Our ESRs Mohammed A. Abo Arab and Safi Ur Rehman Qamar respond to our questions regarding their experience as students of the DECODE project.
1. What motivated you to join the DECODE project?
Safi: I was motivated to join the DECODE project because of its innovative approach and interdisciplinary nature, which aligns perfectly with my research interests in bioengineering and biotechnology. The opportunity to work on cutting-edge projects involving nanoparticles and nanotherapeutics, while collaborating with experts from various fields, is incredibly appealing. Additionally, the DECODE project's focus on real-world applications and societal impact resonates with my career goals of contributing to significant advancements in science and technology.
Mohammed: My motivation to join the DECODE project stems from a profound interest in the intersection of biomedical engineering and advanced computational technologies. With a background in software engineering, electrical communications engineering, and AI complemented by a master’s thesis on a novel registration technique for medical applications, I was drawn to the innovative goals of the DECODE project.
The opportunity to work on developing a cloud platform utilizing Drug-Coated Balloons (DCBs) for Peripheral Artery Disease (PAD) treatment particularly intrigued me. This project aligns perfectly with my passion for image analysis, 3D visualization, and the integration of augmented reality and computational simulations in medical technology. In addition, the chance to contribute to cutting-edge research that can significantly impact patient care and outcomes is incredibly fulfilling.
Furthermore, DECODE's collaborative environment, which brings together experts from various fields and institutions, provides a unique platform for professional growth and knowledge exchange. Engaging with this diverse and dynamic community allows me to expand my expertise, stay abreast of the latest trends and methodologies, and contribute meaningfully to advancements in biomedical engineering. This holistic approach to research and development is what ultimately motivated me to join the DECODE project.
2. Could you describe your specific research focus within the DECODE project and the objectives you aim to achieve?
Safi: Within the DECODE project, my specific research focus is on the development and application of nanoparticle-based systems for therapeutic purposes to treat atherosclerosis. My objectives include understanding the biosynthesis mechanisms of nanoparticles using plant extracts and exploring their potential in making nanoparticles incorporated nanofibers for drug coated balloons. By achieving these objectives, I aim to contribute to the development of innovative and effective therapeutic solutions that can have a substantial impact on healthcare in cardiovascular and biomedical engineering.
Mohammed: My specific research focus within the DECODE project centers on the development and optimization of the DECODE Cloud Platform, which is designed to enhance the treatment of PAD using DCBs. My work involves integrating various advanced technologies to create a comprehensive and user-friendly platform for researchers, clinicians, and medical professionals.
I am primarily involved in cloud-based platform development, where my objective is to establish a robust cloud infrastructure that supports seamless data processing, storage, and accessibility. Utilizing Django for backend development, RESTful APIs for data communication, and React.js for the frontend, we ensure a scalable and secure platform capable of handling the complex requirements of PAD treatment simulations.
Another key area is the development of advanced 3D visualization tools to provide detailed representations of PAD and the effects of DCB treatments. By integrating WebGL for low computational cost visualization and augmented reality for interactive and immersive experiences, we help users better understand the spatial dynamics and effectiveness of treatments.
Additionally, I work on enhancing the analysis of medical images through web-based Progressive Web Applications (PWAs). We implement tools for image data processing, including filtering, volume rendering, segmentation, and measurement, which improve accessibility and functionality across different devices, making it easier for clinicians to analyze and utilize imaging data.
Finally, I focus on creating a comprehensive data repository that integrates clinical data, imaging data, and treatment outcomes. We develop modules for data collection, storage, and real-time processing, enabling continuous updates and quality control. This facilitates data-driven decision-making and research, enhancing the overall effectiveness of the DECODE project.
3. What are the main challenges you have encountered (or anticipate to encounter) in your research?
Safi: One of the main challenges I anticipated in my research is the complexity of nanoparticle biosynthesis and ensuring their stability and efficacy in therapeutic applications. Additionally, understanding the intricate interactions between nanoparticles and biological systems can be quite challenging. There are also logistical challenges related to interdisciplinary collaboration and integrating diverse methodologies into a cohesive research framework.
Mohammed: In my research within the DECODE project, several significant challenges have arisen, and I anticipate encountering more as the project progresses. These challenges span technical, logistical, and collaborative aspects, each requiring careful consideration and innovative solutions.
One primary challenge is collecting high-quality, comprehensive medical data for PAD, which is critical for accurate simulations, visualizations, and treatment optimizations. Handling this sensitive medical data necessitates stringent data privacy and security measures to protect patient information.
Another major challenge is integrating cutting-edge technologies like 3D visualization, augmented reality, and computational simulations into a cohesive platform. This integration presents significant technical difficulties that require innovative solutions to ensure seamless functionality.
Collaboration and communication are also challenging aspects of the DECODE project. The project involves working with researchers, clinicians, and medical professionals from diverse fields and geographical locations, necessitating effective coordination and communication strategies.
