Promotor, co-promotor, advisor : marianne.rooman@ulb.be, Fabrizio Pucci,

Research Unit : 3BIO - COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

Description

Next Generation Sequencing technologies produces massive amounts of genome data that are revolutionizing biological and medical research, and paves the way towards personalized medicine. Among the exome variants that lead to amino acid mutations, most are neutral in the sense that they only modify the individual’s phenotype, but some are the cause of diseases. The identification of deleterious mutations and their characterization are of prime importance for setting up personalized therapies. This project consists in developing and applying bioinformatics tools to predict disease-causing protein variants and trying to understand why they are so, in terms of protein characteristics such as stability, solubility, flexibility and function, or in terms of DNA characteristics such as its ionisation potential. More specifically, we are currently characterizing, at the molecular level, mutations involved in rare diseases, cancer and neurodevelopmental disorders such as autism spectrum disorder. The project is in collaboration with geneticists and clinicians (e.g., Hôpital Erasme, BE, Dana Farber Cancer Institute, USA, University of California San Diego School of Medicine, USA).

Promotor, co-promotor, advisor : marianne.rooman@ulb.be, Fabrizio Pucci,

Research Unit : 3BIO - COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

Description

Maintaining global health requires the development of generic and versatile technologies that allow fast and effective responses to the large variety of disorders, in particular cancer and emerging infectious diseases. Among these, monoclonal antibodies (mAbs) play an important role. Indeed, antibodies can bind antigens, such as bacterial or viral proteins or proteins expressed in cancer cells, to trigger the human immune response. In this project, we will build a bioinformatics pipeline for the design of mAbs that can bind with high affinity a specific target antigen. For that purpose, we will rely on experimentally characterized antibody-antigen complexes and their binding affinity values, detect informative sequence- and structure-based features, and combine them into a predictor using artificial intelligence techniques. The mAbs that we will design will be tested in vitro by experimental collaborators. While the project is focused on the design of a generic pipeline, it can be applied to specific case studies such as chronic lymphocytic leukemia, on which we are currently collaborating with cancer immunologists (Institute Bordet, BE).

Promotor, co-promotor, advisor : marianne.rooman@ulb.be, Fabrizio Pucci,

Research Unit : 3BIO - COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

Description

The renin-angiotensin system (RAS) is an important pathway that plays a key role in many physiological functions among which inflammation and blood pressure regulation. Its dysregulation is related to multiple pathological conditions such as hypertension and acute respiratory distress syndrome, just to mention some of them. In this project, we will use the ordinary differential equation formalism to study and predict the evolution of RAS under different perturbations. Currently, we are studying the effect of SARS-CoV-2 on RAS and how the administration of an endogenous peptide could rescue the severity of the disease. Extension of the RAS model perturbation to other diseases such as sepsis, septic shock or cardiogenic shock is also possible, as clinical data will soon be available. This project is in collaboration with the Intensive Care Unit of the Hôpital Erasme.

Promotor, co-promotor, advisor : marianne.rooman@ulb.be, Fabrizio Pucci, Dimitri Gilis,

Research Unit : 3BIO - COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

Description

Deep Learning algorithms are revolutionizing biomolecular science. For example, the AlphaFold2 and RosettaTR algorithms recently succeeded in pushing the accuracy of 3D protein structure prediction close to that of experimental methods. In this line of research, we will explore complex deep learning architectures to predict targeted biophysical characteristics of proteins. We propose two subtopics. In the first, pretrained attention-based language models (LM), such as ProteinBert, will be used and fine-tuned on downstream tasks such as protein localization or melting temperature predictions. Depending on the availability of computational resources, we will also consider direct training of BERT-like models which use masked LM approaches. The second subtopic is focused on the exploration of generative models for protein design.

Promotor, co-promotor, advisor : marianne.rooman@ulb.be, Fabrizio Pucci,

Research Unit : 3BIO - COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

Description

Proteins carry out a large variety of biological functions in living organisms. Some proteins, for example, act as particularly specific and efficient catalysts. The possibility to exploit the functional properties of proteins in industrial applications (food industry, chemical processes, pharmaceutical developments, etc.) is extremely interesting; however, one of its major limitations is that proteins generally lose their stability and activity under non-physiological conditions. The ability to design modified proteins that remain structured and active at higher (or lower) temperatures is therefore an important objective of research. Moreover, the understanding of how changes in the coding sequence of proteins affect their biophysical properties is essential in fundamental research such as molecular evolution and phylogeny. This project consists in developing efficient and fast computational tools to predict changes in stability, solubility or interactions of proteins upon mutations, which are applicable on a genome-wide scale. This software will be applied to rationally modify proteins of industrial interest and increasing their efficiency within a given application, or to study fundamental questions of interest in biophysics and molecular evolution. This project can be done within our group only, or in collaboration with experimental laboratories in academia or industry where the predictions will be tested.

Promotor, co-promotor, advisor : dimitri.gilis@ulb.be, - ,

Research Unit : 3BIO - COMPUTATIONAL BIOLOGY AND BIOINFORMATICS LAB

Description

Context

The olfactory system relies on protein receptors expressed by olfactory neurons. These olfactory receptors belong to the family of G protein-coupled membrane receptors (GPCR). The relationships between odorant molecules, targeted olfactory receptors and odour perception are complex and not yet well understood. In addition, it has been shown that some olfactory receptors are expressed in tissues other than the olfactory epithelium and may have a physiological or potentially therapeutic role.

Project

This project consists in developing artificial intelligence approaches, allowing (1) to predict the olfactory receptor(s) targeted by an odorant molecule, and (2) to design de novo a molecule able to activate a given olfactory receptor. It is carried out in collaboration with the group of Prof. I. Langer (Faculty of Medicine), which experimentally characterises these systems. The master thesis topics related to this project can be entirely (bio)informatics or include an experimental part.

Contact person

For more information please contact : dimitri.gilis@ulb.be

Promotor, co-promotor, advisor : dimitri.gilis@ulb.be, - ,

Research Unit : 3BIO - COMPUTATIONAL BIOLOGY AND BIOINFORMATICS LAB

Description

Context and project

Allergy represents an important public health problem. On the one hand, we are developing bioinformatics tools to predict whether a protein corresponds to a food allergen. These tools are based on machine learning techniques. Such tools are very important for the development of new food products. On the other hand, we are studying certain structural and dynamic properties of house dust mite allergens.

Contact person

For more information please contact : dimitri.gilis@ulb.be

Promotor, co-promotor, advisor : amin.shavandi@ulb.be, Oseweuba OKORO ,

Research Unit : 3BIO- BIOMATTER

Description

attached pdf document

Promotor, co-promotor, advisor : amin.shavandi@ulb.be, - , Pejman ghaffari

Research Unit : 3BIO-BIOMATTER

Description

Hydrogel-based scavengers of ROS and oxygen generators for mitigating inflammation

The development of certain diseases such as atherosclerosis, myocardial infarction, cancer, and chronic inflammation has been linked to high levels of ROS (reactive oxygen species). Therefore, it is crucial to create materials that can reduce the harmful effects of excessive ROS generation locally. However, hypoxia (a condition of low oxygen levels) can worsen inflammation by causing abnormal ROS production.To address this issue, the proposed solution is to develop modified methacrylate silk fibroin hydrogels (SiMA) that contain calcium peroxide-encapsulated fluorinated hyaluronic acid (HA) particles. The objective is to alleviate hypoxia and scavenge ROSs. To achieve this goal, several steps must be taken: A) Conjugate perfluorocarbon groups onto HA, B) Encapsulate calcium peroxide into fluorinated HA particles, C) Modify silk fibroin with methacrylate groups and catalase, D) Incorporate the synthesized particles into modified SiMA gels, E) Evaluate the physical and chemical properties of the developed hydrogels. This research aims to create a hydrogel that can reduce the harmful effects of excessive ROS generation locally and alleviate hypoxia, which could be beneficial in treating diseases linked to high levels of ROS.

Related literature: [1] Z. Li, Y. Zhao, H. Huang, C. Zhang, H. Liu, Z. Wang, M. Yi, N. Xie, Y. Shen, X. Ren, A Nanozyme‐Immobilized Hydrogel with Endogenous ROS‐Scavenging and Oxygen Generation Abilities for Significantly Promoting Oxidative Diabetic Wound Healing, Advanced Healthcare Materials 11(22) (2022) 2201524. [2] J. Ding, Y. Yao, J. Li, Y. Duan, J.R. Nakkala, X. Feng, W. Cao, Y. Wang, L. Hong, L. Shen, A reactive oxygen species scavenging and O2 generating injectable hydrogel for myocardial infarction treatment in vivo, Small 16(48) (2020) 2005038.

Contact: Pejman.ghaffari.bohlouli@ulb.be, and Amin.shavandi@ulb.be

attached pdf document

Promotor, co-promotor, advisor : amin.shavandi@ulb.be, - , Pejman Ghaffari

Research Unit : 3BIO-BIOMATTER

Description

Chronic wounds in diabetics can be difficult to treat due to a complex and severe inflammatory microenvironment that includes biofilm formation, excessive reactive oxygen species (ROS), hypoxia, and insufficient nitric oxide (NO) synthesis. To address these challenges, we propose synthesizing core-shell particles that can generate both O2 and NO simultaneously and control their release rate to mitigate hypoxia and prevent infection. We hypothesize that by encapsulating calcium peroxide (CaO2) into polycaprolactone (PCL) particles, we can generate H2O2 and O2 gradually through a reaction with water. The produced H2O2 can then react with guanidine groups on chitosan to generate NO. Perfluorocarbon groups (PFCs) on chitosan will form an NO and O2 buffering shell that can trap excess gas release and release it in a controlled, sustained manner. To achieve this aim, several steps are required: A) Conjugating 40-45% PFC groups on the chitosan chain, B) Replacing the remaining amine groups of chitosan with guanidine groups through a chemical reaction, C) Synthesizing core-shell particles that generate and control the release of O2 and NO, D) Evaluating the kinetics of generated O2, H2O2, and NO from the particles, and E) Evaluating the physical and chemical properties of the developed materials. The proposed research aims to develop a novel approach to address the complex and severe inflammatory microenvironment in chronic wounds in diabetics using core-shell particles that generate both O2 and NO and control their release rate, potentially leading to improved healing outcomes.

Related literature: [1] C. Tu, H. Lu, T. Zhou, W. Zhang, L. Deng, W. Cao, Z. Yang, Z. Wang, X. Wu, J. Ding, Promoting the healing of infected diabetic wound by an anti-bacterial and nano-enzyme-containing hydrogel with inflammation-suppressing, ROS-scavenging, oxygen and nitric oxide-generating properties, Biomaterials 286 (2022) 121597.

Contact: Pejman.ghaffari.bohlouli@ulb.be, and Amin.shavandi@ulb.be

attached pdf document

Promotor, co-promotor, advisor : amin.shavandi@ulb.be, - , julia.siminskastanny@ulb.be

Research Unit : 3BIO-BIOMATTER

Description

Project title

The project aims to solve an open issue in a certain domain of application.

By providing oxygen and nutrients to the cells, as well as eliminating metabolic waste, vascularization is a vital factor in the success of tissue engineering and yet one of its main challenges. Despite multiple advantages, natural polymers used for hydrogels creation have poor mechanical properties limiting their applications. Melt-electro-writing (MEW) offers the possibility to modify the physical characteristics of multi-material constructs comprising fibers and provide a scaffolding to enhance cell survival and ingrowth properties. Such multi-material MEW processes can be adapted to a wide range of mechanical properties, and thus enable target tissue-specific adjustments to obtain ideal scaffold properties. Reinforcing MEW frames embedded in hydrogel can affect the toughness and elastic modulus of the construct, helping to maintain the designed dimensions and architecture. Keeping that in mind this project combines MEW approach and extrusion printing of a soft hydrogel material to overcome current limitations associated with the creation of artificial vasculature. Additionally, it will investigate whether microstructure fibers can facilitate the specific alignment of cells. The projects’ tasks will cover, the design and fabrication of PCL (polycaprolactone) grids and fibers utilizing melt-electrowritting technique, followed by a process of extrusion printing of soft hydrogel material (gelatin and hyaluronic acid) to provide a cell-friendly interaction site. Composite scaffolds of preferable properties in terms of cell adhesion and durability will be further tested with in-house prepared PDMS chips, by subjecting the scaffolds to a continuous flow condition. Hopefully, the resulting scaffolds can become promising matrices to support vascularization processes addressing the challenge of angiogenesis within hydrogel-based tissue scaffolds.

Related literature: • https://doi.org/10.1038/s41598-022-24275-6 • https://doi.org/10.3389/fbioe.2020.00793 • https://doi.org/10.1002/adhm.201800418

Contact: julia.siminskastanny@ulb.be and amin.shavandi@ulb.be

attached pdf document

Promotor, co-promotor, advisor : amin.shavandi@ulb.be, - , julia.siminskastanny@ulb.be

Research Unit : 3BIO-BIOMATTER

Description

Lack of a vasculature system within a three-dimensional tissue model can significantly hinder the practical application of such constructs, especially in vivo. Blood vessels are vital to ensure cellular survival and enable tissue restoration first ex vivo and then in vivo. Therefore, the project is guided by a hypothesis that the vascularization of the artificial tissue can be overcome by developing a melt-electrowritten substrate in a form of a lattice decorated with growth factors (GFs) that could help to guide angiogenic processes in matrices composed of different hydrogels for tissue regeneration. Briefly, the projects’ tasks will cover, the design and fabrication of PCL (polycaprolactone) grids with different pore geometries utilizing melt-electrowritting technique, followed by a chemical modification of the polymer (amination) to ease the process of scaffolds decoration with GFs. Subsequently, PCL scaffolds will be tested for their cytocompatibility, stability in simulated body fluid (SBF), and their resistance to tensile stress. MEW scaffolds showing the best properties in terms of cell adhesion and durability will be further tested with in-house prepared PDMS chips, by subjecting the scaffolds to a continuous flow condition. Hopefully, the designed PCL scaffolds can become promising matrices for the guidance of angiogenic processes in hydrogel materials helping the creation of artificial tissues with clinically relevant dimensions.

