Marilyn directed me to a brief paper on good writing. "... papers in the well-written category ... ... have a direct voice that enables the reader to quickly sort out what is being tested and why. Relevant literature is not just cited, but contextualized. At the end of the paper I have learned not just what the new data suggest but how that new information fits within the broader sweep of the field." Theresa Woodruff provides some valuable pointers to help give your writing impact. Check out the full text at https://academic.oup.com/endo/article/159/11/3657/5139758
Following on from my previous post, here is a time-saving suggestion for reshaping your data using recent versions of Excel, using unPivot.
Say you have data in a table like this (lets call this table 1):
and you want to convert to "long-format" like this:
This conversion could involve lots of cutting and pasting, dragging and dropping fill down .... etc., but most of the hard work can be done automatically if you have a recent version of Excel with the Power Query Editor.
From time to time I get asked to help with a statistical analysis. When I ask for the data I often get a spreadsheet like this. OK, I can read this and sometimes make sense of it, but there are a number of important issues including:
how much work is involved in laying out these tables? For example, calculating averages and SEM requires multiply entering the relevant functions for each column for each group, or a lot of cutting and pasting of formulae and double checking that it worked as expected.
is this format easy to import into a statistics program? The answer to this is clearly NO!
How easy is it to regroup the data, filter the data, graph the data? Not very easy at all!
With a little bit of learning, this can all be done so much easier. Here is a suggestion.
Recently published in the prestigious journal Nature Genetics is another marsupial genome, this time it is the iconic koala, a superb effort by a diverse team of specialists including Marilyn.
The paper was highlighted by a cover picture on the printed journal and a commentary by Darren J Burgess in the journal: Nat Rev Genet. 2018 Sep;19(9):533. doi: 10.1038/s41576-018-0039-5.
At least in the northern half of Australia, koala populations are ‘vulnerable’ due to habitat loss and widespread disease. The team sequenced the koala genome, producing a complete and contiguous marsupial reference genome, including centromeres, a notoriously difficult region. Among the discoveries is a proliferation of cytochrome P450 genes. These code for enzymes that can detoxify plant toxins, allowing them to survive on a harsh diet of eucalypt leaves.Koalas' ability to smell, taste and moderate ingestion of plant secondary metabolites may be due to expansions in the vomeronasal and taste receptors. The team identified novel milk proteins that protect young in the pouch and annotated immune genes important for response to chlamydial disease. Historical demography showed a substantial population crash coincident with the decline of Australian megafauna, while contemporary populations had biogeographic boundaries and increased inbreeding in populations affected by historic translocations. A key finding was identification of genetically diverse populations that require habitat corridors and instituting of translocation programs to aid the koala’s survival in the wild.
I recently came across http://phylopic.org/ which has a very useful library of animal silhouettes that may be useful when you are preparing phylogenetic tree diagrams and the like. I've added a tammar, since there wasn't one there, and there are lots of other nice silhouettes of all sorts of living things, indexed by taxonomy or with text search.
The images come in a range of sizes plus thumbnail 64 pixels square, For the tammar image I uploaded, the sizes range from 64x31 px up to the original 4444x2159 pixels. For many there are also SVG (scaled vector graphics) versions. This is a vector format that you can scale to whatever size you need without pixellation. Note that PowerPoint does not always play nicely with SVG, but there are many free apps that can scale and convert SVG to formats PowerPoint will work with. These include Inkscape, Libre Office. Adobe illustrator will also handle SVG if you have this (expensive) application on hand (and the extensive knowledge to use it).
For some species there are multiple images to chose from - eg Homo sapiens sapiens - here is a link to some of the silhouettes in a lineage tree of H sapiens that goes back to the beginning of life.
If you have created silhouettes that you want to share, it is simple on the PhyloPic site to add a new silhouette and place it in its correct taxonomic place.
PhylPic also has a programming interface so if you need, you may be able to grab the images programmatically if you have large jobs.
Here is the scenario. You have just spent ages constructing a beautiful multi panel figure with lettering and immuno or in situ micrographs. It all looks great the blue DAPI staining contrasts beautifully with the red target staining. Here is a sub panel of one recently prepared by Teruhito.
And then, horror, you discover the journal will only publish the figures in monochrome. The default option is to export the figure as, say, a high resolution TIFF file (at least 300 dpi), open the image in photoshop (or the free, open source alternative GIMP, but I will use photoshop as the example here), and change the mode to grayscale.
Here is the result. Alas, all those nice red highlights are grey, and look exactly like the converted blue bits. It is impossible to see which cells are stained positively and which are just bright blue DAPI staining. Blue and red are contrasting. Grey converted red is the same as grey converted blue.
