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Posts Tagged ‘Literature review’

My first paper

January 30, 2012 2 comments

Back in June, I had submitted my first paper for publication. It was a literature review which forms the basis of my thesis, and seeing as I was still in the beginning of my PhD and had time to perfect it etc, I decided to aim high, and submitted to the top journal in my area. I knew that it would be hard to achieve, especially since reviews are commonly written by experienced academics, rather than a lowly PhD student, and many other students in my group had found it quite difficult to get theirs published. But Oh well, to the enthusiasm of a new student. We submitted and from day to day I waited for a reject email to come back.

Alas months passed by and no response was received from the journal. Then the day I went home for Christmas (i.e. 6 months after first submission), my supervisor emailed me saying she received a communication saying I got a major revision for the paper. I was quite disheartened, but after seeing the comments I got and talking to my sister, said that if they did not reject it outright they must think I have something right. So over Christmas, I spent time working on the changes requested, discussed them when I went back to Dublin 3 weeks later and submitted just before the deadline of 4 weeks.

Then just a few minutes ago I received an email from my supervisor, saying that the paper has now been accepted, and we now need to await the schedule for publication etc. I cannot believe how happy this has made me feel and I am glad that I aimed high. So this is my advice to anyone who is in the beginning of their PhD, from the first day start writing up something. From the first week I started, when my supervisor told me to ‘read papers about the area’, I starting putting together a document. It mainly consisted of copy and paste parts or summaries of the different articles, pasted in an incoherent manner under a couple of broad topics. I also started my referencing from the start, using RefWorks, as it is what is available on campus here. Once I had read a number of papers, I organised the copy and paste parts into more coherent sections and rewrote them into paragraphs. But since I already had a number of pages of quotes it was quite easy to achieve. Suddenly, I had a literature review of the different areas I was investigating. I collated the different sections and beefed up some areas and made the document flow.

A couple of drafts later, and it was ready for submission. My advice at this point, especially if you are still towards the start of your PhD, is to aim high. It is better to aim high, get rejected and submit to a slightly lower journal. And you keep getting comments that way which improves your manuscript and writing. Getting the major revisions just before Christmas is quite disheartening, but it is so worth it now.

Good luck with your writing 🙂

Getting back into the swing of things

After my Easter holiday, I was finding it quite hard to get back to work, so that last week I mainly did paper work and no experimental work as such. I did not feel as productive, but I did manage to finish all the documentation (reports, poster, plans) for next week’s ATWARM meeting in Germany.

On a positive note, I had a meeting with the supervisor who had not yet seen my literature review last Wednesday, and he seemed pleased with the way it looks. He suggested some further changes which I also finalised last week and I resent it to him as requested and am now awaiting further comments. Hopefully he approves with the changes so that I could resend it to all the supervisors and can get the ball rolling.

Last week I also got the new HPLC column I ordered just before going on holiday. I will get to working on the HPLC tomorrow to see how this works out using the previous conditions. In theory they are identical columns, just that this one is new and therefore should be ‘better’. But I am learning to expect the unexpected, so will wait and see.

Hopefully this week is more productive, and I get some actual lab work done, since I will be away most of next week for the meeting in Germany.

Research Progresses

April 19, 2011 2 comments

After the ENVIRON conference I got back into my HPLC method development and literature review work. Regarding my literature review my supervisors and I have decided on a target journal for submission, and I have looked at the guide for authors and formatted my document to their requirements e.g. reference style, sections etc. At least Refworks, which I use as a reference manager, had the journal style inputted, and it corresponded to the journal’s requirements, and therefore it was easy enough to achieve. I have now sent my review to a supervisor who has not yet seen it and had requested to see it after I carry out the changes of the three supervisors who had seen the previous draft.

HPLC method development has also progressed well. I have now separated 10 of the analytes (out of 11), with good peak separation and got a good calibration curve. For two of the analytes (i.e. analytes 10 and 11) no peak separation occurs. However they absorb at different wavelengths and therefore I can use wavelength separation for them. Unfortunately the HPLC I am currently using doesn’t have a DAD. However the LC-MS detector has a DAD and therefore I could save time from having to do all analyses twice. I have discussed the HPLC method with one of my supervisors who knows the area most, and he gave me some suggestions re some ghost peaks (small peaks coming out even in the blank), and I will try them out in the coming weeks. Once that is finished, I hope that the LC-MS would have been fixed and I can get onto it (it has been broken down since before the 10th March, so we will see).

Today I am off for an Easter trip around Ireland with the rest of the family who are visiting from all over Europe. I can’t wait to get a break and be back and work!