Related literature: • https://doi.org/10.1038/s41598-022-24275-6 • https://doi.org/10.3389/fbioe.2020.00793 • https://doi.org/10.1002/adhm.201800418

Contact: julia.siminskastanny@ulb.be, amin.shavandi@ulb.be

attached pdf document

Promotor, co-promotor, advisor : amin.shavandi@ulb.be, - , julia.siminskastanny@ulb.be

Research Unit : 3BIO-BIOMATTER

Description

The lack of a functioning vasculature system within a tissue model can remain a significant barrier to the practical application of such constructs, especially in vivo. Therefore, the project is guided by a hypothesis that the vascularization of the artificial tissue can be overcome by developing new 3D-printing strategies using methacrylated gelatin (GelMA) and hyaluronic acid (HA) biomaterial inks. Conventional extrusion bioprinting requires a high-viscosity bio ink to improve the printability and high stiffness to support itself to keep shape fidelity, which subsequently has negative effects on cell viability, migration, or functioning. Nevertheless, low-viscosity inks cannot be printed as standalone structures. In cases such a support bath that offers temporary and omnidirectional support can stabilize the soft and overhanging material, preventing structure collapse before solidification. As such a new method called freeform reversible embedding of suspended hydrogels (FRESH) can be an alternative way to create vascular channels. In this project, a support bath consisting of a gelatin slurry will be used to support the creation of vascular-branched scaffolds from gelatin-hyaluronic acid hydrogels. Light curable biomaterial ink will be used to 3D print vessels, by the extrusion of the material in a vertical manner. Following the photocuring, gelatin term-reversible bath will be dissolved, revealing the printed vessel structure. In this project you will focus on the optimization of a crosslinking method employing visible light photo-crosslinking and investigation of inks and hydrogels rheological behavior, to determine the most promising formulation for FRESH printing. The last step will cover the fabrication of 3D hydrogel scaffolds (in the form of tubes) and their characterization. Quantitative characterization of embedded printing will be performed using cross-sectional images of the printed structure before and after the removal of the suspension bath. Hopefully, the resulting hydrogels may become promising materials to obtain vessel-like structures with branched organization, which is not possible using conventional 3D printing techniques.

Related literature: • https://doi.org/10.1021/acsami.0c05096 • https://doi.org/10.1016/j.tibtech.2019.12.020 • https://doi.org/10.1016/j.procir.2022.06.064

Contact: julia.siminskastanny@ulb.be, amin.shavandi@ulb.be

attached pdf document

Promotor, co-promotor, advisor : amin.shavandi@ulb.be, - , pejman.ghaffari.bohlouli@ulb.be

Research Unit : 3BIO-BIOMATTER

Description

Antimicrobial polycaprolactone 2D wound dressing by melt electrowetting method

Most of the available wound dressings are ineffective and suffer from limitations such as poor antimicrobial activity, inability to provide suitable moisture to the wound, and poor mechanical performance. Inappropriate wound dressings can result in a delayed wound healing process. Nano-size range scaffolds have triggered great attention because of their high capability to deliver bioactive agents, high surface area, improved mechanical properties, mimic the extracellular matrix (ECM), and high porosity. Polycaprolactone (PCL), a bioresorbable and biocompatible, synthetic polymer with Food and Drug Administration approval for use in the human body, has been selected as scaffold material due to its mechanical stability, flexibility, and superior melt processing properties. To increase PCL's biological functionality bioactive and expand their application, this project aims to conjugate antimicrobial agent on the PCL surface. We hypothesize that by aminolysing of ester groups of PCL, it would replace primary amino groups with guanidine groups that are potent antibacterial agents. To achieve this goal, it is required A) To develop a 2D scaffold by electro writing method based on PCL, B) To aminolyze the surface of the scaffolds by immerging it in isopropyl alcohol solutions of ETDA, EDEA, and HMD (10 wt/vol%) under stirring to ensure that the whole scaffold will be aminolyzed, C) To replace primary amino groups on PCL surface with guanidine groups, D) To study physicochemical properties of antimicrobial PCL scaffolds.

See the following articles for further details about the topic. 1-3

1. Toledo, A.; Ramalho, B.; Picciani, P.; Baptista, L.; Martinez, A.; Dias, M., Effect of three different amines on the surface properties of electrospun polycaprolactone mats. International Journal of Polymeric Materials and Polymeric Biomaterials 2021, 70 (17), 1258-1270.
2. Zhao, Y.-T.; Zhang, J.; Gao, Y.; Liu, X.-F.; Liu, J.-J.; Wang, X.-X.; Xiang, H.-F.; Long, Y.-Z., Self-powered portable melt electrospinning for in situ wound dressing. Journal of nanobiotechnology 2020, 18 (1), 1-10.
3. Piyasin, P.; Yensano, R.; Pinitsoontorn, S., Size-controllable melt-electrospun polycaprolactone (PCL) fibers with a sodium chloride additive. Polymers 2019, 11 (11), 1768.

attached pdf document

Promotor, co-promotor, advisor : amin.shavandi@ulb.be, - ,

Research Unit : 3BIO-BIOMATTER

Description

Antibacterial printable marine-based hydrogels

The design of 3D printable bio-based hydrogels with enhanced mechanical properties and minimal chemical modification can open new opportunities in the field of biomedical applications. A facile and safe approach is proposed to prepare mechanically reinforced chitosan-based hydrogels via a phenolated polyelectrolyte complex (PHEC) and enzyme-mediated crosslinking. PHEC will be formed between phenolated chitosan and alginate, leading to the formation of in situ phenol-functionalized microfibers. By replacing amino groups with phenol groups, the antibacterial activity of chitosan will be decreased, which has a critical role in tissue engineering. Therefore, to compensate for the antibacterial activity of the chitosan and increase the antibacterial activity of the system, the guanidine groups will be conjugated on the remaining amino groups of chitosan. To achieve this goal, it is required A) To conjugate phenol groups on chitosan and alginate, B) To synthesize a printable hydrogel based on phenolated chitosan and alginate by enzymatic crosslinking, C) To achieve a 3D hydrogel by 3D printing device, D) To conjugate guanidine groups on remaining amino groups of chitosan on 3D hydrogel surface by immersing the gel into guanidine solution, and E) To characterize physicochemical properties of 3D gels.

Please read the following articles for further details about the topic.1-2 1. Jafari, H.; Delporte, C.; Bernaerts, K. V.; Alimoradi, H.; Nie, L.; Podstawczyk, D. A.; Tam, K. C.; Shavandi, A., Synergistically complexation of phenol functionalized polymer induced in-situ microfiber formation for 3D printing of marine-based hydrogel. Green Chemistry 2022. 2. Zhang, X.; Fan, J.; Lee, C.-S.; Kim, S.; Chen, C.; Lee, M., Supramolecular hydrogels based on nanoclay and guanidine-rich chitosan: injectable and moldable osteoinductive carriers. ACS applied materials & interfaces 2020, 12 (14), 16088-16096.

Contact: amin.shavandi@ulb.be

attached pdf document

Promotor, co-promotor, advisor : alain.delchambre@ulb.be, - , Rami.Taheri@ulb.be

Research Unit : BEAMS (BIO- ELECTRO- AND MECHANICAL SYSTEMS)

Description

Project title

The project aims to solve an open issue in a certain domain of application.

Contact

• Name Contact Person: Tim Cleys • Business: Helicus • E-mail address: tim.cleys@helicus.com

Problem Statement and Motivation

Helicus is an Antwerp based startup, working to realize the transport of medical goods (e.g. biomedical samples, pharmaceutical products and donor blood) via drones. Helicus is developing an ecosystem of partners supporting unmanned aviation between medical actors across a city or region: the Helicus Aero Initiative (HAI). More concretely, HAI aims to provide a solution for integrated automated drone fleet management for medical goods.

Some of the deliveries that need to happen in the medical drone sector will be to destinations that do have a fixed/safe landing spot. An example of such a scenario is the delivery of an automated external defibrillator (AED) to a emergency site, such as the location of an accident. In this case, landing the drone will not be possible, so a solution is needed to design packaging for such an AED, and a method to lower this package onto a site. This solution needs to be secure, repeatable, and compliant with standards that exist within the aviation world.

Thesis Statement

Research question:

• Evaluate last design of AED packaging and winching system to hoist for emergency scenarios
• Adapt design for commercialization/industrialization
• Build prototype
• Test prototype
• Integrate the solution (controlled and monitored) into the existing Helicus Command and Control Center.

More Information

• Preferably a duo thesis • Fields of activity: mechanical design, medical equipment, programming • Hybrid: online/Helicus office at Sint Pietersvliet 7, 2000 Antwerp

attached pdf document

Promotor, co-promotor, advisor : bernardo.innocenti@ulb.be, - ,

Research Unit : BEAMS - BIOMECHANICS

Description

Project title

Biomechanical analysis of implant position in mobile bearing knee prosthesis with conventional and ultra-congruent insert

Context

Mobile-bearing knee prostheses are very sensitive to implant position. The posterior slope is a common mistake performed during surgery. Ultracongruent inserts are currently developed to improve stability. The idea of this study is to provide biomechanical evidence on the effect of changing the posterior slope in knee prosthesis in standard and ultra-congruent insert

Objective

Analyze the change in biomechanics during walking and squatting induce by different posterior slope positions in mobile-bearing knee implant

Methods

different models and configurations will be developed using finite element analysis similar to [Innocenti2020]

Prerequisite

None, biomechanical knowledge and finite element modeling could help but are not mandatory

Contact person

For more information please contact : bernardo.innocenti@ulb.be

references

Innocenti2020

Promotor, co-promotor, advisor : bernardo.innocenti@ulb.be, - ,

Research Unit : BEAMS - BIOMECHANICS

Description

Project title

Analysis of the effect of patellar laxity in different hinged knee prostheses

Context

Hinged total knee arthroplasty is used in case of severe revision implant (implant after implant) characterized by severe bone loss and reduced ligament stability. Two different possibilities exist for the hinged implants: rotating hinged and fixed hinge; while the first option allows flexion extension and internal-external knee motion, the second only allows flexion extension. Some surgeons fear that fixed hinged over-constrained the knee joint, while some others propose such designs in the case of patellar instability, however, no biomechanical guideline is currently available.

Objective

To be able to investigate the motion (kinematics) and forces (kinetics) of both a fixed and rotating knee prosthesis and to check the joint performance in presence of patellar stability and in the case of patellar laxity.

Methods

finite element model, based on: [Bori2022], [Bori2023]

Prerequisite

None, biomechanical knowledge and finite element are suggested but not mandatory

Contact person

For more information please contact : bernardo.innocenti@ulb.be

references

Bori2022 Bori2023

Promotor, co-promotor, advisor : alain.delchambre@ulb.be, - , Charlotte Deroubaix

Research Unit : BEAMS - BIOMECHATRONICS

Description

Electromagnetic linear actuator for arm prosthesis

Context

Generally, rotative motors are used as driving sources of prostheses and active orthoses to help restore lost abilities resulting from an amputation or a disease. However, reproducing natural movements with this type of actuator remains challenging, this is why the development of actuators with an action closer to that of a muscle has been emerging for years. Electromagnetic linear actuators could be an interesting solution, as they would have the potential to replicate the contraction and elongation principle of muscles.

Objective

The goal of the master thesis will be :

• To determine through a literature review if this type of actuator would be better adapted to an arm prosthesis for amputees, or to an active arm orthosis for people who have lost muscles strength,
• To define a full requirements list of the actuator for the chosen option,
• To adapt and optimize the existing actuator to meet the requirements,
• To develop a first proof of concept

Skills

• CAD software,
• Matlab,
• Electromagnetism,
• Prototyping

Contact persons

For more information please contact : Alain Delchambre (alain.delchambre@ulb.be), Charlotte Deroubaix (charlotte.deroubaix@ulb.be)

attached pdf document

Promotor, co-promotor, advisor : antoine.nonclercq@ulb.be, - , Romain Raffoul

Research Unit : BEAMS - BIOMECHATRONICS

Description

Gastric motility tracking setup

Context

To treat obesity, gastric electrical stimulation (GES) has been investigated in the last few decades with promising pre-clinical results. If long-term clinical trials demonstrate efficacy in inducing and sustaining weight loss, GES would have the advantage of offering a minimally invasive, long-term, reversible, and adjustable alternative to bariatric surgery, which is currently the gold-standard treatment but suffers from invasiveness and restrictions.

Despite its potential benefits, the underlying physiological mechanisms that mediate the effects of gastric stimulation are not fully understood. The stomach's movements and distention are particularly interesting, which may be closely linked to feelings of fullness and satiety.

Specialized monitoring systems are required to accurately measure these motions, ranging from a few millimeters in smaller animal models like rats to centimeters in dogs, in all three spatial dimensions. Before proceeding to clinical trials, it is necessary first to establish proof-of-concept using phantoms or ex vivo models.

Work

This master thesis aims to design, implement and validate a gastric motility monitoring setup. Various options will be considered, evaluating their pros and cons and classifying them based on practical trials. Creating a test bench is part of the project. It could be done by creating a phantom and/or using ex-vivo stomachs from rats, combined with the engineering of a motion generator. As the final application might be used on larger animals such as dogs, scalability should be one of the multiple criteria to fulfill.

Major steps include: - Define the technical requirements of the setup - Draw a state of the art of the existing motion tracking techniques - Creating a test bench (phantom and/or ex-vivo stomach + motion generator) - Prototyping the theoretically best motion tracking setups - Practical trials and measurements - Evaluation of the best solution - Improvement and scalability

Contact persons

For more information please contact : Antoine Nonclercq (antoine.nonclercq@ulb.be), Romain Raffoul (romain.raffoul@ulb.be)

attached pdf document

Promotor, co-promotor, advisor : antoine.nonclercq@ulb.be, - , Romain Raffoul

Research Unit : BEAMS - BIOMECHATRONICS

Description

Behavioral video analysis to assess gastric electrical stimulation

Context

To treat obesity, a promising method is gastric stimulation. The BEAMS department has investigated this therapy in the past years, and in vivo testing has been reached. Dogs have been implanted successfully, and by monitoring the amount of food ingested during the stimulation period with respect to the reference period, significant differences have been shown.

During the test periods of several weeks, each dog has been monitored by video cameras to analyse their behaviour. Those data remain currently unused, and a lot of information could be extracted from it in terms of reaction to the stimulation. Rather than watching the videos with a human eye and writing down the different times stamps and behaviours, an engineering approach is most suitable: creating a behaviour tracking algorithm, in coordination with veterinary surgeons and behavioural experts.

Work

This master thesis aims to propose an algorithm tracking different characteristics of the behaviour linked to the satiety feeling or wellbeing of the dogs. This will allow a comparison of the different periods of the tests (reference, gastric-stimulation, reference post-stimulation etc) and enlighten the effects of the gastric stimulation.

