Danuta Liberda-Matyja, a chemist at the SOLARIS National Synchrotron Radiation Center, sheds light on her research using synchrotron radiation. In an interview with Coopernicus, she talks about her discoveries in the lab, the prospects for their application and her plans for the future.
Although she did not plan to pursue a career in science, Danuta Liberda-Matyja, is currently working on innovative projects at the SOLARIS National Synchrotron Radiation Center. Laughing, she admits that in high school she was an average student, able to devote herself only to those subjects that really interested her. She completed her bachelor’s degree in environmental protection at Jagiellonian University, after which she returned to her native Silesia. There, at the University of Silesia, she completed a master’s degree in data analysis in chemistry (known as chemometrics). When she was looking for a job after graduation, she came across an offer from the Institute of Nuclear Physics in Krakow. It was the HOMING project led by Dr. Tomasz Wróbel on histopathological classification of pancreatic tissues, using machine learning. Currently, she is working on accelerating cancer diagnostics in tissues, using infrared radiation, as part of subsequent grants. This topic is also closely related to her dissertation submitted to the Jagiellonian University where she studied in the Biomedical Sciences program. “The standard approach is that a biopsy is taken, which is then stained. Later, a histopathologist evaluates this tissue for cancerous changes. This process takes a long time, several weeks or even a month. And the World Health Organization predicts that the number of cancer patients will continue to increase,” Liberda-Matyja explains.
That’s why there is a need for a method that would speed up diagnosis. Faster diagnosis, she notes, also means an accelerated time frame for starting treatment. Liberda-Matyja’s findings are a promising step in that direction. The tests involve taking a sample of unstained tissue, which is illuminated with infrared radiation under a microscope.
“Depending on the biochemical composition, part of this radiation is selectively absorbed by the sample, the light that is not absorbed follows to the array detector. In our research, we obtain information about the sample in the form of so-called spectra and tissue images”
The data acquired in this way, is used to train machine learning models. Algorithms such as random forest or neural networks are used. The result of this method is a computer stained image of the tissue. In such an image, it is possible to distinguish, for example, between healthy and cancerous tissue – each is stained in a different color. Such a stained slice, in the future, could provide great support for histopathologists in evaluating difficult cases, she argues. Liberda-Matyja adds that a second method is also being developed:
This is rapid screening, during which a computer recognizes whether a patient has cancer or not. Introducing this approach into the clinic would allow histopathologists to focus on evaluating cancer cases. In addition to this research, she is also participating in Dr. Tomasz Wróbel’s SONATA project, on the orientation of macromolecules in tissues.
“In the case of cancer, for instance in breast tissues, the fibers that make up the microenvironment of cancer organize themselves in different ways. The organization of these fibers can affect the progression of the disease as well as the penetration of the drug to the pathologically altered site”
Internship abroad
One of the methods she uses in her research, based on neural networks, Liberda-Matyja learned during a month-long internship in Germany. The trip was inspired by research conducted under a Preludium grant she received. The goal of the grant, she says, was to build a breast cancer detection model that is robust.
“A model built based on samples from a few patients will not work well on the entire population. Acquiring a large number of samples from hundreds or even thousands of patients and then measuring them with infrared radiation is a time-consuming process, so it is difficult to obtain material to train the model. Particularly in the case of breast tissue, it is an additional challenge to obtain samples from healthy patients, due to the highly developed diagnostics in the steps preceding biopsy collection”
Just how time consuming the process is can be shown by Liberda-Matyja’s research to date. The research team in which she works took as long as five years to study pancreatic tissue. During that time, they measured 600 biopsies, from 250 patients.
“In the Preludium grant, my goal was to create simulated samples, spectra of breast tissue. I saw great potential in using neural networks for this purpose. In Germany, at the University of Bochum, there is a bioinformatics group that is applying neural networks to tissue classification,”
This internship was her first research trip abroad to develop her own research project. Despite the initial stress, she quickly found her feet and managed to analyze all the data she brought. She adds that it was a very fruitful time. She also didn’t notice much difference between the way research was conducted in Germany and Poland. Although she says this may be related to the scale of SOLARIS research where she works. It is one of the leading research units and the only one of its kind in Central and Eastern Europe. “You can’t say that we are lagging behind our neighbors. During the internship, it was a true exchange of information: I also introduced something from myself, showing how we analyze our data with an emphasis on pre-processing.”
