This project is progressing well since the last blog post. The experimental work should be finished in a few months. I hope to publish two papers on the work that has already been done and two more on the remaining lab work. I have 11 months of funding remaining for this project, and it looks like I should be finished within that time frame.

Experimental work update

As mentioned in the last blog post, this stage of the research is to finish testing the materials. With the UV curing and settling experiments finished and data analysed, the next experiment to complete is the microbiology work.

The first method that was trialled to test the anti-microbial properties of the additives was loading the powder onto filter paper disks and testing bacterial growth on an agar plate. This method showed that only one additive was killing bacteria, so a second method was trialled to check if the same result was produced.

The method I am testing at the moment is a microtiter well plate method. This test is automated to measure the cloudiness of the growth medium hourly over two days. The cloudier the medium, the more bacteria in that well. Since I am using powders in the medium, the liquid is already cloudy before the bacteria starts to grow so it is nearly impossible to detect any growth. I will keep trying with lower concentrations of powder, but I may have to look at other test methods. An example of such could be testing whether the bacteria are alive after being in contact with the cured anti-microbial resins, rather than testing the additive on its own.

Thesis in three

Earlier in the month I entered a competition called ‘thesis in three’. The goal of this competition is to describe your thesis to a non-specialist audience in three minutes using three slides. The slides transition automatically so timing is crucial.

I usually do quite well in presentations but this time I chose to learn a script word for word. I had plenty of practice in the days leading up to the heat of the competition. On the day, I lost my place for a few seconds. I recovered and finished what I had to say but it threw off my timing and I went over time slightly. I did not get through but was happy with the judges’ feedback and have some pointers to work on for any similar presentations in the future.

Conferences

I hope to apply for two conferences over the summer – one material-related one and one 3D printing one. It is great to see these events going back to normal with in-person conferences and meet-ups allowed to resume. If I have learnt anything from the thesis in three competition, I will practice key points relating to the message I want to get across rather than learning any text word for word.

This week I have been drafting a poster for the HRI Research Day as part of University of Limerick’s Research Week 2022. Making presentations is a skill that I have developed since starting the PhD. As I am doing the PhD with the school of design, there is always emphasis to do a very clear poster with a visual poster rather than walls of text.

Supervision

This semester I have been supervising a Masters student in the lab. Their research goal is to create a radiopaque spine phantom for patient-specific surgical training.

This is my first opportunity to supervise a student and it is a task I am enjoying. This semester we have been meeting three times a week. I am managing my time well and it is not negatively affecting my own tasks.

Research update

My main research update from this year is that the experiments as part of my PhD have started. This year I have been focusing on the material selection aspect of my work.

To recap, the material aspect of my project can be broken into three stages: additive identification, material selection and material characterization. First, 17 additives were selected which were either metal oxides or metal nanoparticles. The material selection stage of the research involves assessing additives based on their performance and deciding which one performed best overall. The criteria that the additives will be tested under included UV curing, settling and antimicrobial properties.

The UV curing experiments were carried out in February and the data has been analysed. The settling experiments are finished with the analysis in progress and the microbiological tests are also in progress. Once there is a single additive chosen, this will be 3D printed and characterized by mechanical testing and further antimicrobial testing – to make sure that 3D printed parts can kill bacteria.

Design of experiments

One of the most difficult aspects of my PhD journey so far has been planning and designing experiments. Even though it is interesting, it took a long time to get right. Similar to the literature review blog post, the first step is to check if any other published work has been done on a similar topic. For the material selection stage of this project, I am using adapted methods found in literature for my experiments. Each experiment needed to be modified slightly for this project. An important aspect while conducting a research project is being able to justify the methods being used when defending the work.

Undertaking these PhD experiments has been my first time having to think about how best to test anything. During school, my undergraduate degree and Master’s degree, the test methods were always given in advance, for practicality. Because of this, the last three years have involved a huge amount of learning and trying to think in a way I never had to before. It is crucial to design an experiment so that you are measuring exactly what you are trying to measure, since unaccounted for factors can affect the results.

Setbacks with experiments

There have been setbacks with the material selection experiments, some of which are due to poor planning.