Major steps included: - Familiarize yourself with the format of the monitoring and the common image processing tools - Meet the behavioural experts and rediscuss what is feasible and/or interesting to analyse - Develop an algorithm to extract data such as timestamps and linked actions - Improve the algorithm step by step, behaviour by behaviour - Analyse the statistical differences between the different periods of the experiment

Contact persons

For more information please contact : Antoine Nonclercq (antoine.nonclercq@ulb.be), Romain Raffoul (romain.raffoul@ulb.be)

attached pdf document

Promotor, co-promotor, advisor : antoine.nonclercq@ulb.be, - , Sofiana Mootassim-Billah

Research Unit : BEAMS - BIOMECHATRONICS

Description

Project title

DEVELOPMENT OF AN ACOUSTIC COUGH ANALYSIS METHOD

Context

This master thesis proposal is part of a doctoral thesis project centered on the evaluation of swallowing disorders in patients with head and neck cancer. Radiation-associated dysphagia (RAD) is defined as impaired swallowing efficiency/safety following (chemo)radiotherapy in head and neck cancer (HNC) patients. In a RAD framework, the risk of impaired coughing may lead to lung aspiration and fatal lung infection (1-3). The two hallmarks of RAD are residue (food sticking in the mouth/throat) and aspiration (food entering the airways) (4-5). The latter ideally results in a cough reflex protecting the airways and lungs. In HNC-patients, the efficacy of this elicited cough is often diminished due to changes in the local physiology (sensory deterioration) (6-7). As such, up to 83% of HNC-patients are at risk of lung aspirations and consequent lung infections (8-9), fatal for one third of them (9-11). Although cough efficacy is considered as a reliable predictor of aspiration in the framework of dysphagia, cough investigation has been minimal in patients with RAD. Coughing is generally assessed perceptually (auditorily) during a clinical swallowing evaluation by clinicians. However, the agreement between clinicians with regard to cough scoring is very low (12).
Acoustically, a cough sound is a superposition of turbulence noise – presumably due to the air jet passing through the glottis – and lower frequency noise – presumably generated by the airflow modulated by the vibrations of the vocal folds, false vocal cords and aryepiglottic folds. Because cough is a transient signal, existing software for speech analysis are not appropriate.  Indeed, the assessment of voice quality is based on sustained voiced speech sounds, selected for reasons of technical feasibility and ease of reproducibility of the analysis. Therefore, developing new acoustic cough analysis methods might provide valid and objective measurements.

Objective

The goal of this project is to develop an objective assessment method using acoustic features related to voluntary and reflexive coughs as biomarkers of dysphagia/aspiration in HNC-patients with RAD.  At present, a program for cough analysis is available (prototype). Automatic segmentation enables to measure the cough duration. The analysis involves temporal features: the amplitude contour, the sample entropy and the kurtosis. These features report respectively the strength, the unpredictability (turbulence noise due to the air jet) and the impulsive quality (burst) of the signal. The analysis also includes spectral features obtained via a spectral decomposition of the relative cough signal energy into several frequency bands (0-400Hz, 400-800Hz, 800-1600Hz, 1600Hz-3200Hz, >3200Hz). 

Methods

The aims of the proposal are the following. Firstly, the comparison of voluntary and reflexive coughs in healthy subjects based on the above-mentioned temporal and spectral features. This study focuses on healthy subjects to obtain reference values and to examine the reliability of the cough analysis under development. Secondly, provided a reliability of the cough analysis, the development of a clear and intuitive interface of the existing analysis software that enables the software to be used easily by clinicians and that also offers a readable display of the data.

Prerequisite

• Python

Contact person

Antoine Nonclercq (anoncler@ulb.ac.be) Dirk Van Gestel (dirk.vangestel@hubruxelles.be) Sofiana Mootassim-Billah (s.mootassim-billah@hubruxelles.be)

references

1. M. J. Awan et al., “Late radiation-associated dysphagia (late-RAD) with lower cranial neuropathy after oropharyngeal radiotherapy: A preliminary dosimetric comparison,” Oral Oncol., vol. 50, no. 8, pp. 746–752, 2014, doi: 10.1016/j.oraloncology.2014.05.003.
2. D. I. Rosenthal, J. S. Lewin, and A. Eisbruch, “Prevention and Treatment of Dysphagia and Aspiration After Chemoradiation for Head and Neck Cancer,” J. Clin. Oncol., vol. 24, no. 17, 2006, doi: 10.1200/JCO.2006.06.0079.
3. S. N. King, N. E. Dunlap, P. A. Tennant, and T. Pitts, “Pathophysiology of RadiationInduced Dysphagia in Head and Neck Cancer,” Dysphagia, vol. 31, no. 3, pp. 339–351, 2016, doi: 10.1007/s00455-016-9710-1.
4. Hammond CS. Cough and aspiration of food and liquids due to oral pharyngeal. Dysphagia. 2008;186:35-40.
5. Madhavan A, Carnaby GD, Crary MA. ‘Food sticking in my throat’: videofluoroscopic evaluation of a common symptom.
6. Rosenbek JC, Robbins JA, Roecker PDEB, Coyle JL, Wood JL. A penetration-aspiration scale. Dysphagia. 1996;11:93-98.
7. Lee JY, Kim D, Seo KM, Kang SH. Usefulness of the simplified cough test in evaluating cough reflex sensitivity as a screening test for silent aspiration. Ann Rehabil Med. 2014;38(4):476-484.
8. Rogus-Pulia N, Pierce MC, Mittal BB, Zecker SG, Logemann JA. Changes in swallowing physiology and patient perception of swallowing function following Chemoradiation for head and neck cancer. Dysphagia. 2014;29:223-233.
9. Nguyen NP, Frank C, Moltz CC, et al. Aspiration rate following chemoradiation for head and neck cancer: an underreported occurrence. Head Neck Radiother. 2006;80:302-306.
10. Xiong J, Krishnaswamy G, Raynor S, Loh KS, Lay ALH, Lim CM. Risk of swallowing-related chest infections in patients with nasopharyngeal carcinoma treated with definitive intensity modulated radiotherapy. Head Neck. 2016;38(1):1660-1665.
11. Xu B, Boero IJ, Hwang L, et al. Aspiration pneumonia after concurrent chemoradiotherapy for head and neck cancer. Cancer. 2015; 121(8):1303-1311.
12. H. Laciuga, A. E. Brandimore, M. S. Troche, and K. W. Hegland, “Analysis of Clinicians ’ Perceptual Cough Evaluation,” Dysphagia, vol. 31, no. 4, pp. 521–530, 2016, doi: 10.1007/s00455-016-9708-8

Promotor, co-promotor, advisor : antoine.nonclercq@ulb.be, - , Louis Vande Perre

Research Unit : BEAMS - BIOMECHATRONICS

Description

Infrared neural stimulation mechanism modeling

Supervising staff

Antoine Nonclercq (antoine.nonclercq@ulb.be), Louis Vande Perre (louis.vande.perre@ulb.be).

Background

Neurostimulation is widely used to treat chronic conditions. It is usually performed by electrical stimulation of tissues. However, it suffers from several shortcomings, including stimulation artifacts, low spatial resolution, incompatibility with magnetic resonance imaging, and the order in which nerve fibers are activated is not physiological. Optical stimulation could overcome all these shortcomings. Among the optical nerve stimulation techniques, infrared neural stimulation (INS) is very promising because it does not require any prior genetic modification. INS consists of nerve activation due to transient exposure to infrared light. Our team has developed an experimental setup capable of compound action potential (CAP) elicitation in an excised rat sciatic nerve with the help of INS [1], [2]. The setup simultaneously records the nerve electrophysiological activity and the temperature at the surface of the nerve to link the CAP triggering and temperature gradients. However, numerical modeling would be helpful to investigate further why heat accumulation results in larger CAP amplitude. Moreover, modeling the light diffusion could help us better monitor the thermal gradients induced in the nerve based on the surface temperature measurements. In the literature, three main hypotheses are currently considered as the underlying mechanism of INS: membrane capacitance change [3]–[7], membrane nanoporation [8], [9] or thermosensitive ion channels [10], [11] could be responsible for the axon depolarization. Therefore, the precise modeling of INS is complex, but numerous axon modeling could be used to explore the impact of temperature on the nerve cell. For the sake of simplicity, this project could rely on the Hodgkin-Huxley (HH) model, extensively used in neuroscience, which has already been adapted in the context of the INS [12]–[14]. However, Forrest argues that this simplistic model does not conveniently include thermodynamics considerations in action potential triggering [15]. Therefore, another model than the one developed by Hodgkin and Huxley might be considered. Regarding the heat diffusion in the nerve during INS, previous work already investigated how temperature evolves at different spots in the nerve [16], [17]. However, these models do not fully describe the type of thermal gradients we observed in our experiments. Based on these works, a new model could be developed to analyze the results of our ex-vivo experiments better.

Work

The main goal of this project is to reuse the existing axon model or develop a similar model to investigate the impact of a rapid temperature increase on the membrane. The action potential (AP) elicitation will be based on a change in membrane capacitance, at least for the first model iteration. In parallel, modeling of the heat diffusion - to better quantify the spatiotemporal temperature gradients in our experiments - could be achieved.

This work is exploratory and will require creativity and autonomy.

Bibliography

[1] L. vande Perre et al., “A Setup for Conduction Velocities and Temperature Gradients Measurements during Infrared Neurostimulation,” in 2022 IEEE Biomedical Circuits and Systems Conference (BioCAS), 2022, pp. 453–457. doi: 10.1109/BioCAS54905.2022.9948671. [2] J. Cury et al., “Infrared neurostimulation in ex-vivo rat sciatic nerve using 1470 nm wavelength,” J Neural Eng, vol. 18, no. 5, p. 056018, 2021, doi: 10.1088/1741-2552/abf28f. [3] B. I. Pinto, C. A. Z. Bassetto, and F. Bezanilla, “Optocapacitance: physical basis and its application,” Biophys Rev, vol. 14, no. 2, pp. 569–577, 2022, doi: 10.1007/s12551-022-00943-9. [4] M. Plaksin, E. Shapira, E. Kimmel, and S. Shoham, “Thermal Transients Excite Neurons through Universal Intramembrane Mechanoelectrical Effects,” Phys Rev X, vol. 8, no. 1, p. 11043, 2018, doi: 10.1103/PhysRevX.8.011043. [5] M. G. Shapiro, K. Homma, S. Villarreal, C. P. Richter, and F. Bezanilla, “Infrared light excites cells by changing their electrical capacitance,” Nat Commun, vol. 3, no. March, pp. 310–376, 2012, doi: 10.1038/ncomms1742. [6] Z. Ebtehaj, A. Hatef, M. Malekmohammad, and M. Soltanolkotabi, “Computational Modeling and Validation of Thermally Induced Electrical Capacitance Changes for Lipid Bilayer Membranes Irradiated by Pulsed Lasers,” Journal of Physical Chemistry B, vol. 122, no. 29, pp. 7319–7331, 2018, doi: 10.1021/acs.jpcb.8b02616. [7] G. Bondelli et al., “Shedding Light on Thermally Induced Optocapacitance at the Organic Biointerface,” Journal of Physical Chemistry B, vol. 125, no. 38, pp. 10748–10758, 2021, doi: 10.1021/acs.jpcb.1c06054. [8] H. T. Beier, G. P. Tolstykh, J. D. Musick, R. J. Thomas, and B. L. Ibey, “Plasma membrane nanoporation as a possible mechanism behind infrared excitation of cells,” J Neural Eng, vol. 11, no. 6, 2014, doi: 10.1088/1741-2560/11/6/066006. [9] C. C. Roth, R. A. Barnes, B. L. Ibey, R. D. Glickman, and H. T. Beier, “Short infrared (IR) laser pulses can induce nanoporation,” Clinical and Translational Neurophotonics; Neural Imaging and Sensing; and Optogenetics and Optical Manipulation, vol. 9690, p. 96901L, 2016, doi: 10.1117/12.2214892. [10] E. S. Albert et al., “TRPV4 channels mediate the infrared laser-evoked response in sensory neurons,” J Neurophysiol, vol. 107, no. 12, pp. 3227–3234, 2012, doi: 10.1152/jn.00424.2011. [11] E. Suh, A. D. Izzo, M. Otting, J. T. Walsh, and C. Richter, “Optical stimulation in mice lacking the TRPV1 channel,” Proceedings of SPIE - The International Society for Optical Engineering, vol. 7180, no. February, pp. 71800S–1, 2009, doi: 10.1117/12.816891. [12] S. Fribance, J. Wang, J. R. Roppolo, W. C. de Groat, and C. Tai, “Axonal model for temperature stimulation,” J Comput Neurosci, vol. 41, no. 2, pp. 185–192, 2016, doi: 10.1007/s10827-016-0612-x. [13] M. J. Alemzadeh-Ansari, M. A. Ansari, M. Zakeri, and M. Haghjoo, “Influence of radiant exposure and repetition rate in infrared neural stimulation with near-infrared lasers,” Lasers Med Sci, vol. 34, no. 8, pp. 1555–1566, 2019, doi: 10.1007/s10103-019-02741-4. [14] C. A. Maldonado, B. D. Wooley, and J. J. Pancrazio, “The excitatory effect of temperature on the Hodgkin-Huxley model,” Impulse: The Premier Undergraduate Neuroscience Journal, pp. 1–7, 2015, [Online]. Available: http://impulse.appstate.edu/sites/impulse.appstate.edu/files/Maldonado et al..pdf [15] M. D. Forrest, “Can the Thermodynamic Hodgkin-Huxley Model of Voltage-Dependent Conductance Extrapolate for Temperature?,” Computation, vol. 2, pp. 47–60, 2014, doi: 10.3390/computation2020047. [16] Zhou, R. et al. 2022. “Theoretical simulation of the selective stimulation of axons in different areas of a nerve bundle by multichannel near-infrared lasers.” Medical and Biological Engineering and Computing. 60, 1 (2022), 205–220. DOI:https://doi.org/10.1007/s11517-021-02475-y. [17] Liljemalm, R. et al. 2013. “Heating during infrared neural stimulation.” Lasers in Surgery and Medicine. 45, 7 (2013), 469–481. DOI:https://doi.org/10.1002/lsm.22158.

attached pdf document

Promotor, co-promotor, advisor : antoine.nonclercq@ulb.be, Nicolas Gaspard (Head of Department of Neurology, Erasme), Lise Cottin

Research Unit : BEAMS - BIOMECHATRONICS

Description

Brain connectivity investigation during seizures in the intensive care unit

Supervising staff

Antoine Nonclercq (antoine.nonclercq@ulb.be), Nicolas Gaspard (Head of Department of Neurology, nicolas.gaspard@hubruxelles.be), Lise Cottin (lise.cottin@ulb.be).