Working at SOLARIS
The SOLARIS National Synchrotron Radiation Center, is a unique research unit.
The hall itself is impressive:
“It houses a huge concrete ring (accumulation ring), with a circumference of as much as 96 meters. Inside it are located 12 sections of huge blocks of electromagnets, which help accelerate the electrons in the ring and maintain their path of motion along the orbit. When the electrons’ motion path is curved, synchrotron radiation can be acquired,”
She adds that such radiation has a very wide range, from X-rays to infrared. At SOLARIS, infrastructure can be built in each of the 10 sections to extract radiation with a different range of energy or parameters, which is made available for so-called research lines where measurements are made. At the moment at SOLARIS there are 7 test lines made available to users and 3 more are under construction.
“This makes it possible to test a variety of samples using this radiation,”
For example, the CIRI (Chemical Infrared Imaging) line on which Liberda-Matyja works examines biomaterials, among other things, thanks to the non-destructive nature of the radiation. But there are also lines that deal with studying materials such as photovoltaic panels, for example.
“Interestingly, the synchrotron is open to scientists from all over the world. People can come to us and do their research free of charge, they just have to apply for research time,”
Such a research line design is a big challenge. The infrared beam obtained must be introduced to the microscopes on which the scientists conduct their research, Liberda-Matyja says. She notes that there are few such infrastructures in the world, and the research being conducted at SOLARIS is truly inspiring. “The daily life of the linemen at the synchrotron is very interesting, scientists come to us with different samples. And so one day we can measure, for example, parrot feathers, and the next day works of art or cosmetics. You never know what research challenge will surprise you the next day,” Liberda-Matyja says. She adds that this daily interaction with something new makes her work very interesting and provides more and more challenges.
Scholarship from the Foundation for Polish Science
Liberda-Matyja encountered scientific challenges not only in her work, but also during her PhD.
“We as scientists apply for grants and research money all the time. A person encounters various setbacks over the years. During the doctorate there comes a moment of just being overwhelmed, in my case it was after two years. Things don’t always work out, sometimes you have to take a few steps back and do something again.”
However, when she was awarded the START Grant, given by the Foundation for Polish Science, she felt that what she was doing was appreciated by the academic community.
“Being awarded this grant was a big reward for me. It also encouraged me to continue what I was doing and gave me a break from this bleak everyday life of what I was struggling with in my daily work.”
The START scholarship is also a resource she greatly appreciates and plans to use for trips abroad or a postdoc.
Future prospects
Currently, Liberda-Matyja and the team she works for are nearing completion of the construction of the entire CIRI research line at SOLARIS. This will be the culmination of a four-year project. During this summer, the installation of the research line is planned, and in the fall the opening of the resulting infrastructure with access for researchers, she announces.
“This is something I am very much looking forward to.”
Liberda-Matyja also wants to go on another foreign internship and postdoc. She says she wants to gain experience in another research group and further develop her career.
“There are a lot of opportunities for development at the synchrotron, but it’s a challenge that’s fun to face,”
She is also fascinated by technological developments based on the synchrotron, which often provide unique measurement capabilities.
Purpose-driven career
In addition to conducting innovative research, Liberda-Matyja is also involved in a number of initiatives that popularize science and help others who are on a similar path. She says that despite the fact that it’s sometimes difficult when conducting research and attending conferences, it’s worth getting involved in the additional activities. She emphasizes the role of consciously building one’s resume.
“For example, evaluating funding applications submitted by doctoral students is an activity benefiting the academic community and one that also allows you to learn a lot. It is also a valuable experience that we can include in our resume,”
During her Ph.D. studies, she was a representative of doctoral students, and currently leads tours at SOLARIS. Both students and pupils take part in them.
“If there is no event we can get involved in, we can try to come up with something ourselves, share an original idea. Often this is noticed and the response is positive,”
she concludes, adding that the trips for PhD students in the School of Natural Sciences were her initiative.
Another venture she enjoys participating in is the annual Malopolska Night of Scientists, where various experiments are prepared during the event. Liberda-Matyja says it is inspiring to interact with people, of almost any age.
“You can see the engagement, especially for children it’s something that they will remember and that can interest them. And maybe even pull them towards science.”
Fot. Unsplash