A few times experiments have been postponed because essential materials or supplies had not been delivered on time. This is not so bad as there is always other work to be done, such as drafting literature reviews or making literature summaries for future papers.

There were issues encountered while setting up the settling tests. For this experiment, I was taking time-lapse images every hour as the powder settled out of suspension. The main issue was that the light sources I was using as a back light were curing the resin. This resulted in the final experiment using a red LED light source and in a dark box since the ambient lab lighting was even curing the resin. This set back added a few weeks to the experiment overall.

It is important to be able to deal with and overcome these setbacks as part of the PhD process, and learn to not take issues with an experiment personally. This is something that I am still learning to do.

A literature review is a summary of the state of the art literature for a given topic. This involves finding and searching through a range of academic papers that relate to the topic. The key points are taken from each and inform a well-written narrative which usually serves as an introduction or background to give context to a written document. At this stage of my project, I will only discuss my methods for organizing the information taken from papers, and the writing process will be discussed in a later post.

For the past few weeks, I have been reading literature that relates to my PhD and making summaries of any interesting points from academic papers. I have been doing this task on and off for the past three years and I will likely be adding to my literature review document until I am nearly finished my PhD thesis.

Up until now, I have completed two formal literature reviews: one as part of my undergraduate final year project and one as part of my Master’s thesis. The following is what I have learned from conducting previous literature searches:

• Focus is crucial to nailing a literature review
• Summarise your findings
• Document anything that is interesting (or could be relevant)

For me, it is extremely important to be able to focus when reading a paper. Looking for a particular piece of information such as a specific method that was used, makes it easy to efficiently extract information from a paper. I like to do my literature reviews with an empty schedule so that I can get through as many papers as possible while remaining focused on the topic.

Usually, reading any paper front to back is a waste of time. It is much more time efficient to take notes of the relevant sections. So far, I have been adding to my literature review document in sections – which allows me to focus and skim through parts of relevant papers without reading them all in full. Reading without taking notes means that the information may be forgotten when it is the time to write. Well-documented notes are crucial for referencing the correct source of your information.

My advice to any students commencing a literature review would be to first ask why and how you are going to do this search, before ever opening a new search tab.

Firstly, why are you doing this literature search?

• Primarily, to check that the work you are about to do has not already been done – this could save you from doing experiments in some cases. You may also want to follow existing methods rather than re-inventing the wheel
• To find the niche where your work fits into the existing research. You are more than likely building on the research of others, it is important to check what has been done and where your work fits among the existing work.
• To get familiar with the writing style of the journal you are submitting to.
• Improving your own writing style

Secondly, how are you going to do this literature search? For me, the most efficient literature review method is as follows:

1. Decide what area of the literature you are researching
2. Collect papers from a quick systematic search
3. Set up an excel sheet with different headings of information that you will be interested in
4. Go through the papers and take out information from each
5. Record the information

I use a single excel document with a different spreadsheet for each topic of the project. I like to give each paper its own row within the relevant spreadsheet. I summarise anything that could be used for when I am writing. I highlight the cells with key papers so I know to come back to these when I am eventually writing. In the past, I used to read papers and write summary paragraphs but these paragraphs never made it to the final written draft. It makes more sense to summarise everything now so that I can easily catch up on the topics and write with a better flow when I am drafting the thesis. My PhD Literature review spreadsheet has the following topics: 3D printing with UV curable composites, cystic fibrosis, feeding tubes, general microbiology, Gram positive bacteria, and metal oxides. These topics should fit nicely to give a comprehensive background to my project when it is time to write.

This blog post describes my method and motive for doing literature reviews and my recommendations for any students that were starting a literature search for the first time. Like anything else, it is a case of trial and error to find what works best.

Working on campus

In my last blog post, I gave an update on the realities of working from home. I am glad to be able to say that I have been working on campus again for the past few weeks, but life has definitely not returned to normal.