Context

This project will be performed in collaboration and with the help of the Department of Neurology at the CUB Hôpital Erasme.

Epilepsy is a disorder of the brain characterized by an enduring predisposition to generate epileptic seizures and by the neurobiologic, cognitive, psychological, and social consequences of this condition (Fisher et al. 2005). Epilepsy has variable etiologies, may affect both children and adults, and has an annual incidence of 4–8/1000. In about a third of epileptic patients, seizures do not respond to conventional anti-epileptic drugs.

Management of epileptic patients in the Intensive Care Unit (ICU) is challenging. The ability to anticipate an upcoming seizure would be valuable both for patient management and as a predictor of treatment adequacy.

Recently, a technique has gradually gained prominence in forecasting epileptic seizures: the investigation of brain connectivity, characterizing how highly specialized brain regions communicate with each other (Ismail and Karwowski 2020). Indeed, epilepsy is widely believed to result from disrupting healthy brain network properties (van Mierlo et al. 2014). By modeling the brain as a connectivity graph, the interactions between its regions can be studied formally, allowing quantitative characterization and interpretation of the specific patterns observed (Farahani, Karwowski, and Lighthall 2019; van Diessen et al. 2015).

Although brain connectivity has been increasingly studied in recent years in epilepsy, the organizational changes in the brain network around a seizure are not yet clear, and the literature shows great discrepancies between articles. It is commonly accepted that the brain is organized in a small-world structure, characterized by a larger number of smaller and denser clusters of connected nodes. When the occurrence of a seizure disrupts this structure, this efficient organization for information transfer tends towards more random or ordered patterns (Ponten, Bartolomei, and Stam 2007; Kramer, Kolaczyk, and Kirsch 2008; Schindler et al. 2008; Srinivas et al. 2007; Kramer et al. 2010; Wu, Li, and Guan 2006; Percha et al. 2005; Christodoulakis et al. 2012). An explanation for these disagreements is that most of the studies focused on small and specific patient groups, for which conclusions were consistent but difficult to compare since they were obtained under different conditions (van Mierlo et al. 2014). They also show the need for a deeper investigation of the connectivity mechanisms present in epilepsy.

Work

This work aims to investigate the organizational features of brain connectivity during seizures to understand the pathological mechanisms underlying epilepsy better. The evolution of the connectivity in that framework will be evaluated. In that regard, these patients' connectivity will be investigated during background activity, just before, during, and after a seizure. Besides, if results are conclusive, a comparison of the analysis on EEG from these patients with the one on EEG from epileptic patients (i.e., characterized by recurrent – rather than isolated – seizures) is also considered.

Recording of electroencephalographic signals (EEG) from patients in the Intensive Care Unit (ICU) will be provided.

Bibliography

Christodoulakis, Manolis, Maria Anastasiadou, Savvas S. Papacostas, Eleftherios S. Papathanasiou, and Georgios D. Mitsis. 2012. “Investigation of Network Brain Dynamics from EEG Measurements in Patients with Epilepsy Using Graph-Theoretic Approaches.” IEEE 12th International Conference on BioInformatics and BioEngineering, BIBE 2012, 303–8. https://doi.org/10.1109/BIBE.2012.6399693. Diessen, E. van, T. Numan, E. van Dellen, A. W. van der Kooi, M. Boersma, D. Hofman, R. van Lutterveld, et al. 2015. “Opportunities and Methodological Challenges in EEG and MEG Resting State Functional Brain Network Research.” Clinical Neurophysiology 126 (8): 1468–81. https://doi.org/10.1016/J.CLINPH.2014.11.018. Farahani, Farzad V., Waldemar Karwowski, and Nichole R. Lighthall. 2019. “Application of Graph Theory for Identifying Connectivity Patterns in Human Brain Networks: A Systematic Review.” Frontiers in Neuroscience 13 (JUN). https://doi.org/10.3389/FNINS.2019.00585/FULL. Fisher, Robert S., Walter Van Emde Boas, Warren Blume, Christian Elger, Pierre Genton, Phillip Lee, and Jerome Engel. 2005. “Epileptic Seizures and Epilepsy: Definitions Proposed by the International League Against Epilepsy (ILAE) and the International Bureau for Epilepsy (IBE).” Epilepsia 46 (4): 470–72. https://doi.org/10.1111/J.0013-9580.2005.66104.X. Ismail, Lina Elsherif, and Waldemar Karwowski. 2020. “A Graph Theory-Based Modeling of Functional Brain Connectivity Based on EEG: A Systematic Review in the Context of Neuroergonomics.” IEEE Access. Institute of Electrical and Electronics Engineers Inc. https://doi.org/10.1109/ACCESS.2020.3018995. Kramer, Mark A., Uri T. Eden, Eric D. Kolaczyk, Rodrigo Zepeda, Emad N. Eskandar, and Sydney S. Cash. 2010. “Coalescence and Fragmentation of Cortical Networks during Focal Seizures.” The Journal of Neuroscience : The Official Journal of the Society for Neuroscience 30 (30): 10076–85. https://doi.org/10.1523/JNEUROSCI.6309-09.2010. Kramer, Mark A., Eric D. Kolaczyk, and Heidi E. Kirsch. 2008. “Emergent Network Topology at Seizure Onset in Humans.” Epilepsy Research 79 (2–3): 173–86. https://doi.org/10.1016/J.EPLEPSYRES.2008.02.002. Mierlo, Pieter van, Margarita Papadopoulou, Evelien Carrette, Paul Boon, Stefaan Vandenberghe, Kristl Vonck, and Daniele Marinazzo. 2014. “Functional Brain Connectivity from EEG in Epilepsy: Seizure Prediction and Epileptogenic Focus Localization.” Progress in Neurobiology 121 (October): 19–35. https://doi.org/10.1016/J.PNEUROBIO.2014.06.004. Percha, Bethany, Rhonda Dzakpasu, Michał Zochowski, and Jack Parent. 2005. “Transition from Local to Global Phase Synchrony in Small World Neural Network and Its Possible Implications for Epilepsy.” Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics 72 (3 Pt 1). https://doi.org/10.1103/PHYSREVE.72.031909. Ponten, S. C., F. Bartolomei, and C. J. Stam. 2007. “Small-World Networks and Epilepsy: Graph Theoretical Analysis of Intracerebrally Recorded Mesial Temporal Lobe Seizures.” Clinical Neurophysiology : Official Journal of the International Federation of Clinical Neurophysiology 118 (4): 918–27. https://doi.org/10.1016/J.CLINPH.2006.12.002. Schindler, Kaspar A., Stephan Bialonski, Marie Therese Horstmann, Christian E. Elger, and Klaus Lehnertz. 2008. “Evolving Functional Network Properties and Synchronizability during Human Epileptic Seizures.” Chaos (Woodbury, N.Y.) 18 (3). https://doi.org/10.1063/1.2966112. Srinivas, Kalyan V., Rishabh Jain, Subit Saurav, and Sujit K. Sikdar. 2007. “Small-World Network Topology of Hippocampal Neuronal Network Is Lost, in an in Vitro Glutamate Injury Model of Epilepsy.” The European Journal of Neuroscience 25 (11): 3276–86. https://doi.org/10.1111/J.1460-9568.2007.05559.X. Wu, Huihua, Xiaoli Li, and Xinping Guan. 2006. “Networking Property during Epileptic Seizure with Multi-Channel EEG Recordings.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 3973 LNCS: 573–78. https://doi.org/10.1007/11760191_84/COVER.

attached pdf document

Promotor, co-promotor, advisor : antoine.nonclercq@ulb.be, Nicolas Gaspard (Head of Department of Neurology, Erasme), Lise Cottin

Research Unit : BEAMS - BIOMECHATRONICS

Description

Machine learning method to forecast epileptic seizures from brain connectivity

Supervising staff

Antoine Nonclercq (antoine.nonclercq@ulb.be), Nicolas Gaspard (Head of Department of Neurology, nicolas.gaspard@hubruxelles.be), Lise Cottin (lise.cottin@ulb.be).

Context

This project will be performed in collaboration and with the help of the Department of Neurology at the CUB Hôpital Erasme.

Epilepsy is a disorder of the brain characterized by an enduring predisposition to generate epileptic seizures and by the neurobiologic, cognitive, psychological, and social consequences of this condition (Fisher et al., 2005). Epilepsy has variable etiologies, may affect both children and adults, and has an annual incidence of 4–8/1000. In about a third of epileptic patients, seizures do not respond to conventional anti-epileptic drugs.

Management of epileptic patients in the Intensive Care Unit (ICU) is challenging. The ability to anticipate an upcoming seizure would be valuable both for patient management and as a predictor of treatment adequacy.

Recently, a technique has gradually gained prominence in forecasting epileptic seizures: the investigation of brain connectivity, characterizing how highly specialized brain regions communicate with each other (Ismail and Karwowski 2020). Indeed, epilepsy is widely believed to result from disrupting healthy brain network properties (van Mierlo et al. 2014). By modeling the brain as a connectivity graph, the interactions between its regions can be studied formally, allowing quantitative characterization and interpretation of the specific patterns observed (Farahani, Karwowski, and Lighthall 2019; van Diessen et al. 2015).

Machine learning techniques are often used on EEG data to accurately and automatically predict a patient's condition, such as at risk of seizure or not for ICU patients. However, research using machine learning techniques to analyze connectivity parameters extracted from connectivity graphs or even directly analyze connectivity networks has been much less explored.

In addition to exploring the potential of machine learning in analyzing connectivity networks, it would be valuable to compare its performance to more traditional classification methods. This would help determine whether machine learning techniques can provide more accurate predictions. Another important aspect to consider is the trade-off between model complexity and interpretability. While more complex models may offer higher performance, they can also be more difficult to explain and interpret. Understanding this correlation and finding a balance between accuracy and interpretability is crucial in ensuring that these models are reliable and can be used effectively in clinical settings.

Work

This work aims to design, implement and assess a machine-learning method to predict subsequent seizures based on brain connectivity. Recording of electroencephalographic signals (EEG) from patients in the Intensive Care Unit (ICU) will be provided.

Bibliography

Diessen, E. van, T. Numan, E. van Dellen, A. W. van der Kooi, M. Boersma, D. Hofman, R. van Lutterveld, et al. 2015. “Opportunities and Methodological Challenges in EEG and MEG Resting State Functional Brain Network Research.” Clinical Neurophysiology 126 (8): 1468–81. https://doi.org/10.1016/J.CLINPH.2014.11.018. Farahani, Farzad V., Waldemar Karwowski, and Nichole R. Lighthall. 2019. “Application of Graph Theory for Identifying Connectivity Patterns in Human Brain Networks: A Systematic Review.” Frontiers in Neuroscience 13 (JUN). https://doi.org/10.3389/FNINS.2019.00585/FULL. Hamilton, William L. 2020. “Graph Representation Learning.” Vol. 14. Ismail, Lina Elsherif, and Waldemar Karwowski. 2020. “A Graph Theory-Based Modeling of Functional Brain Connectivity Based on EEG: A Systematic Review in the Context of Neuroergonomics.” IEEE Access. Institute of Electrical and Electronics Engineers Inc. https://doi.org/10.1109/ACCESS.2020.3018995. Mierlo, Pieter van, Margarita Papadopoulou, Evelien Carrette, Paul Boon, Stefaan Vandenberghe, Kristl Vonck, and Daniele Marinazzo. 2014. “Functional Brain Connectivity from EEG in Epilepsy: Seizure Prediction and Epileptogenic Focus Localization.” Progress in Neurobiology 121 (October): 19–35. https://doi.org/10.1016/J.PNEUROBIO.2014.06.004.

attached pdf document

Promotor, co-promotor, advisor : antoine.nonclercq@ulb.be, Nicolas Gaspard (Head of Department of Neurology, Erasme), Lise Cottin

Research Unit : BEAMS - BIOMECHATRONICS

Description

Study of parameter's influence in brain connectivity estimation

Supervising staff

Antoine Nonclercq (antoine.nonclercq@ulb.be), Nicolas Gaspard (Head of Department of Neurology, nicolas.gaspard@hubruxelles.be), Lise Cottin (lise.cottin@ulb.be).

Context

This project will be performed in collaboration and with the help of the Department of Neurology at the CUB Hôpital Erasme.

Epilepsy is a disorder of the brain characterized by an enduring predisposition to generate epileptic seizures and by the neurobiological, cognitive, psychological, and social consequences of this condition (Fisher et al., 2005). Epilepsy has variable etiologies, may affect both children and adults, and has an annual incidence of 4–8/1000. In about a third of epileptic patients, seizures do not respond to conventional anti-epileptic drugs.

Management of epileptic patients in the Intensive Care Unit (ICU) is challenging. The ability to anticipate an upcoming seizure would be valuable both for patient management and as a predictor of treatment adequacy.

Recently, a new technique to investigate epilepsy emerged: the investigation of brain connectivity, characterizing how highly specialized brain regions communicate with each other (Ismail and Karwowski 2020). Indeed, epilepsy is widely believed to result from a disruption of healthy brain network properties (van Mierlo et al. 2014). By modeling the brain as a connectivity graph, the interactions between its regions can be studied formally, allowing quantitative characterization and interpretation of the specific patterns observed (Farahani, Karwowski, and Lighthall 2019; van Diessen et al. 2015).

Brain connectivity estimation is undertaken by graph theory. While this framework offers classical steps for constructing connectivity networks, the impact of the many parameters involved at each stage has received little attention in the literature. Yet, these parameters can significantly influence the results obtained, and are therefore crucial in the evaluation.

Work

This work aims to design and implement a method for brain connectivity analysis with graph theory based on the current framework available at our lab, and validate it on electroencephalographic signals (EEG) from patients at the Intensive Care Unit (ICU). More specifically, key parameters in evaluating brain connectivity will be reviewed, and their impact on the final connectivity results will be assessed. Recording of electroencephalographic signals (EEG) from patients at the Intensive Care Unit (ICU) will be provided.

