — well here we go (again): Too detailed? I will be asked to shorten and be more concise; too concise? I will be asked to expand.

 Middle ground seems to be hard to find — or rather seems to be a function of how willing Reviewers are to look up cited literature. 
I’d rather go with short, sweet and properly cited — at least next time, when I will be Reviewer 2 ūüėČ

The Canadian Mercury Science Assessment is now published

The assessment provides current information about Hg emissions, transformation and environmental impact from a Canadian perspective.

I was the lead author of the “Emissions” chapter of the report and together with D. Niemi and Y. Fan-Li, I have summarized past, current and projected future emissions using Canadian and global data.

Find a summary here: http://www.ec.gc.ca/mercure-mercury/default.asp?lang=En&n=32909A5D-1

Talk at the MUSCLE Cluster Conference at Bishop’s University

I have attended and presented at the “Connecting Through Climate Change” meeting at Bishop’s University (where I also teach). I was asked to present results from my Arctic Research and very interesting discussions followed with researchers from the Universit√© de Sherbrooke and Bishop’s University.

What’s going on here…today…

Things have been busy in the last few months… and here is why.

Research-wise, I have continued the urban air quality data project, where I statistically analyse 10+ years of hourly pollution data from major Canadian Cities, mostly using Matlab. The modelling component of the project aims at understanding the underlying atmospheric reactions, especially the involvement of halogens. I employ the CAABA/MECCA box model for this task.

I am also finishing up my chemometric modelling work¬†for the MYCOSPEC project. I presented results at the Mycotoxin Summer Talks in Tulln, Austria last summer and at the 5th¬†MoniQA International Conference “Food and Health – Risks and Benefits” in Porto, Portugal last fall.

On the teaching side, I have been teaching Analytical Chemistry (lecture and lab) in the fall and currently Chromatography and the Atmosphere and Ocean lab are on my teaching schedule. Courses are going well and I really enjoy the interaction with students!

Working with netCDF data in Matlab

It took a bit of time, but here are some simple procedures to work with netCDF output that I get from my atmospheric chemistry model runs in Matlab.

Here is an example for pollutant concentrations obtained in .nc format from a CAABA/MECCA run:

% Read 4D-double data from .nc file for the following variables
time = ncread('caaba_mecca.nc','time');
o3_data = ncread('caaba_mecca.nc','O3');
oh_data = ncread('caaba_mecca.nc','OH');
no_data = ncread('caaba_mecca.nc','NO');
no2_data = ncread('caaba_mecca.nc','NO2');
ch4_data = ncread('caaba_mecca.nc','CH4');
co_data = ncread('caaba_mecca.nc','CO');

% Extract concentration data from 4D double matrix and write to new variable
o3_data2 = squeeze(o3_data(1,1,1,:));
oh_data2 = squeeze(oh_data(1,1,1,:));
no_data2 = squeeze(no_data(1,1,1,:));
no2_data2 = squeeze(no2_data(1,1,1,:));
ch4_data2 = squeeze(ch4_data(1,1,1,:));
co_data2 = squeeze(co_data(1,1,1,:));

Starting here you can resume regular Matlab code to work with the variables defined

Common elements, when importing pollution and meteorological data

Well, there is only one thing that the data have in common … they are available in csv format. But this is it.

Whether you download from providers such as Metro Vancouver, the City of Montreal, the Ontario Ministry of the Environment and Climate Change (OMECC) or Environment Canada — all of them set up their data tables in a different fashion; data from the OMECC are¬†formatted in an especially exotic fashion (hourly data columns!), whereas other providers basically stick to a date/time column(s), followed by data columns. Hourly data are the norm for Criteria Air Pollutants, but e.g., merging precipitation data, which is reported as cumulative daily value is more challenging.

So — first task is to cut away explanatory lines (if any — I’d rather have these; Environment Canada is pretty thorough here), harmonise data flags (I do this mostly in vim), find out what empty cells are (< LOD?, no data?, units used?… depends on the provider, so find and talk to the responsible person;¬†good luck!), arrange all data in the same fashion and finally merge it¬†into a common data table (in Matlab).

Bottom line: Open data is good, but open data formats and documentation not so much!

Focus on research for the summer

I have successfully completed my Winter term teaching. I taught two courses, the Atmosphere and Ocean Lab at McGill University and the Chromatography Lab at Bishop’s University. I also supervised an Honour’s student at Bishop’s University, who graduated at the beginning of June (Congratulations, Kaylee!).

Now it is time to focus on my research projects again. I continue collaborating on the Mycospec project, where I develop chemometric models from mid-infrared data in Matlab. With model development and validation complete for the current data sets — a bagged decision tree algorithm turned out to be the best choice, I provide support for software development, while waiting for new infrared data to come in.

I also started a new, exciting project, looking at air pollutant concentrations (especially ozone) in major Canadian cities in the last 10 years. After initial statistical analysis, I have started a modelling exercise using the CAABA/MECCA box model to better understand the mechanisms responsible for certain observed pollution scenarios. This is shaping up to be very interesting.

Chemistry Departmental Seminar Series at Bishop’s University

With the help of the other faculty members, I have initiated and administered the Chemistry Departmental Seminar Series at Bishop’s University during the last academic year. I have secured funding from the Speaker’s Committee for student lunches with the speaker prior to the seminar and to cover speaker’s expenses.

The seminar was primarily targeted at undergraduate students to provide them with information about current research, future employment and graduate studies. Speakers were faculty members, graduate students and professionals from various fields of chemistry in order to provide different perspectives about chemistry-related activities.

Here is the list of speakers.¬†We started off with 15–20 students and faculty in the audience during the fall term and had an audience of 25–30 during the winter term. The seminar programme was put together with suggestions from students and faculty members. Faculty took turns hosting the speaker and student lunches.

Winter 2015

  • √Čloic Colombo, CHUS, Medicinal Chemistry, New inhibitors of matriptase for treatment of influenza viruses
  • Kaylee Saunders, Bishop’s University, Department of Chemistry, Characterization and Comparison of Neat Alternative Fuels and their Corresponding Combustion Residues
  • Frederic-George Fontaine, Universit√© Laval, D√©partement de Chimie, Molecular Geopolitics
  • Ian Butler, McGill University, Department of Chemistry, An Overview of the Applications of Molecular Spectroscopy in Art Forensics: Infrared and Raman Spectroscopy

Fall 2014

  • Avik Ghoshdastidar, McGill University, Department of Chemsitry Pharmaceuticals, Pesticides, Mercury and First Year Students ‚ÄĒ Journeys of a Grad Student in Chemistry
  • Patrick Ayotte, Universit√© de Sherbrooke, D√©partement de Chimie, Life and death of a snowflake; Or how to read the global atmospheric archives in a carrot?
  • Daniel Fortin, Universit√© de Sherbrooke, D√©partement de Chimie, Understand the chemistry and physical properties with molecular and electronic structures. See inside the molecular world!

New article in press

An article that I co-authored (and edited; 500+ references!) is now published¬†— find it on the ACS Chemical Reviews webpage:

P.A. Ariya, M.¬†Amyot, A.¬†Dastoor, D.A.¬†Deeds, M.¬†Subir, A. Feinberg, G. Kos, A.¬†Poulain, A.¬†Ryjkov, K.¬†Semeniuk, K.¬†Toyota,¬†Mercury Physicochemical and Biogeochemical Transformation in the Atmosphere and at Atmospheric Interfaces: A Review,¬†Chemical Reviews¬†115 (2015)¬†3760‚Äď3802, 10.1021/cr500667e