Every morning I must sign in at the Main Building then walk across a tunnel to the Foundation Building where my desk and lab are. Our office has moved downstairs temporarily so that all staff that are back to work are on the same level (the basement). We must walk back to the main building to use the toilets as the toilets in our building are closed. Our building is basically closed apart from a few members of our research group. Every evening we have to fill out a contact tracing form, listing anybody we have been in contact with for 15 minutes or more within a distance of 2m. There is also a one-way system in place and plenty of hand sanitisers as in most buildings at the moment. UL students are due to return at the end of September which will change our current set up. Hopefully the Foundation Building will be opened and toilets back up and running.

I really have missed the lab over the past few months and I am delighted to be back. The social aspect is another advantage of being physically ‘back to work’. I am delighted to have a regular routine back. I tried my best to continue working Monday to Friday, 9am to 5pm while working from home but this was rarely the case. I often felt guilty for not getting enough done during the day, due to all the distractions at home, and ended up working later than 5pm and a few hours over the weekend. I am glad to get out of this habit now that I am physically back at work.

PhD update

At the time of writing my previous blog, I had just submitted an abstract for a 3D printing conference. I was accepted to talk at this conference and presented remotely in July. This was my first time presenting at a conference. I was happy with my presentation but disappointed that there were no comments or feedback from the others that had tuned in. As the topics I am working on are all medical-based it might be best to stick to 3D printing in medicine conferences only in future as I believe people attending these conferences would have more interest in my work.

Before returning to work, I completed the paper that I had been working on during the summer months. This paper was submitted to a journal but unfortunately it was rejected (I received the rejection email this morning). There was less scientific data in this paper than the first one we submitted and this was the primary reason for rejection. This paper is a material selection paper on how we chose the additive for radiopaque 3D printing. This is the second paper submitted as part of my PhD, the first paper was accepted for publication but has not yet been published.

The next step in my research is choosing a single additive for antimicrobial 3D printing. I have now narrowed down the search to 10-20 additives based on a list of criteria. I am currently working on a lab work plan for the PhD and mapping out what experiments need to be done. Each round of testing should eliminate additives so that we are left with the best candidate for antimicrobial 3D printing. I reckon that I will have approximately one year of lab work, a few months of clinical work (this is highly dependent on the covid-19 situation in 12 months time), and a year to write up subsequent papers and my thesis.

During the first research project (radiopaque 3D printing) I made lots of mistakes, which is probably fair for the first project that I have led myself. The biggest mistake was not taking good enough notes and not documenting some experimental conditions. This meant that a lot of work had to be repeated, wasting time and materials. I have learnt from what went wrong with the first project and I am writing short reports for each experiment with a method section to avoid any repetition at a later stage. This will hopefully make writing papers and my thesis easier when the time comes.

Overall, I am definitely excited to be back to work and I am quite happy with the research plan for the remainder of the PhD. I reckon that I am well on track to finish within the four years (currently half way through year 2).

I am now officially into the second year of my PhD. For the first year of my project I had been keeping my to-do list on my computer and deleting tasks as they were completed. This method had me feeling that I was not achieving much and forgetting what I had accomplished in the previous weeks, and therefore feeling that I was not getting enough done. Last week I got a diary for planning work. Each evening I have been making a to-do list for the following day, ticking each task off as they are completed. The main reason for getting a diary was to have the satisfaction of ticking a task as being complete rather than just deleting it. I now feel more satisfied that I am achieving my goals each week. 

On a completely different note, yesterday all UL staff and students received an email to say the campus would be closing due to the COVID-19 virus. To start with, the campus is closed from now until the 29^th March (10 working days), however, it seems that the university could be closed for a number of weeks.  

How will COVID-19 affect my PhD work?  

For the next month I was not planning lab work or clinical work, so the main difference is that I will be doing my planned ‘desk work’ from home rather than on campus. I always prefer to work on campus as I enjoy the routine of getting up, going to work, doing all my work there and getting to relax when I come home in the evenings. I am usually more productive on campus, but I will have to learn to keep my usual routine while working remotely.  

One of my main research goals for this year is to conduct a clinical study on feeding tubes, as the problem needs to be fully identified before thinking of a solution. This work will be delayed if this situation continues for more than a few weeks, which is looking likely. In the meantime, I am still working on the ethics application. Ethics applications can take months to get approved so the sooner we can submit this the better, even if the actual clinical work will be delayed.  