Bibliography

Diessen, E. van, T. Numan, E. van Dellen, A. W. van der Kooi, M. Boersma, D. Hofman, R. van Lutterveld, et al. 2015. “Opportunities and Methodological Challenges in EEG and MEG Resting State Functional Brain Network Research.” Clinical Neurophysiology 126 (8): 1468–81. https://doi.org/10.1016/J.CLINPH.2014.11.018. Farahani, Farzad V., Waldemar Karwowski, and Nichole R. Lighthall. 2019. “Application of Graph Theory for Identifying Connectivity Patterns in Human Brain Networks: A Systematic Review.” Frontiers in Neuroscience 13 (JUN). https://doi.org/10.3389/FNINS.2019.00585/FULL. Fisher, Robert S., Walter Van Emde Boas, Warren Blume, Christian Elger, Pierre Genton, Phillip Lee, and Jerome Engel. 2005. “Epileptic Seizures and Epilepsy: Definitions Proposed by the International League Against Epilepsy (ILAE) and the International Bureau for Epilepsy (IBE).” Epilepsia 46 (4): 470–72. https://doi.org/10.1111/J.0013-9580.2005.66104.X. Ismail, Lina Elsherif, and Waldemar Karwowski. 2020. “A Graph Theory-Based Modeling of Functional Brain Connectivity Based on EEG: A Systematic Review in the Context of Neuroergonomics.” IEEE Access. Institute of Electrical and Electronics Engineers Inc. https://doi.org/10.1109/ACCESS.2020.3018995. Johann. 2022. “Easy Plot EEG Brain Network Matlab.” Mierlo, Pieter van, Margarita Papadopoulou, Evelien Carrette, Paul Boon, Stefaan Vandenberghe, Kristl Vonck, and Daniele Marinazzo. 2014. “Functional Brain Connectivity from EEG in Epilepsy: Seizure Prediction and Epileptogenic Focus Localization.” Progress in Neurobiology 121 (October): 19–35. https://doi.org/10.1016/J.PNEUROBIO.2014.06.004.

attached pdf document

Promotor, co-promotor, advisor : antoine.nonclercq@ulb.be, - , Maxime Verstraeten

Research Unit : BEAMS - BIOMECHATRONICS

Description

Design and manufacturing of a capacitive strain sensor to monitor bladder activity

Supervising staff

Antoine Nonclercq (antoine.nonclercq@ulb.be), Maxime Verstraeten (maxime.verstraeten@ulb.be).

Context

“Neurogenic bladder” usually defines bladder and sphincter dysfunctions related to a neurological disease or a condition such as a spinal cord injury (SCI). Clinical manifestations include detrusor overactivity leading to incontinence and detrusor sphincter dyssynergia which can result in irreversible kidney damage. A neurogenic bladder has tremendous repercussions on patients’ physical and psychological well-being, constituting a financial burden on healthcare systems.

To prevent most of these issues, patients rely on uncomfortable bladder management techniques such as clean intermittent catheterization, which often lead to urinary tract infections and subsequent renal failure if managed incorrectly or in poor conditions. Being able to monitor and predict bladder contractions, as well as rising intravesical pressure, would allow patients to adapt their management techniques and increase their quality of life. Moreover, it would be possible to stimulate the afferent nerves in a closed feedback loop to refrain from their urge to urinate. Therefore, monitoring bladder activity in SCI patients is a top research priority.

One of the possibilities for monitoring bladder activity is its deformation. A resistive strain gauge is its simplest implementation but presents two major flaws: - The elasticity of a standard strain gauge is low. It is, therefore, not correctly following the bladder deformation. The flexibility, stretchability, and durability are also limited, and the measurement presents some hysteresis. - Measuring the gauge strain requires a relatively high current flow which is to be avoided in an implant design because of limited battery capacity and risk of overheating.

A capacitive strain sensor (i.e., a sensor whose capacitance changes depending on its strain) has been designed to overcome these limitations. It comprises a stretchable silver-coated fabric, acting as electrodes, and silicone, acting as the dielectric. The change in the sensor capacitance largely depends on the variation in the geometric structure of the electrodes and the dielectric layer. This increases the linearity of the measurements and removes any hysteresis behavior. Multiple designs exist and should allow a greater elasticity of the measuring device, which the anchoring on the bladder wall will benefit from. Two different designs have been investigated.

The 3-layer design is a simple sandwich of fabric electrodes around a single dielectric layer. When stretched, the silicone layer gets thinner, and the capacitance increases as the electrodes get closer.

The interdigital design is a succession of fabric electrodes in the same 2D plane, separated by silicone. Similarly, the electrodes get closer as the sensor is stretched, and the capacitance increases.

Although the sensors are promising, the manufacturing technique may still benefit from improvements, and the fabrication parameters could be tuned. For example, some sensors fail as a short circuit between the electrodes appears in some configurations and others fail due to the high impedance connection between the measuring wires and conductive fabric. The sensors have also not been completely characterized (baseline capacitance depending on the configuration, capacitance-to-strain relationship, drift, hysteresis, susceptibility to EMI, functionality in a humid environment, …).

Work

This master thesis aims to design the manufacturing process of a capacitive strain sensor to measure the bladder wall's deformation and assess its feasibility and performance with a test bench. A specific mechanical anchoring device must also be designed for the sensor to be well attached to the bladder wall and to measure its deformation accurately.

This will require a complete state-of-the-art review to select the best capacitive sensor designs for the application, followed by the actual implementation and assessment of the sensor and the anchor. The main assessment criteria are the power required to measure the deformation, the range of deformation, the elasticity of the sensor, the durability, the hysteresis behavior, and the anchoring capabilities.

Current prototypes must be reproduced to understand their functionality and assess their failure points or limitations. Fabrication parameters (electrode gap, dielectric thickness, size, …) will be varied on new prototypes to optimize the design.

Additional solutions, such as using conductive ink, silicone, or silicone mix, can also be investigated. Additional evaluation criteria, design requirements, and improvements can be discussed during the work.

attached pdf document

Promotor, co-promotor, advisor : antoine.nonclercq@ulb.be, - , Marie Dawant

Research Unit : BEAMS - BIOMECHATRONICS

Description

Supervising staff

Antoine Nonclercq (antoine.nonclercq@ulb.be), Riëm El Tahry (riem.eltahry@saintluc.uclouvain.be) and Marie Dawant (marie.dawant@ulb.be)

Context

Epilepsy is a neurological disease affecting 50 million people worldwide associated with increased mortality, stigma, psychiatric co-morbidity, and high economic costs. The world health organization characterizes epileptic seizures as: “Seizure episodes are a result of excessive electrical discharges in a group of brain cells. Different parts of the brain can be the site of such discharges. Seizures can vary from the briefest lapses of attention or muscle jerks to severe and prolonged convulsions” (World Health Organization 2023). In the patients diagnosed with epilepsy (representing an active incidence of 4/8 people over 1000 (Brodie et al. 2012)), one-third do not respond to epileptic drugs or partially without controlling the seizures and are classified as refractory epileptics. Vagus nerve stimulation (VNS) is an adjunctive treatment for refractory epilepsy in patients who are unsuitable candidates for anti-epileptic drugs or resective surgery. VNS uses an implanted pulse generator that delivers trains of electrical pulses to the left cervical vagus nerve. Although widely used, two-thirds of these implanted patients present an insufficient response or an absence of response to VNS (Ben-Menachem 2002). The identification of biomarkers to assess VNS efficacy pre-operatively would be crucial to reduce the number of non-responders.

In this context, our department, in collaboration with the Institute of NeuroScience (IoNS) at the Cliniques Universitaires of UCLouvain is aiming to develop new ways to assess clinical response to VNS prior to device implantation. The analysis of the evoked response potential (ERP) presented in this project could offer new possibilities to assess VNS responsiveness.

P300 is the positive peak deflection appearing at 300 ms in an ERP, classically elicited using an “oddball paradigm”. The oddball paradigm consists of a series of stimuli, either visual or auditive, which are embedded target stimuli with a low presentation probability. The patient is asked to only recognize the stimuli, eliciting a brain response recorded by an electroencephalogram (EEG). Recently, P300 has been investigated as a biomarker in people implanted with VNS devices by various works. On the one hand, P300 amplitude has been shown to be smaller in VNS responders prior to therapy when the device is turned ON (Hödl et al. 2020). On the other hand, patients’ responses to VNS show an increase in P300 after therapy (> 18 months after implantation) when the device is turned ON (De Taeye et al. 2014).

Various pre-processing steps are applied to the raw recordings to extract “epochs” (timeframes of typically 1200 ms containing the patient’s electrical brain response to one stimulus) before averaging them to obtain the mean differential waveform.

ERP P300 analysis in epileptic patients implanted with VNS stimulating device is an emerging field in literature, although already widely used in neuroscience. Experimental design, recording parameters, post-processing, and metrics all influence to some extent the resulting waveform.

Work

Our group already developed a framework to evoke and record P300 during three experimental conditions: 1. “VNS OFF”: when the VNS is turned completely OFF, 2. “VNS Low”: when the VNS is turned ON, 3.” VNS Low”: only when the VNS is actively stimulating.

This research project aims to implement different metrics to determine how the P300, based on the current framework available at the department, differs in responders from non-responders. Beyond the amplitude and latency of the P300, brain connectivity analysis is an emerging tool based on graph theory in the analysis of P300. Already intensively used to evaluate how highly specialized brain regions communicate with each other; recent works have exploited its use in the scope of P300 ERP analysis in healthy subjects.

Major steps in this work include: - Familiarization with signal processing applied to evoked response potential and physiological background underlying ERP elicitation
- Familiarization with brain functional connectivity applied to evoked response potential and physiological background underlying ERP elicitation
- Exploring how the data processing parameters influence the P300 waveform in time-domain analysis - Implementing a framework for brain connectivity analysis using different association metrics - Analyzing the statistical differences between sets of P300 ERP in VNS epileptic responders and non-responders

References

Ben-Menachem, Elinor. 2002. “Vagus-Nerve Stimulation for the Treatment of Epilepsy.” Lancet Neurology. Lancet Publishing Group. https://doi.org/10.1016/S1474-4422(02)00220-X. Brodie, M J, S J E Barry, G A Bamagous, J D Norrie, and P Kwan. 2012. “Patterns of Treatment Response in Newly Diagnosed Epilepsy.” Hödl, S., S. Carrette, A. Meurs, E. Carrette, A. Mertens, S. Gadeyne, L. Goossens, et al. 2020. “Neurophysiological Investigations of Drug Resistant Epilepsy Patients Treated with Vagus Nerve Stimulation to Differentiate Responders from Non-Responders.” European Journal of Neurology 27 (7): 1178–89. https://doi.org/10.1111/ene.14270. Kabbara, Aya, Mohamad Khalil, Wassim El-Falou, Hassan Eid, and Mahmoud Hassan. 2016. “Functional Brain Connectivity as a New Feature for P300 Speller.” PLoS ONE 11 (1). https://doi.org/10.1371/journal.pone.0146282. Luck, Steven J. (Steven John). 2005. An Introduction to the Event-Related Potential Technique. Taeye, Leen De, Kristl Vonck, Marlies van Bochove, Paul Boon, Dirk Van Roost, Lies Mollet, Alfred Meurs, et al. 2014. “The P3 Event-Related Potential Is a Biomarker for the Efficacy of Vagus Nerve Stimulation in Patients with Epilepsy.” Neurotherapeutics 11 (3): 612–22. https://doi.org/10.1007/s13311-014-0272-3. World Health Organization. 2023. “Epilepsy.” Fact Sheet - Epilepsy . February 9, 2023.

attached pdf document

Promotor, co-promotor, advisor : jerome.dohet-eraly@ulb.be, Frank DUBOIS,

Research Unit : BEAMS-BIOMECHATRONICS

Description

Titre (français) : Analyse d’objets épais en microscopie par holographie numérique : aspects métrologiques.

Titre (anglais) : Analysis of thick objects in digital holographic microscopy : metrological aspects.

Promoteur : Jérôme Dohet-Eraly (Beams-BioMechatronics) ; contact : jerome.dohet-eraly@ulb.be Co-promoteur : Frank Dubois (Beams-BioMechatronics, frank.dubois@ulb.be)

Bref descriptif : La microscopie par holographie numérique (MHN) est une technologie particulièrement performante permettant d’extraire à partir des images enregistrées, en chaque point, non seulement l’intensité lumineuse, comme en imagerie classique, mais aussi la phase du champ optique émanant de l’échantillon, liée direction de propagation de la lumière. L’enregistrement de cette information complète confère de nombreux avantages à cette technologie, notamment, grâce à un traitement numérique, la remise au net automatique d’images pourtant enregistrées floues ainsi que l’imagerie quantitative de la phase optique. En microscopie en transmission, en première approximation, la phase optique est souvent considérée comme proportionnelle à l’épaisseur optique de l’échantillon. Cependant, pour les objets relativement épais, la validité de cette approximation doit être étudiée. C’est l’objectif de ce mémoire. Pour ce faire, trois axes principaux seront suivis : (1) l’étude de l’imagerie en MHN d’objets d’épaisseur variable ; (2) la mise au point d’une méthode permettant d’évaluer quantitativement les variations d’épaisseur de ces objets ; et (3) la validation expérimentale à l’aide d’un microscope fonctionnant en transmission et en réflexion. Les développements seront d’un intérêt majeur en ce qui concerne les aspects métrologiques de la MHN. Le mémoire couvrira les aspects théoriques, algorithmiques et expérimentaux.

Promotor, co-promotor, advisor : jean-francois.determe@ulb.be, François Horlin, Jean-François Determe

Research Unit : BEAMS-EE

Description

Developing an acquisition chain for real-time gait parameter estimation using high-frequency radars

Context

Recently, high-frequency radars have been shown to be effective, privacy-preserving and economic solutions to the problem of estimating over time human health parameters (breathing frequency, gait analysis, etc.).

Another more traditional and well-established solution for gait analysis is based on motion capture (MoCap) (using markers or markerless) as well as other approaches based on LIDAR (Light Detection and Ranging) sensors. The Kinect system is a notable example that partially relies on a camera and a LIDAR system that can be used for movement reconstruction. However, MoCap measurement setups are usually expensive and not as mobile as radar systems. Moreover, camera-based systems (MoCAP and Kinect) suffer from low illumination and may lead to privacy issues.

The goal of this Master’s thesis is to develop a robust radar-based gait measurement system that can work offline (providing raw measurements with optional pre-processing) or in real-time (providing a graphical user interface displaying the movement of the body as well as graphs of joint movements). The prospective student is expected to i) program a complete and documented acquisition chain using a high-end computer (endowed with a high-end CPU as well as a recent high-end consumer graphics card, such as an Nvidia RTX 3080) ii) determine to what extent this acquisition process can be ported in real-time to an embedded computer like the Jetson Nano or the newer and more powerful Jetson Orin Nano platform (which also comprise a CPU and a GPU, but slower than in the high-power computer) iii) develop a graphical visualization solution of the movement and the main gait parameter estimates iv) (optional) implement into the visualization solution the estimates provided by the third-party system that is the Kinect system.