But all is not lost. By using a more sophisticated approach to the conversion, you can mute the blue and bring up the red, as illustrated below.
We were delighted that the National Health and Medical Research Council has awarded us funding to continue our investigations into hypospadias over the next 3 years. Hypospadias, a failure of the correct formation of the penis, is the second-most common birth defect, occurring in around 1% of boys. It causes distress to both newborn and parents, requiring surgical intervention, and is a burden of cost and is a risk to the child. Furthermore, it is frequently associated with other abnormalities. We have a novel model in which we can induce penis abnormalities and define the link between hormonal exposures and defective penis differentiation.
Microsoft, in their wisdom, cripple PowerPoint's abilities to export slides to high resolution graphic files, and by default they compress images imported to a mere 220 pixels per inch or less. Here are a couple of tricks to improve things.
NOTE: more recent versions of Powerpoint might already be configured so that slides saved as jpg files are at high resolution (try it with your computer/software and see. My system converts an A4 sized slide to 8980 x 6349 pixels which is 768 pixels per inch, so plenty of resolution). However you still need to make sure that Powerpoint is not reducing the resolution of the images you put on the page (see below) or you will get a high resolution output of blurry / pixelated images.
Caveat: if you insert low resolution images into PowerPoint, you cannot increase the usable resolution by exporting to a higher resolution. You just get large pixelated files. If you insert high res files but let Powerpoint "compress" the images, you will reduce the resolution of the images and will lose detail that you cannot recover (see 1 below).
1. Tell PowerPoint not to automatically compress imported images.
Open PowerPoint.On the File menu choose Options. In the options dialog choose Advanced. In the right panel under Image Size and Quality select Do not compress images in file.
This setting will stay with the file, but you will need to reapply it for new files where you want the highest resolution in your images. There is probably a way to make this the default... stay tuned.
Also, don't use the "compress pictures" functionality unless you are happy with reduced resolution/quality of your images.
2. Change the export resolution for PowerPoint slides
This step involves editing the registry. The registry is a database maintained by the system of all the relevant settings that allow programs to work. If you muck up the registry, things might not work afterwards. If you are unsure, get expert assistance. That said, it isn't difficult if you follow the instructions here: https://support.microsoft.com/en-us/help/827745/how-to-change-the-export-resolution-of-a-powerpoint-slide [UPDATE 2018-04-17: this URL no longer works. Try https://answers.microsoft.com/en-us/office/forum/office_2013_release-powerpoint/how-to-change-the-powerpoint-export-resolution-of/786f5a11-2c31-4234-95a3-d28943fa2987 or look up how to edit the registry (a quick look on google should do it, or ask your local friendly windows guru). Locate HKEY_CURRENT_USER\Software\Microsoft\Office\15.0\PowerPoint\Options. Add or edit DWORD ValueExportBitmapResolution. Set this to the desired resolution. Note that whatever resolution is set in registry, older versions of Powerpoint will not export files with more than 3072 pixels on the longest side. On my new installation of office 365 they seem to have fixed this bug so it exports at the specified resolution.
Since this change is done in the registry, it will be in operation whenever you use PowerPoint from then on. Note that if you upgrade to a new powerpoint, the registry change may not be copied to the new version (It seems to have carried through with my recent upgrade to office 365) so you may need to repeat the process after each version upgrade.
Note that no matter how high you set the resolution in the registry PowerPoint will not export slides as image files with sides greater than 3072 pixels - that is usually enough, but may not be for some applications [UPDATE 2018-04-17: note that the current office365 has fixed this - see above]. The next section has an approach that gets around this limitation.
3. Alternative -- export by printing to a PDF file
This is less convenient but does not need changes in the registry. Print the slide (or slides) using a PDF writer. WIth Adobe's PDF writer you can set a high resolution (the default is to compress large images to 150 ppi). In the print dialog with Adobe PDF selected choose Properties
In the Document properties dialog, choose a setting with high dpi settings such as Press quality:
Or you can edit one of the other settings and change the images compression properties to whatever resolution you want.
If you don't have adobe PDF writer, there are lots of alternative free programs such as Foxit PDF, Bulllzip PDF or CutePDF Writer which can give high quality PDF output, allowing you to configure the graphics resolution settings to your needs.
Once you have the slide(s) saved as a PDF file containing embedded high resolution images you can save them as image files from Acrobat (paid version) or open them using programs such as (expensive) Adobe photoshop or Adobe Illustrator, or (free, open source programs) GIMP (sim to photoshop) or Inkscape (sim to Illustrator), from where you can export to whatever graphic file format you require.