Another difference is that I won’t see any of my work colleagues face-to-face for a few months. Any meetings will be over the phone or skype, which I don’t think will be as productive as face-to-face meetings, but we will make do for this short-term restriction.  

This semester I am taking two modules (microbiology & immunology and academic writing) and teaching tutorials for one module (industrial organisation). Lectures will be delivered online for all three and I will be doing voice recordings of my tutorials from home. The lab work for microbiology & immunology looks like it will need to be cancelled/postponed. At this stage, lecturers are trying to come up with alternatives for the end of semester exam in the possibility that we will still not be allowed on campus by May. The only advantage I am seeing to teaching from home is that I now only have to deliver my tutorials once, rather than five times a week. This will hopefully give me some more time for my own work. 

Most of this blog is about how I reckon the next month to six weeks will work out for me. I will do a follow up blog about what working from home was actually like, and whether I was able to keep to my regular routine during this time.  

In October I submitted my first paper to a 3D printing journal. This is the first paper in which I was able to plan experiments, carry these experiments out and write about my findings. I had previously been involved with a paper as part of my masters project, but I did very little work on my own for this. I was constantly under supervision in the lab due to UL’s rules in relation to taught masters students. This time I was working as a PhD student and was allowed to work independently. If/when this paper gets published I will summarise the results in a blog post of its own. As it is still not guaranteed to be published I cannot go into the specific details yet.

At the start of January we received an email from the editor of the journal to say that major revisions were required for the paper before they could consider it for publication. We were invited to make changes as suggested by their reviewers and re-submit our manuscript. Most of the requests were asking for more data to support what we were saying. And in most cases, these images/graphs already existed and just needed to be dug out and cleaned up before being added to the paper.

The deadline for returning the revised paper was last week and this was definitely one of my busiest week since starting the PhD. My ordinary work schedule is usually from 9am to 4-6pm, depending on my work load that day. I usually don’t do any more work in the evenings or weekends unless I have a presentation or an important deadline. However, the last two weeks have been hectic trying to get the paper finished on time. I worked all of last weekend which was the first weekend that I have worked since starting the PhD (last March). I also worked longer hours during the week to get the paper finished. Even though last week was a tough week, it is satisfying to finally send off the updated and definitely improved paper. Hopefully it will be accepted!

I have definitely noticed that a lot of the corrections from my supervisors are relating to how I am phrasing sentences rather than the content of that sentence. Apart from a handful of lab reports, the undergraduate final year project and the masters project, I have not done any other scientific writing. I have decided to take an academic writing module this semester as I feel that I need practice in this area. I have already missed two weeks of this but the lecturer has allowed me to register anyway and catch up with material in my own time.

This module only has one compulsory hour per week, along with two online lectures. In addition to this, I am taking a module called ‘Immunology & Microbiology’ and I am teaching tutorials for a third module. Even though I am involved with three modules this semester, I have been very lucky with my timetable. All three are on Tuesday to Thursday only. This leaves me Monday and Friday to do any clinical work at the hospital when it comes to it. I hope to complete an ethics application this semester and begin the clinical side of the CF work as soon as this gets accepted.

Science week this year was in the middle of November and UL’s Research Week was the first week of December. I have been quite busy so I am only getting to finish the November/December blog now.

Science Week 2019

As part of science week 2019 I spoke to a local sixth class about 3D printing and also got involved with the SOPHia project (indirectly).

I spoke to the primary school class about 3D printing in general. I had prepared a short presentation (mainly cartoons, images and time-lapses) with the intention of talking for 10 minutes and then having a 10 minute class discussion. I was pleasantly surprised that the class grasped the concept of 3D printing very quickly and were blown away by the models I brought to pass around. The students had plenty of intelligent questions and the class discussion went on for 40 minutes.

The SOPHia project student science competition final also took place during science week. A school group that I had visited in September had been shortlisted for the SOPHia project final in UL. This involved doing a physics project and presenting the project in a poster which was then judged by researchers from the UL physics department. The girls did a project on the uptake of physics among students in their school and highlighted that less girls were taking physics despite girls being as interested in the subject as boys. They also included my visit in their poster as I was brought in as a female role model to promote physics. I was genuinely delighted that the girls ended up winning as they had put so much time and effort into this project!