Thus, the student should be interested in high-performance programming on single-CPU systems (in C and C++) and high-performance programming on GPUs (CUDA and/or OpenCL). A basic knowledge of digital signal processing is recommended but not mandatory. A basic knowledge of telecommunication and/or radar systems is an advantage.

Objectives and steps

• Get familiar with state-of-the-art radar signal processing algorithms and gait parameter extraction algorithms • Develop a first real-time-capable acquisition and pre-processing chain on a high-end computer • Determine if porting the acquisition chain to a Jetson Nano or a Jetson Orin Nano platform is possible and carry out this task if possible • Develop a graphical visualization solution

Contact person

Jean-François Determe, jean-francois.determe@ulb.be François Horlin, francois.horlin@ulb.be Solbosch campus, building U, level. 5, BEAMS-EE department

Promotor, co-promotor, advisor : jean-francois.determe@ulb.be, François Horlin, Jean-François Determe

Research Unit : BEAMS-EE

Description

Multiple-antenna, high-frequency radars for gait analysis

Context

Recently, high-frequency radars have been shown to be effective, privacy-preserving and economic solutions to the problem of estimating over time human health parameters (breathing frequency, gait analysis, etc.).

Another more traditional and well-established solution for gait analysis is based on motion capture (MoCap) (using markers or markerless) as well as other approaches based on LIDAR (Light Detection and Ranging) sensors. The Kinect system is a notable example that partially relies on a camera and a LIDAR system that can be used for movement reconstruction. However, MoCap measurement setups are usually expensive and not as mobile as radar systems. Moreover, camera-based systems (MoCAP and Kinect) suffer from low illumination and may lead to privacy issues.

Commercially available high-frequency radar systems often feature multiple antennas, thereby allowing for a clever combination of measurements on each antenna to improve signal-to-noise ratio (SNR). The multi-antenna front-end may also enable engineers to perform beamforming to better isolate joint movements: when using a mono-antenna radar, all movements are superimposed and their separation is based on expected movement patterns and algorithms distinguishing movements trajectories over time; having multiple antenna should allow us to create beams in software that preferentially target specific body parts (e.g., torso or hands). This is particularly useful as body parts have varying radar cross sections (RCSs) and the movement of body parts with high RCS may overshadow that of other parts with low RCS in comparison.

Objectives and steps

Get familiar with radar front-ends, state-of-the-art radar signal processing algorithms and gait parameter extraction algorithms • Write a state-of-the-art about multiple-antenna, high-frequency radar systems used in biomedical applications identical or similar to gait analysis • Implement and compare these solutions using radar hardware available at OPERA-WCG and BEAMS-EE to quantify to what extent multiple-antenna front-ends improve upon mono-antenna ones when paired with appropriate signal processing algorithms (validation of joint movement reconstruction shall be carried out using an independent Kinect measurement system) • Propose improvements to existing algorithms for the specific case of gait parameter estimation

Contact person

Jean-François Determe, jean-francois.determe@ulb.be François Horlin, francois.horlin@ulb.be Solbosch campus, building U, level. 5, BEAMS-EE department

Promotor, co-promotor, advisor : gilles.bruylants@ulb.be, - , Victor Lepeintre

Research Unit : EMNS

Description

Design of nucleic acids coated nanomaterials for RNA delivery in specific organs.

The project aims to solve an open issue in a certain domain of application.

Context

Chemotherapy drugs such as cyclophosphamide are highly gonadotoxic and lead to ovarian reserve depletion, causing infertility and thus strongly affecting the quality of life in young patients. The EMNS laboratory works in collaboration with the Research Laboratory of Human Reproduction (LRRH) and the Laboratoire d'Histologie générale, Neuroanatomie et Neuropathologie (LHNN) from the Erasme hospital to develop new RNA Delivery Systems based on gold nanoparticles. MiRNAs are small non-coding molecules, which offer new promising approaches in cancer therapy but also in fertility preservation. However, these miRNA have to be delivered to the right organ, which requires the development of new targeted delivery systems.

Objective

The main objective of the project is to develop a new vector for nucleic acids delivery in selected organs based on Gold nanoparticles (GNPs) are promising vectors: gold nano spheres and gold nano rods. In this study, we propose a new approach of GNPs surface functionalization based on calix[4]arenes which can be used to control the anchoring of synthetic miRNA nucleotides and/or of other ligands (peptides) for organ specific targeting (brain or avory depending on the application).

Methods

Particles will be synthesized and functionalized with a first layer of calixarenes. Different chemistries will be tested to attached the nucleic acids strands and a targeting ligands to these particles with defined densities.

Contact person

For more information please contact : Victor.lepeintre@ulb.be

references

Retout, M., Cornelio, B., Bruylants, G., & Jabin, I. (2022). Bifunctional Calix[4]arene- Coated Gold Nanoparticles for Orthogonal Conjugation. Langmuir, 38, 9301-9309. Retout, M., Blond, P., Jabin, I., & Bruylants, G. (2021). Ultrastable PEGylated Calixarene- Coated Gold Nanoparticles with a Tunable Bioconjugation Density for Biosensing Applications. Bioconjugate chemistry, 32(2), 290-300.

Promotor, co-promotor, advisor : gilles.bruylants@ulb.be, - , Alessia Fantoni

Research Unit : ENGINEERING OF MOLECULAR NANOSYSTEMS

Description

Development of Lateral Flow Assays based on Organic Molecular Receptors

Context

Lateral flow assays (LFAs), as the COVID-19 rapid self-test, are a critical tool in the field of in vitro diagnostics (IVD). These simple and rapid tests play a pivotal role in the diagnosis and management of various diseases, providing quick and accurate results without the need for complex laboratory equipment or extensive sample preparation. LFAs have gained widespread recognition and adoption due to their simplicity, portability, cost-effectiveness, and rapid turnaround time, making them invaluable in a variety of healthcare settings. These tests are usually based on the use of gold nanoparticles (AuNPs) functionalized with an antibody (Ab) that provides specificity to the test thanks to its selective binding to its antigen. However, antibodies are difficult to manipulate due to their poor stability in solution, they are known to induce reproducibility issues and are highly expensive. Organic molecular receptors do not present these drawbacks, however there are usually poorly soluble and therefore cannot be used to functionalize the AuNPs directly in water. In this context, the EMNS laboratory aims at developing a general methodology to extend the field of LFAs to molecular organic receptors by incorporating them in amphiphilic layer grafted onto the particles.

Objective

The main objective will be the design of the surfactant molecules composing the amphiphilic layer: anchoring group, size and nature of the lipophilic and hydrophilic parts of the molecules, loading capacity. A proof of concept will be developed based on organic receptors already known in the EMNS laboratory and tested for their binding properties in aqueous environments.

Contact person

For more information please contact : Alessia.Fantoni@ulb.be

references

[Gosselin, B., Retout, M., Dutour, R., Troian Gautier, L., Bevernaegie, R., Herens, S., Lefèvre, P., Denis, O., Bruylants, G., & Jabin, I. (2022). Ultrastable Silver Nanoparticles for Rapid Serology Detection of Anti-SARS-CoV-2 Immunoglobulins G. Analytical chemistry, 94, 7383-7390. doi:10.1021/acs.analchem.2c00870]

Promotor, co-promotor, advisor : hennie.valkenier@ulb.be, - ,

Research Unit : ENGINEERING OF MOLECULAR NANOSYSTEMS

Description

Project title

Transport of organic anions across lipid membranes

Context

Transport of ions across membranes is an important process in biology. Specialized proteins embedded within the cellular membranes take care of this. In our laboratory, we seek to mimic the action of these proteins with synthetic molecules that can transport ions across membranes.

Objective

Many important molecules in biology have anionic phosphate or carboxylate groups and could thus be considered ‘organic anions’. The aim of this project is to study the impact of the organic group on the transmembrane transport of these organic anions using synthetic transporters.

Methods

The project will consist of: • Preparation of liposomes as membrane models • Incorporation of synthetic transporters in the membranes of these liposomes • Use of these liposomes to study the transmembrane transport process of different organic anions using fluorescence spectroscopy and an ion selective electrode • Study the effect of pH on the transport and on diffusion • Analysis of the data by fitting the curves • Comparison of the results obtained for different anions and different transporters

Prerequisites

• Organic Chemistry
• Spectroscopy

Contact person

For more information please contact : hennie.valkenier@ulb.be

Promotor, co-promotor, advisor : adrian.munteanu@vub.be, Nastaran Nourbakhsh Kaashki,

Research Unit : ETRO

Description

Object Detection on Low-cost Edge Devices

Object detection is a computer vision technique for locating instances of objects in images or videos. Although this area has attained great progress, it is still a challenging topic when it comes to embedded devices. During this project, the performance of state-of-the-art object detection methods will be evaluated on low-cost Edge devices, such as Nvidia Jetson Nano, Google Coral, NXP iMX8M Plus and so forth.

Background

• Programming skills (Python/C++)
• Experience with computer vision and image processing techniques
• Experience with deep-learning-based methods is a plus.
• The student must sign an NDA before starting the project.

Contact person

If you are interested, please send your resume and transcript to nknourba@etrovub.be (Dr. Nastaran Nourbakhsh), and adrian.munteanu@vub.be (Prof. Adrian Munteanu)

Promotor, co-promotor, advisor : lesley.de.cruz@vub.be, - , Andrei Covaci

Research Unit : ETRO

Description

Urban thermal comfort modelling with deep learning

Context

When considering the impact of meteorological conditions (such as heat waves) on human health, it is not enough to only look at the individual meteorological variables. It is often the combination of these meteorological variables with the physical factors surrounding a person that will determine the thermal comfort that this person feels. e.g., the perceived higher temperature and thermal discomfort due to standing in the clear sun during summer or perceived lower temperature due to the wind blowing during the winter (wind chill).

To quantify thermal comfort, certain indices, such as the Universal Thermal Climate Index (UTCI) or the Physiological Equivalent Temperature (PET) score, were proposed [1]. With these indices (both expressed in °C), we can easily determine whether a person is subject to heat stress or cold stress. Prior research has already shown that there is a direct link between these indices and excess mortality [2]. It is, therefore, important to understand how these indices will evolve, especially in the context of climate change, the intensification of heat waves and increasing urbanisation.

These indices are computed by computing a human body energy balance model between the person and the surrounding physical environment. Especially the impact of radiation tends to be quite involved, as it is influenced by many environmental factors. This causes the model to be very complex but also computationally heavy. It is, therefore, interesting to look at alternative methods to obtain these thermal comfort indices at a lower computational cost.

With this master's thesis, the aim would be to investigate using machine learning models to emulate thermal comfort scores, such as the UTCI or the PET score [3,4]. Here, you will train and compare machine learning models by using a variety of meteorological variables (temperature, wind speed …) and environmental factors (such as Sky view factor, land cover fractions ...) as input variables and targeting the corresponding thermal comfort scores. In particular, we will use the VLINDER network for the meteorological variables. This network consists of 70+ standardised weather stations placed in varying environment types.

The project is done in collaboration with the Royal Meteorological Institute of Belgium and the Atmospheric Physics group of Ghent University.

Objective

*) Literature study on thermal comfort scores and the usage of machine learning for emulation.

*) Constructing a working machine learning model that outputs the desired thermal comfort score.

*) Comparing and evaluating different types of machine learning models.

*) Calculating the thermal comfort scores for an entire city during an interesting meteorological event (e.g., a heatwave).

Methods

*) Data analysis of meteorological observations *) Software to compute thermal heat indices *) Machine learning and deep learning

Prerequisite

Programming background (e.g., Python)

Background in machine learning

Experience with machine learning frameworks (e.g., TensorFlow or PyTorch)

Strong interest in weather and climate.

Contact person

For more information please contact : lesley.de.cruz@vub.be

references

[1] Zare, Sajad, et al. "Comparing Universal Thermal Climate Index (UTCI) with selected thermal indices/environmental parameters during 12 months of the year." Weather and climate extremes 19 (2018): 49-57.

[2] Di Napoli, Claudia, Florian Pappenberger, and Hannah L. Cloke. "Assessing heat-related health risk in Europe via the Universal Thermal Climate Index (UTCI)." International journal of biometeorology 62 (2018): 1155-1165.

[3] Ketterer, C., & Matzarakis, A. (2016). Mapping the Physiologically Equivalent Temperature in urban areas using artificial neural network. Landscape and Urban Planning, 150, 1-9.

[4] Philippopoulos, Kostas, et al. "A novel artificial neural network methodology to produce high-resolution bioclimatic maps using Earth Observation data: A case study for Cyprus." Science of The Total Environment (2023): 164734.

Promotor, co-promotor, advisor : nikolaos.deligiannis@vub.be, Hichem Sahli , Soha Mahdi - sohasadat.mahdi@vub.be

Research Unit : ETRO

Description

Project title

Automated Icd Classification Using Nlp And Deep Learning Techniques: A Comparative Study On Mimic-Iii Dataset

Context

The International Classification of Diseases (ICD) is a system used to classify diseases and medical procedures. Accurate ICD coding is essential for billing, epidemiological studies, and clinical decision-making. With the advent of electronic health records (EHRs), there is a growing interest in using natural language processing (NLP) and deep learning (DL) techniques to automate the ICD coding process. This study aims to compare the performance of different DL and NLP techniques for ICD classification using the MIMIC-III (Medical Information Mart for Intensive Care III) dataset1,2,3,4,5,6.

Objective

Objectives: • To compare the performance of different DL and NLP techniques (e.g., convolutional neural networks, recurrent neural networks, transformers) for ICD classification using MIMIC-III dataset. • To evaluate the impact of different pre-processing and feature engineering techniques on the performance of the DL models. • To investigate the interpretability and explainability of the DL models for ICD classification.