Some progress is made

Finally, we managed to get the HPLC up and running again (basically I managed to convince the technician to change the tubing to a different type), so I had my first run yesterday, which kept going till this morning. The results are still not totally there, but the R squared values are all higher than 0.9, and those that are low are due to known reasons. So that is a good thing. I should be getting back on the equipment next week for at least 2 days, so that is something to look forward to, and hopefully I can get some good results and progress to the next stage.

Today I also received the last of the comments from my supervisors about my literature review (received from 3 out of 5, which is the most I can expect at the moment: one is out on long-term sick leave and the other said he will see the next draft, which is better after all, because I would not have to join all comments together). That is on the agenda for next week too. Overall the comments were quite manageable. They should not involve too much work, and hopefully I can get through them in a week or so, since most involve removing certain sections, or particular quick to do word changes etc.

However, the supervisors suggested that I look at publishing my literature review, which is what is worrying me the most. They have asked me to suggest journals in which to publish my literature review, and I have no idea where to start looking. I have never published papers before in any journal, so I am at a bit of a loss. They talked about impact factors for the journals, and they said it should not be too low, but I do not want to aim too high. I also know that it is difficult to get literature reviews published, unless it is invited (which this certainly is not). We’ll see how things go.

More HPLC Woes

My HPLC woes continue. I have finally gotten onto the HPLC to do some work, but have not been getting any peaks whatsoever.  I tried a couple of different approaches, but to no avail. Being sick over the past few days certainly does not do anything to help me think or to boost my morale. After carrying out a couple of runs this morning, I decided to take the rest of the day off and have a good rest. I turned over the HPLC to the next person who needs to use it, and hopefully can get access to it, and some work done tomorrow.

On a positive note, I managed to finish my second draft of my literature review yesterday and sent it to all my supervisors for comments and advice. I had sent the first draft to just one supervisor, and had gotten some constructive comments on how to improve it. I will await comments on this draft hopefully in the coming weeks.

Lab Meeting

On Thursday I managed to squeeze in a lab meeting with two of my supervisors on Thursday between the two lab demonstration sessions. Rather than a lab meeting where all of us are present, it was an individual meeting where only myself, the two supervisors (the other is away sick) and the lab post-doc was present. I had not had such a lab meeting in more than a month, so it is good to give a presentation on progress.

First up for discussion was the literature review. One of the supervisors had seen it and all that I had done was work on the changes she suggested. However the other knew that I was working on it, but not on the progress. The changes are by no means completely done, but hopefully I can polish it up somewhat in the coming weeks. I am pleased that there were not many changes suggested by my supervisor, though there are a couple of areas I feel I need to improve.

I then discussed my method development. I have now nearly determined the method for the first few analytes. On Thursday, after the meeting I also received the next few analytes, so what I am doing today is trying to include them in the same method, to reduce sample preparation and analysis time. It was good to present some actual findings in the meeting, and got some good suggestions from one of my supervisors, who is a chemist and knows a whole lot about everything.

As with all of my meetings, it was a short and sweet meeting. I hope I manage to have some good results for the next meeting, whenever that will be. Hopefully I will have nearly finalized my HPLC method, so I can go on to SPE and LC-MS method development. I have some analysis currently running, so hopefully by the end of the weekend I will know a bit better about how much more work is needed. Wish me luck 🙂

Lab Meeting…lost count of the week

January 13, 2011 1 comment

Today was the day of our next lab meeting. It was the first after the Christmas Holidays and as such we had to prepare a short summary of what we had accomplished to date and the way forward for the coming three months. So…what is the plan forward? Well, I hope that in the next couple of months HPLC method development will be largely complete, my literature review will be polished and hopefully have a trial test for another aspect I might be adding to my project.

The supervisors seemed quite pleased with my progress. I hope I manage to accomplish these 3 aspects in these 3 months, and if I will I would certainly be quite pleased with myself. This would allow me to move into LC-MS and SPE development and therefore to move forward in my research quite well. So what do I hope to achieve in the immediate weeks that are coming? I hope to have a first draft of my literature review, an HPLC method which somewhat works (if I manage to get a good blank run it would be perfect at the moment) and have the sites for the preliminary test identified.

I am mostly worried about the site selection for sample collection. I have limited knowledge about Irish environments. If it were Malta it would be quite easy to pinpoint sites. However here it is a whole different kettle of fish. However my supervisors gave me some suggestions of people who they will contact and hopefully could be helpful to me. So we will see how that goes.

Wish me luck 🙂