NCRC Annual Research Symposium 2019

In December I attended the NCRC Annual Research Symposium. The NCRC (National Children’s Research Centre, based in Crumlin) is the organisation that part-funding my research. I did a poster presentation which was my first time presenting my PhD research. The posters were judged by a researcher and a lay person at the same time so it had to have a balance between technical and non-technical language to convey the main objective and goals of the project. There were prizes at the end of the day but I did not win any. The projects currently funded by the NCRC are all so diverse and so interesting. After I had been judged I walked around to look at the range of projects.

Research Week @ UL

This year was UL’s second research week. I was definitely less involved in this year’s research week compared to the previous year. Last year I attended talks and workshops as part of the research week. However, this year I was too busy with my postgraduate progression. Usually this is done by filling a form with all the courses taken, papers published and accomplishments in the previous 12 months. A committee then decides if you have done enough to progress to the next year of research. However, this year has been the first year of including a presentation as well as the standard form. The week of the progression presentation was the same week as the NCRC research symposium. I was very busy preparing for both presentations.

I presented first out of the five PhD students in my department. I was very happy with my presentation and received an email the following week to say that I had progressed into the next year of my research!

I have mentioned in previous blogs that I have been writing my first paper. I am glad to finally announce that I have finished writing and my paper has been submitted to the journal ‘3D Printing and Additive Manufacturing’. We are not expecting to hear back from them for a while. It has been 2 weeks since the paper was submitted and we have not heard anything back which means it probably has not been rejected (most papers get rejected in the first 10 days if they are going to get rejected).

Now that this paper is finished, I can really focus on my PhD topic. The paper was not entirely separate from my funded research, as I was still getting to know the 3D printer, as well as the 3D printing material. It was sort of like a training exercise. I have also now got a taste of what it is like to be involved in writing a journal article. This paper took much longer than I thought it would, but it was my first and I now understand how to better approach writing for next time. I will write a blog post on this paper when it gets published and go into greater detail of the paper content and my main findings.

As part of my PhD, I will be developing a 3D printable antimicrobial material in order to create devices to alleviate some complications associated with PEG feeding tubes for children with Cystic Fibrosis. There are multiple parts to this project, including Cystic Fibrosis, 3D printing, PEG feeding tube complications, material science and microbiology. All of these components are completely different to one another.

In college I studied physics and material science, so the materials portion is the part that I am most prepared for. I have spent a year and a half working with the 3D printer that will be used for my PhD project. I am now confident 3D printing and hacking the 3D printer, although by no means an expert. I have attended 3D printing conferences, and have been reading literature on how 3D printers are currently being used in hospitals. The areas that I feel that I need to brush up on most are Cystic Fibrosis, PEG tubes and microbiology. I am currently taking a microbiology module which will hopefully give me an insight to design an experiment to test antimicrobial properties of the material that will be developed. I have been reading about Cystic Fibrosis and PEG tubes, and chose this topic for an assignment as part of my summer school modules, since I knew it was the area that I was least knowledgeable in.

This week I spoke to my microbiology lecturer about my project and he gave me a list of people around the University that would be good to talk to in relation to testing the material against particular microbes. It looks like I will be able to use some lab space on campus to test antimicrobial properties of the material. This will speed up the testing of the material, as doing these tests off campus could take up a lot more time. When I complete this module I should have the skills required to work independently and grow bacteria myself for testing.

Next week I am meeting a doctor in the local hospital, along with my supervisors. The aim of this meeting is to hopefully allow me to spend a week or more in the Cystic Fibrosis unit to get to know the local CF team and eventually spend time studying what the real-life PEG tube complications are. This will give me a better insight into the issues associated with PEG tubes in order to design devices to alleviate these issues. It is already known that scar tissue and infection at the site where the tube enters the body are issues, but maybe there are other problems that do not appear in the literature. This should form the basis for the devices I design to alleviate some of the PEG tube related problems.

As it stands, everything is running smoothly and the project seems to be coming together nicely. However, this is research and just because everything is going well now does not mean that I won’t encounter a road block in a month’s time.