Methods

Methodology: 1. The study will be conducted in the following steps: 2. Data Preprocessing: The MIMIC-III dataset will be preprocessed to extract relevant text for NLP analysis. 3. Text Preprocessing: Different text pre-processing techniques (e.g., tokenization, stemming, stop word removal) will be applied to prepare the text for NLP analysis. 4. Feature Engineering: Different feature engineering techniques (e.g., word embeddings, contextual embeddings) will be applied to represent the text for DL models. 5. DL Model Selection and Training: Several DL models (e.g., convolutional neural networks, recurrent neural networks, transformers) will be trained using the preprocessed data and selected features. 6. Model Evaluation: The performance of the DL models will be evaluated using standard metrics (e.g., accuracy, F1-score) and compared to identify the best-performing technique. 7. Interpretability and Explainability: The selected DL models will be investigated for interpretability and explainability to understand the decision-making process of the models.

Expected Outcomes: The study is expected to produce the following outcomes: • A comparison of different DL for NLP techniques for ICD classification using MIMIC-III dataset4. • An evaluation of the impact of different pre-processing and feature engineering techniques on the performance of the DL models. • A set of recommendations for the selection of the most appropriate DL for NLP technique for ICD classification based on the dataset characteristics. • A deeper understanding of the interpretability and explainability of the DL models for ICD classification.

Prerequisite

• Strong programming skills are required for this project, particularly in Python. • Experience with deep learning frameworks, especially PyTorch, is a plus. • Familiarity with natural language processing is also desirable. • Good communication skills and the ability to document code and results are helpful.

Contact person

For more information please contact : Soha Mahdi sohasadat.mahdi@vub.be

references

1. C. Yan, X. Fu, X. Liu, Y. Zhang, Y. Gao, J. Wu, and Q. Li, “A survey of automated International Classification of Diseases coding: development, challenges, and applications,” Intelligent Medicine, vol. 2, pp. 161–173, Aug. 2022.
2. F. Teng, Y. Liu, T. Li, Y. Zhang, S. Li, and Y. Zhao, “A review on deep neural networks for ICD coding,” IEEE Transactions on Knowledge and Data Engineering, pp. 1–1, 2022.
3. J. Xu, X. Xi, J. Chen, V. S. Sheng, J. Ma, and Z. Cui, “A Survey of Deep Learning for Electronic Health Records,” Applied Sciences, vol. 12, p. 11709, Nov. 2022.
4. A. E. Johnson, T. J. Pollard, L. Shen, L.-w. H. Lehman, M. Feng, M. Ghassemi, B. Moody, P. Szolovits, L. Anthony Celi, and R. G. Mark, “MIMIC-III, a freely accessible critical care database,” Scientific Data, vol. 3, p. 160035, May 2016.
5. J.Mullenbach,S.Wiegreffe,J.Duke,J.Sun,andJ.Eisenstein,“Explain- able Prediction of Medical Codes from Clinical Text,” in Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long Papers), (New Orleans, Louisiana), pp. 1101–1111, Association for Computational Linguistics, 2018.
6. Z. Zhang, J. Liu, and N. Razavian, “BERT-XML: Large Scale Auto- mated ICD Coding Using BERT Pretraining,” in Proceedings of the 3rd Clinical Natural Language Processing Workshop, (Online), pp. 24–34, Association for Computational Linguistics, 2020.

Promotor, co-promotor, advisor : bruno.da.silva@vub.be, Johan Stiens ,

Research Unit : ETRO (VUB)

Description

Project title

Remote Photoplethysmography (rPPG) monitoring

Context

Photoplethysmography (PPG) is a non-invasive method for detecting cardiovascular pulse waves that travel through the human body. It is based on the determination of the optical properties of vascular tissue by means of a probe, which consists of an LED-PD configuration (Light Emission Diode – Photodetector). Analog techniques are commonly used to determine the intensity of the light received by the photodetector. In these, the intensity of the light reaching the PD is measured and the variations, caused by changes in blood volume, are amplified, filtered and recorded as a voltage signal.

Remote PPG is the same principle as traditional PPG measurements but it is a contactless measurement. It measures the variance of red, green, and blue light reflection changes from the skin, as the contrast between specular reflection and diffused reflection. Specular reflection is the pure light reflection from the skin. Diffused reflection is the reflection that remains from the absorption and scattering in skin tissue, which varies by blood volume changes.

Objective

The main objective of this thesis is the measurement of raw PPG signals using rPPG. The signal quality obtained should be compared with traditional PPG systems. The student must compare and evaluate the signals obtained in terms of signal resolution, SNR (Signal to Noise Ratio), SQI (Signal Quality Index), system complexity and power consumption. Simple Heart Rate and SpO2 algorithms can be implemented to demonstrate the system application.

Prerequisite

• Interested in physiological sensing • Basic knowledge of signal processing • Programming experience (python, C/C++ and/or Matlab)

Contact person

For more information please contact : bruno.da.silva@vub.be

References

Yang, Cheng, Gene Cheung, and Vladimir Stankovic. "Estimating heart rate and rhythm via 3D motion tracking in depth video." IEEE Transactions on Multimedia 19.7 (2017): 1625-1636.

Lai, Marco, et al. "Perfusion monitoring by contactless photoplethy smography imaging." 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019). IEEE, 2019.

attached pdf document

Promotor, co-promotor, advisor : bruno.da.silva@vub.be, - ,

Research Unit : ETRO (VUB)

Description

Project title

FPGAs for Biomedical Applications

Context

In the last year our research group has develop an open source educational kit based on photoplethysmography (PPG) called PPG EduKit [1]. The PPG technology is the same that you can find in pulse oximeters or smartwatches, and allow to retrieve your heart rate or your blood oxygen level among others. The algorithms to retrieve these physiological parameters are running on microcontrollers or multicore devices using the PPG Edukit, which is basically an Arduino shield.

Objective

The goal of this thesis is to perform these computations on an FPGA. The Pynq board is a perfect platform for that since it is compatible with Arduino shields, it has a framework which uses Python while includes a system-on-chip FPGA as a main core. The goal of this project is to adapt the existing code [3] to run on the FPGA, or at least, be integrated in the Python framework.

Prerequisite

• Interest in biomedical signal processing and FPGAs
• Experience in C/C++ is recommendable

Contact person

For more information please contact : bruno.da.silva@vub.be

References

[1] Solé Morillo, Ángel, et al. "PPG EduKit: An Adjustable Photoplethysmography Evaluation System for Educational Activities." Sensors 22.4 (2022): 1389. [2] http://www.pynq.io/ [3] https://gitlab.com/etrovub/wearables/publications/PPG-EduKit

attached pdf document

Promotor, co-promotor, advisor : bruno.da.silva@vub.be, - ,

Research Unit : ETRO (VUB)

Description

Project title

Evaluation of Low-Power Strategies for Biomedical Wearable Devices

Context

Wearable devices are power-constrained embedded devices. Such a power limitation becomes critical when considering front ends composed of arrays of sensors. The additional computational power demand quickly drains the battery level if an efficient power management is not considered. Nowadays microcontrollers offer different low-power modes, which can be exploited towards power efficiency and longer battery life.

Objective

The objective of this master thesis is to evaluate the available low-power modes of microcontrollers to be exploited towards power efficient biomedical wearable devices. Several realistic applications in the biomedical domain will be used for this evaluation. The ultimate goal is to propose general guidelines to exploit power modes for biomedical devices.

Prerequisite

• Interested in embedded systems, wearables and/or hardware accelerators.
• Experience with Python, C/C++ and/or Matlab programming languages.

Contact person

For more information please contact : bruno.da.silva@vub.be

attached pdf document

Promotor, co-promotor, advisor : bruno.da.silva@vub.be, - ,

Research Unit : ETRO (VUB)

Description

Project title

Remote Sensing Using Sensor Arrays

Context

Sensors arrays are been widely adopted for multiple applications, from arrays of cameras on smartphones, non-invasive sensor arrays for patient monitoring [1] or bringing new applications [2]. The proper combination of the gathered data is, however, not fully exploited. Moreover, the use of AI to exploit the acquired data from sensor arrays is not widely adopted (yet).

Objective

This thesis intends to evaluate existing data fusion techniques, combined with AI, for homogeneous and heterogeneous sensor arrays. Different applications related to noninvasive physiological monitoring and remote sensing will be used to evaluate and exploit these techniques.

Kind of Work: * Literature study of existing solutions and their limitations. * Evaluation of the most interesting solutions exploiting the additional data from the sensor array * Interface the sensor array and embed the data fusion

Prerequisites

• Interest in embedded systems and AI.
• Experience with Python and/or C/C++.

Contact person

For more information please contact : bruno.da.silva@vub.be

References

[1] Lin, Feng, et al. "Smart insole: A wearable sensor device for unobtrusive gait monitoring in daily life." IEEE Transactions on Industrial Informatics 12.6 (2016): 2281-2291.

[2] da Silva, Bruno, et al. "A Multimode SoC FPGA-based acoustic camera for wireless sensor networks." 2018 13th International Symposium on Reconfigurable Communication-centric Systemson- Chip (ReCoSoC). IEEE, 2018.

attached pdf document

Promotor, co-promotor, advisor : denis.terwagne@ulb.be, - , Denis Terwagne

Research Unit : FRUGAL LAB / FABLAB ULB

Description

Unconventional Water Ressources : Optimizing Fog Nets

This project aims to develop unconventional water harvesting systems such as fog nets to harvest atmospheric water in water-scarce regions of the world.

Context

As scarcity of water is expected to intensify with global warming, unconventional water sources such as advective fogs may become essential [1]. In numerous arid regions, nets are used to harvest such water droplets. However, many current fog nets are either not durable or expensive, and have poor performances for short time or low intensity fog events.

A crucial societal challenge is to produce scalable, low-cost fog nets that are efficient and durable.

To solve this societal problem, we strive to do so in a frugal, low-tech way [2,3]. Our approach is to connect to the people on the ground who are living the challenge [4], to use frugality as a creative constraint, to ask nature for solutions [5] that we seek to understand fundamentally from a physical perspective. All of this opens the door to innovative solutions that are fostered by digital fabrication technologies and the interdisciplinary community of the Fab Lab ULB. These solutions developed in the lab will eventually be tested and deployed in the field.

This project will be carried out in the Frugal Lab research facility and the Fab Lab ULB in Usquare, within an energetic and interdisciplinary community of researchers, students, technicians and citizens.

Objective

The objective of this Master Thesis will be to design and optimize fog nets based on the latest experimental measurements and design rules established in the laboratory.

In particular, we will focus on the geometry of structures to generate air flows conducive to water collection.

Ultimately, prototypes might be deployed on fiel in Morocco with NGO Dar Si Hmad [5] with whom we collaborate.

Methods

In this Master Thesis, the master student will use digital fabrication tools to design the nets, will use experimental test benches for net efficiency measurements and will interact with the interdisciplinary community of the Frugal Lab and the FabLab ULB mobilized around the deployment of this project.

Prerequisite

• An interest
  • in digital fabrication and hands-on experiments,
  • in working in interdisciplinary and fablab environment.
  • in solving societal challenges

Contact person

For more information please contact : Denis.Terwagne@ulb.be

references

• [1] UN-Water Analytical Brief on Unconventional Water Resources
• [2] Frugal Science
• [3] Low-tech, wikipedia
• [4] NGO Dar Si Hmad, Morocco
• [5] Ask Nature website

Promotor, co-promotor, advisor : christine.decaestecker@ulb.be, - , Adrien.Foucart@ulb.be, Arthur.Elskens@ulb.be

Research Unit : LISA

Description

Project title

In medical image analysis, it is often useful to combine information from several imaging modalities, such as in-vivo CT and ex-vivo microscopy. Interpretation of this information requires good colocalization of the corresponding regions of the organ in the different modalities. Image registration consists of finding the best image transformation to create a correspondence between the regions of a reference image and the corresponding regions of a target image.

Context

This topic is proposed within the framework of the ProTherWal project, which aims to develop and better understand proton therapy. It is funded by the Walloon Region and is conducted in collaboration with laboratories from several French-speaking universities in Belgium. The data are provided by the Centre for Microscopy and Molecular Imaging (CMMI) of the Biopark of Gosselies. They include in-vivo µCT images of mice, ex-vivo µCT images of liver lobes extracted from mice, and high resolution images of whole tissue slides.

Objective

The objective is to study and implement image segmentation and/or registration techniques that can facilitate the different steps of the in-vivo / ex-vivo registration process. They may relate to any of the following steps:

• Registration of the in-vivo µCT image to the ex-vivo µCT image
• Segmentation of the liver lobes in the in-vivo µCT
• Registration of the ex-vivo µCT to whole tissue slide images
• Segmentation of regions of interest in whole tissue slide images

The exact specifications of the thesis objectives will be determined with the student at the beginning of the thesis.

Prerequisite

• Python
• Image processing techniques (INFO-H-500)
• Interest in pattern recognition and image analysis (cf INFO-H-501)

Contact person

For more information please contact : Adrien Foucart - Adrien.Foucart@ulb.be, Arthur Elskens - Arthur.Elskens@ulb.be, Christine Decaestecker - Christine.Decaestecker@ulb.be.

references

Oliveira, 2012 - Medical image registration: a review Bandi, 2017 - Comparison of different methods for tissue segmentation in histopathological whole-slide images Kiemen, 2022 - CODA: quantitative 3D reconstruction of large tissues at cellular resolution Goubran, 2015 - Registration of in-vivo to ex-vivo MRI of surgically resected specimens: A pipeline for histology to in-vivo registration

Promotor, co-promotor, advisor : olivier.debeir@ulb.be, agiotis@tuc.gr,

Research Unit : LISA

Description

Study of the dynamics of co-current flow of oil and water in porous subsurface by image processing

Context

The project is done in collaboration with Pr Andreas Giotis of the School of Mineral Resources Engineering Technical University of Crete.

A series of image sequences have been taken using a special microscopic setup to study the displacement of droplets (ganglias) on a substrate.

Different locomotion patterns related to experimental settings can be qualitatively observed.

Objective

A first exploratory approach will try to identify different image processing approaches (object based of pixels based) to extract physical features of interest.