Additionally, validating the simulations and visualizations against real-world clinical outcomes is crucial to ensure their accuracy and reliability. This process involves rigorous validation and clinical trials to confirm the effectiveness of the developed technologies.
4. Collaboration is a key aspect of the DECODE project. How has your collaboration with other ESRs and project partners affected your work within the project?
Safi: Collaboration with other Early-Stage Researchers (ESRs) and project partners from POLIMI, Italy and University of Montpellier, France has been immensely beneficial to my work within the DECODE project. It has provided me with access to a wealth of knowledge and expertise from different fields, which has enhanced the quality and scope of my research, especially understanding nanoparticle incorporation into nanofibers. Through collaborative efforts, we have been able to tackle complex problems more effectively and innovate more rapidly. These interactions have also fostered a supportive research environment where ideas are freely exchanged and refined.
Mohammed: I have been greatly influenced by the saying, “Alone we can do so little; together we can do so much.” — Helen Keller. Collaboration is indeed a cornerstone of the DECODE project, profoundly influencing my work and progress. Working closely with other ESRs and project partners has not only enriched my research but also significantly advanced the overall objectives of the DECODE project.
One of my primary collaborations is with the ESRs based in Athens, who have been instrumental in providing the necessary datasets for the DECODE Cloud Platform. This collaboration has ensured access to high-quality, comprehensive data, which is critical for developing accurate simulations and visualizations. Their expertise in data collection and initial processing has streamlined my work, allowing me to focus on integrating and analyzing this data within the platform.
Another vital collaboration is with the ESRs at MedApp in Krakow, Poland. Together, we have worked on integrating different modules such as segmentation and centerline extraction into the DECODE Cloud Platform. Their specialized knowledge and technical skills have been crucial in ensuring that these modules function seamlessly within the platform, enhancing its overall capabilities and performance.
My secondment at AGH University in Krakow marked a significant milestone in my research. During this period, I collaborated intensively with the team at MedApp and AGH University on the 3D volume rendering and WebGL visualization aspects of the project. This hands-on experience and direct interaction with experts in these fields accelerated my understanding and implementation of advanced visualization techniques. The collaborative environment fostered innovative solutions and provided valuable feedback that refined my work.
Being part of a network of 15 researchers has exposed me to a diverse range of expertise and perspectives. Regular meetings, workshops, and collaborative sessions have facilitated the exchange of ideas and best practices. This interdisciplinary approach has not only broadened my knowledge base but also inspired new research directions and methodologies that I might not have considered independently.
The collaborative efforts within the DECODE project have significantly impacted my work by providing essential datasets and technical resources, facilitating the integration of complex modules and technologies, offering diverse insights and feedback that enhance the quality and applicability of my research, and accelerating the development process through shared knowledge and collective problem-solving.
5. Given the interdisciplinary nature of the DECODE project, how have you incorporated components from different disciplines into your research?
Safi: The interdisciplinary nature of the DECODE project has enabled me to incorporate various components from different disciplines into my research. For example, I have integrated principles from cell biology, chemistry, and biomedical engineering to develop and optimize nanoparticle-based therapeutic systems. This holistic approach has allowed me to address research questions from multiple perspectives, leading to more robust and comprehensive findings.
Mohammed: Inspired by the principle “Great things are done by a series of small things brought together.” — Vincent Van Gogh, the DECODE project inherently requires an interdisciplinary approach, combining elements from biomedical engineering, computer science, data analysis, and clinical medicine. Here’s how I have integrated these diverse components into my work:
In the realm of biomedical engineering, I have collaborated with biomedical engineers to ensure accurate simulation of Drug-Coated Balloons (DCBs) and their efficacy for PAD treatment. Incorporating clinical data from PAD patients into these simulations and visualizations ensures they reflect real-world scenarios, enhancing their relevance and accuracy.
From the perspective of computer science and engineering, I have utilized advanced computing techniques to develop a scalable and secure cloud platform, employing backend frameworks like Django and RESTful APIs, along with frontend technologies such as React.js. In addition, I have created detailed and interactive visual representations of arterial structures and DCB interactions using computer graphics and WebGL technology.
In data science and machine learning, my collaboration with data scientists has been crucial in developing and optimizing machine learning algorithms for image processing and segmentation. I have also implemented computational modeling techniques such as the Finite Element Method (FEM) and agent-based modeling to predict PAD treatment outcomes, furthering the predictive capabilities of the DECODE platform.
The development of tools for processing and visualizing DICOM images has been a significant aspect of my work in medical imaging and visualization. These tools, which incorporate techniques like volume rendering, filtering, and measurement, facilitate better diagnosis and treatment planning.
Clinical collaboration and validation have been essential to ensure the practical applicability of my research. I have worked closely with clinicians to refine simulations and visualizations to meet healthcare needs and conducted clinical trials to validate the accuracy and effectiveness of the DECODE platform, aiming to translate research into real-world clinical benefits.
Participating in interdisciplinary training and workshops organized by DECODE partners has broadened my understanding and facilitated the effective integration of different components into my research. These sessions have provided valuable insights and fostered a collaborative environment, essential for the success of the DECODE project.
6. How do you plan to make the most of the training and support you are receiving as an ESR in the DECODE project?
Safi: As an ESR in the DECODE project, I plan to make the most of the training and support by actively engaging in workshops, seminars, and collaborative projects. I will also seek mentorship and guidance from experienced researchers to enhance my skills and knowledge. Additionally, I will leverage the resources and networking opportunities provided by the project to establish strong professional connections and further my research career.
Mohammed: As an ESR in the DECODE project, I plan to maximize the training and support received by leveraging multidisciplinary training, actively engaging in collaborative activities, and applying the skills gained to advance my research. To achieve this, I will take several key actions:
First, I will leverage multidisciplinary training to deepen my expertise in scientific and technological areas, while also enhancing complementary skills such as project management and communication. This dual focus will enable me to become more effective in both my technical work and in coordinating with my peers and stakeholders.
Second, I will actively engage in collaborative activities, building a strong professional network with peers and experts. This engagement will facilitate the integration of interdisciplinary knowledge into the DECODE Cloud Platform, ensuring that the platform benefits from a broad spectrum of insights and innovations.
Third, I will apply the training to research and development by implementing advanced techniques and continuously optimizing the platform. Utilizing feedback from collaborators and end-users will be crucial for continuous improvement and ensuring that the platform meets the highest standards of efficacy and usability.
By fully engaging with the DECODE project's opportunities, I aim to enhance my research capabilities, contribute significantly to the project's goals, and prepare for future challenges in the field of biomedical engineering.
7. Can you share any results or insights from your research so far, and how do they contribute to the overall objectives of the DECODE project?
Safi: So far, my research has yielded promising results in the biosynthesis of nanoparticles using plant extracts and their application in targeting cancer cells and atherosclerosis. These findings contribute to the overall objectives of the DECODE project by providing a foundation for developing new therapeutic strategies that are both effective and environmentally sustainable. The insights gained from my research also help to advance our understanding of the interaction between nanoparticles and biological systems, which is crucial for their safe and effective use in medicine.
Mohammed: First, the development of the DECODE Cloud Platform architecture has been completed, including the design of its workflow. This design incorporates a multi-layer hierarchical framework that integrates various modules such as data collection, image processing, computational modeling, and visualization tools.
Additionally, advanced visualization techniques have been integrated into the platform. By incorporating WebGL-based 3D visualization, augmented reality (AR), and virtual reality (VR), the platform enables detailed, real-time interaction with 3D models of arterial structures and DCB behavior.
Furthermore, the DECODE platform has been optimized as a Progressive Web Application (PWA), achieving high scores in performance (91%), accessibility (90%), best practices (83%), and SEO (100%), as assessed by Google's Lighthouse tool.
The platform also features advanced data processing and computational modeling capabilities. It includes sophisticated modules for image processing, segmentation, and 3D reconstruction, which facilitate detailed and accurate analysis of medical images. Additionally, techniques such as the Finite Element Method (FEM) and agent-based modeling have been integrated to simulate and predict the behavior and efficacy of DCB treatments.
8. What are your long-term aspirations beyond the project and how has your participation in the DECODE project influenced them?
Safi: My long-term aspirations beyond the DECODE project include continuing my research in bioengineering and contributing to the development of innovative medical technologies. The experience and knowledge gained through my participation in the DECODE project have significantly influenced my career trajectory by equipping me with advanced research skills and a strong professional network. This project has also reinforced my commitment to interdisciplinary collaboration and translational research, aiming to bridge the gap between laboratory discoveries and clinical applications.
Mohammed: "I'm convinced that about half of what separates successful entrepreneurs from the non-successful ones is pure perseverance." — Steve Jobs
This quote perfectly encapsulates my journey and dedication during my PhD studies and throughout the DECODE project.
First, I aspire to merge academic and industry experience by establishing a start-up focused on innovative medical technologies. Inspired by DECODE’s successful integration of academic research with industry practices, I believe the skills and knowledge I have gained will be instrumental in this venture.
Second, I am passionate about academic contributions and mentorship. I aim to support young researchers by sharing insights from my DECODE experience, helping them merge academic research with practical applications.
Third, I seek to foster international collaboration by facilitating partnerships between my institutions in Greece and Egypt. This will promote continuous research and innovation in biomedical engineering.
The DECODE project has profoundly influenced my career development. It has enhanced my skill set, significantly improving both my technical expertise and interpersonal collaboration skills, which are essential for a successful career in academia, industry, or entrepreneurship.
The exposure to industry practices provided by DECODE has prepared me to navigate market needs and regulatory requirements, crucial for launching and sustaining a successful start-up.
Moreover, the project has allowed me to build a strong professional network, supporting my long-term goals with access to resources, expertise, and potential partnerships.
Comments