The best methods will then be made as automatic as possible to process numerous dataset to get statistically significant measures.

see also [Chevalier2015]

Prerequisite

• image processing

• Python

Contact person

For more information please contact : olivier.debeir@ulb.be, andreas giotis agiotis@tuc.gr

reference

Chevalier2015

Promotor, co-promotor, advisor : olivier.debeir@ulb.be, - , toshna.manohar.panjwani@ulb.be

Research Unit : LISA

Description

Determining the impact of probe and operator-dependent factors on prostate visualization and overall quality of micro-ultrasound images

Microultrasound (MicroUS) is a novel ultrasound-based imaging method that provides a 300% improvement in image resolution in comparison to multi-parametric MRI for prostate cancer screening. MicroUS scanners work at 29MHz with an angled side-fire transducer that reduces wave penetration depth, while providing real-time transrectal imaging similar to transrectal ultrasound (TRUS), but with higher image quality and detection of focal lesions that are generally undetected with TRUS while taking prostate size into consideration. MicroUS is standardized with the Prostate Risk Identification using Micro-Ultrasound (PRIMUS) system, which determines risk stratification, biopsy technique and the course of treatment suitable to the patient. Targeted microUS biopsies are more accurate, safe, quick and convenient for the physician as well as the patient than other biopsy methods. (Gurwin et al., 2022; Laurence Klotz, 2020; Panzone et al., 2022)

Like other ultrasound-based modalities, microUS also uses a handheld transducer. This makes it easy to visualize the complete prostate from the peripheral zone to the anterior including the transition zone. During examination, the side-fire transducer is moved and angled to view the different zones and identify any lesions in ducts that appear as hyper-echoic areas on the image. (Ghai et al., 2016; Luger, 2019)

This process is highly-operator dependent, especially in terms of their skill and experience, transducer positioning and probe pressure applied during examination. This affects the reproducibility of the test and adds ambiguity. The aim is to understand changes in prostate visualization and overall image quality with respect to probe pressure and angle using a phantom that mimics prostate and its surrounding organs along with abnormalities such as lesions and calcifications of the ducts.

Context

The project is done in collaboration with the radiology department of CHIREC - Hôpital Delta.

Prerequisite

• Python
• Image Processing

Contact person

For more information please contact : toshna.manohar.panjwani@ulb.be , olivier.debeir@ulb.be

Promotor, co-promotor, advisor : olivier.debeir@ulb.be, pierre.eisendrath@stpierre-bru.be,

Research Unit : LISA

Description

Endoscopic video sequence automatic annotation

An Esophagogastroduodenoscopy is a very common procedure, it consists in exploring the upper gastro-intestinal tract of the patient with an endoscope.

The operator will visually assess the state of various sites of the upper tract to pose a diagnostic.

One problem is to assess the quality and the completeness of the realised exam.

The assessment is based on the visual quality of the images taken and also on the validation of all the visual sites to be visited.

The aim of the project is to continue a previous work that developed the hardware to enable the video recording of the endoscopic exam sequence by adding temporal sequence analysis.

Context

The project is done in collaboration with Dr Eisendrath of St-Pierre hospital.

Prerequisite

• Python
• Linux (acquisition system based on a Raspberry pi4)

Contact persons

For more information please contact : pierre.eisendrath@stpierre-bru.be, olivier.debeir@ulb.be

attached pdf document

Promotor, co-promotor, advisor : olivier.debeir@ulb.be, nicolas.arribard@ulb.be,

Research Unit : LISA

Description

Cardiac fiber orientation extraction from high resolution CT-SCAN

An exceptional series of high resolution CT-scan of pathological hearts has been acquired.

The objective of the project is to build a 3D distribution of the cardiac muscle orientation (tractography), from these 3D high-resolution micro-CT volumes.

Usually tractography is done using MRI acquisition, however, because the study material is anatomical pieces, 3D CT has been chosen. The work will then focus on developing the technique for this specific type of images.

Once the fiber tensor identified, the anatomical fiber angle (as described in [Straatman21] will be computed and compared between different pathological groups.

Context

The work is done in collaboration with Dr Arribard of the cardiology department of Erasme hospital.

Prerequisite

• Python
• Image processing

Contact person

For more information please contact : nicolas.arribard@ulb.be, olivier.debeir@ulb.be

references

Straatman21

Promotor, co-promotor, advisor : olivier.debeir@ulb.be, kevin.brouboni@hubruxelles.be, Thomas Giot

Research Unit : LISA

Description

Background

Medical image segmentation is a crucial step in many clinical applications, including the body composition analysis (BCA) in radiology for prognosis purposes or in radiation therapy necessary for treatment planning.

Deep learning (DL) has shown remarkable success in medical image segmentation due to its ability to learn complex features from large datasets while being fast and accurate. However, with the growing number of DL-based segmentation algorithms [1,2], it becomes imperative to evaluate and compare their performance to determine their effectiveness in different clinical scenarios.

Goals

1. Conduct a comprehensive literature review on deep learning-based medical image segmentation algorithms.

2. Implement/improve an in-house model and evaluate selected algorithms on a dedicated dataset, including CT and anatomical structures associated.

3. Quantitatively compare the performance of different algorithms using metrics such as Dice similarity coefficient, Jaccard index and BCA metrics.

Prerequisites

• Proficiency in programming languages such as Python and deep learning libraries such as TensorFlow or PyTorch.

• Ability to critically analyze and interpret research papers related to medical image segmentation.

Contact person

For more information please contact : olivier.debeir@ulb.be, kevin.brouboni@hubruxelles.be

references

[1] Wasserthal, Jakob, et al. "TotalSegmentator: robust segmentation of 104 anatomical structures in CT images." arXiv preprint arXiv:2208.05868 (2022).

[2] Sundar, Lalith Kumar Shiyam, et al. "Fully Automated, Semantic Segmentation of Whole-Body 18F-FDG PET/CT Images Based on Data-Centric Artificial Intelligence." Journal of Nuclear Medicine 63.12 (2022): 1941-1948.

Promotor, co-promotor, advisor : olivier.debeir@ulb.be, - , toshna.manohar.panjwani@ulb.be

Research Unit : LISA

Description

Frame-by-frame zonal mapping of prostate in micro-ultrasound images.

Context

Over the last few years, PCa screening has taken an ‘MRI-first’ approach. Multi-parametric MRI (mpMRI) with PI-RADS (Prostate Imaging Reporting and Data System) is routinely used by clinicians as a risk stratification tool in patients with elevated PSA serum. PI-RADS is a scoring system that that focuses on the peripheral and transition zone of the prostate to predict the probability of clinically significant cancer based on T2-weighted(T2W), Diffusion weighted imaging (DWI) and dynamic contrast enhancement (DCE) findings. mpMRI images are also used for mapping lesions for transrectal ultrasound (TRUS)-based targeted biopsy and more recently with micro-ultrasound (microUS).(Gurwin et al., 2022; Panzone et al., 2022)

MicroUS is a novel ultrasound-based imaging method that provides a 300% improvement in image resolution in comparison to mpMRI for prostate cancer screening. The side-fire transducer of microUS works at 29MHz and make it possible to view the cellular and ductal anatomy from the peripheral zone to the anterior including the transition zone. Focal lesions that are generally undetected with TRUS and mpMRI, even in enlarged prostates can be seen as hyper-echoic areas on the image. MicroUS is standardized with the Prostate Risk Identification using Micro-Ultrasound (PRIMUS) system, which determines risk stratification, biopsy technique and the course of treatment suitable to the patient. Overall, microUS with PRIMUS offers a safe, quick, reliable and inexpensive system to screen for prostate cancer and also perform targeted biopsies across all zones of the prostate, irrespective of the size in a clinical setting.(Ghai et al., 2016; Klotz et al., 2021; Laurence Klotz, 2020; Luger, 2019)

Objective

The aim of the current study would be to map the different zones of prostate across a multi-frame microUS DICOM acquired during screening. Computer aided detection (CADe) has been utilized in mpMRI before to help visualize lesions more accurately in peripheral zone. A similar approach to microUS using texture-based features and anatomical segmentation from MRI as an additional input to map and segment the zones of prostate and the lesions in those zones can ease the localization of targets for biopsy. (Ashouri et al., 2023; Greer et al., 2018; Liu et al., 2016)

Prerequisite

• Python

• Image processing

Contact person

For more information please contact : toshna.manohar.panjwani@ulb.be , olivier.debeir@ulb.be

Promotor, co-promotor, advisor : olivier.debeir@ulb.be, ayse.betul.oktay@ulb.be,

Research Unit : LISA

Description

Stress Recognition with Fusion of Multi-Modal Sensor Data

Background

Several studies have been performed on physiological signals collected with wearable devices (such as Empatica E4 wristband) [1,2].

Electrodermal activity, heart rate, skin temperature, and blood volume pulse are the most commonly used physiological data. There are also studies for stress recognition from facial images [3].

Objective

The objective of this project is to detect stress with signals of E4 sensor and facial images. Several data fusion strategies will be investigated on an open dataset that includes data of 25 children playing exergames for physiotherapy.

Prerequisites

• Python

• Signal and Image Processing

• Deep and Machine Learning

Contact person

For more information please contact : ayse.betul.oktay@ulb.be and olivier.debeir@ulb.be

references

[1] Chandra, V., Priyarup, A., Sethia, D. (2021). Comparative Study of Physiological Signals from Empatica E4 Wristband for Stress Classification. In: Singh, M., Tyagi, V., Gupta, P.K., Flusser, J., Ören, T., Sonawane, V.R. (eds) Advances in Computing and Data Sciences. Ihttps://doi.org/10.1007/978-3-030-88244-0_21

[2] Kyamakya K, Al-Machot F, Haj Mosa A, Bouchachia H, Chedjou JC, Bagula A. Emotion and Stress Recognition Related Sensors and Machine Learning Technologies. Sensors (Basel). 2021 Mar 24;21(7):2273. doi: 10.3390/s21072273. PMID: 33804987; PMCID: PMC8037255.

[3] Jeon T, Bae HB, Lee Y, Jang S, Lee S. Deep-Learning-Based Stress Recognition with Spatial-Temporal Facial Information. Sensors. 2021; 21(22):7498. https://doi.org/10.3390/s21227498

Promotor, co-promotor, advisor : olivier.debeir@ulb.be, Nicolas.Pauly@ulb.be, Younes Jourani@hubruxelles.be

Research Unit : LISA & MÉTROLOGIE NUCLÉAIRE - HUB

Description

DIR implementation for contour propagation in H&N adaptive RT

Background

The clinical workflow for patients in radiotherapy involves several steps, such as acquisition of multi- modal imaging (CT for treatment planning, MRI and PET-CT), delineation of targets and organs at risk (OAR), treatment planning and delivery. However, for some specific tuour sites, such as head and neck (H&N) patients, the workflow can experience some adjustments. This is due to anatomical changes during the treatment, which often requires contour adaptation and replanning [1-4].

The delineation process in H&N is time consuming due to the number of OAR at the target proximity. For this reason, many commercial softwares have developed tools to help and speed up this step in the workflow. Deformable image registration (DIR) is widely applied for contour propagation between CTs [5, 6]. However, it remains on the competence of the clinical physicists to implement and validate such workflows.

Deep learning is also an option for this subject with the aim to compare both approaches. #### Objective

Here the goal

Goals

The purpose of this work is to implement and validate a clinical workflow for contour propagation with DIR in MIM software based on 24 H&N patients that underwent adaptive radiotherapy.

Prerequisite

• Programming skills

Contact person

For more information please contact : *olivier.debeir@ulb.be, nicolas.pauly@ulb.be, Sara Poeta (sara.poeta@bordet.be), Younes Jourani (younes.jourani@hubruxelles.be), Kevin Brou Boni (kevin.brouboni@hubruxelles.be) *

references

[1] Schwartz D. et al, Journal of Oncology, 2011, « Adaptive Radiation Therapy for HN Cancer – Can an old goal evolve into new standard ? »

[2] Schwartz D. et al, IJROBP, 2011, « Adaptive Radiotherapy for HN cancer : initial clinical outcomes from a prospective trial »

[3] Castelli J. et al, Acta Oncologica, 2018, « Adaptive radiotherapy for HN cancer »

[4] Morgan H. E. et al, Cancers of the Head & Neck, 2020, « Adaptive radiotherapy for head and neck cancer »

[5] Brock C. et al, Medical Physics, 2017, « Use of image registration and fusion algorithms and techniques in radiotherapy : Report of the AAPM Radiation Therapy Committee Task Group No. 132 »

[6] Husein et al, BJR, 2021, « Clinical use, challenges, and barriers to implementation of deformable image registration in radiotherapy – the need for guidance and QA tools »

Promotor, co-promotor, advisor : olivier.debeir@ulb.be, Nicolas.Pauly@ulb.be, younes.jourani@hubruxelles.be

Research Unit : LISA & MÉTROLOGIE NUCLÉAIRE - HUB

Description

Sensitivity of the gamma index evaluation in the context of bone SBRT

Background

Stereotactic body radiation therapy (SBRT) rises as an effective technique to improve oncological outcome in oligometastatic patients [1-3]. In bone metastasis management, the possibility to deliver high dose per fraction with extreme precision shows excellent response in terms of local control [4-6]. There are international guidelines for target delineation based on some patterns of failure in bones metastasis data and expert consensus [7-8]. These recommendations often support the addition of a large part of adjacent “normal appearing” bone spaces leading to potential dose prescription compromises [9-11].

The delivery of these treatments is complex, with quality assurance measures in place to ensure it is delivered accurately. Patient-specific quality assurance (PSQA) is commonly used to examine the quality of intensity modulated treatment plans, but their ability to detect clinically significant problems is unclear. External audits have found problems with delivered radiation doses despite internal PSQA giving the green light, raising questions about the sensitivity of clinical PSQA procedures [12].

Goals

The purpose of this work is to analyze the sensitivity of the PSQA procedure using the common gamma index evaluation in the context of bone SBRT. The work will contain:

• Recalculation of already delivered plans with known modifications

• Measurement of original and modified plans with standard PSQA tool

• Comparison with advanced PSQA tool (if tool available at the time)

• Correlation with local control and/or survival (if clinical data available at the time)

Contact person

For more information please contact : *olivier.Debeir@ulb.be, nicolas.pauly@ulb.be, Younes Jourani (younes.jourani@hubruxelles.be) *

references

[1] Ost et al. Surveillance or metastasis-directed therapy for oligometastatic prostate cancer recurrence: a prospective, randomized, multicenter phase II trial. 2018, J Clin Oncol 36(5):446-453

[2] Palma et al. Stereotactic ablative radiotherapy for the comprehensive treatment of oligometastatic cancers: Long-term results of the SABR-COMET phase II randomized trial. 2020, J Clin Oncol 38(25):2830-2838

[3] Harrow et al. Stereotactic radiation for the comprehensive treatment of oligometastases (SABR-COMET): extended long-term outcomes. 2022, Int J Radiat Oncol Biol Phys 114(4):611-616

[4] Husain et al. Stereotactic body radiotherapy for de novo spinal metastases: systematic review. 2017, J Neurosurg Spine 27:295-302

[5] Spencer et al. Systematic review of the role of stereotactic radiotherapy for bone metastases. 2019, J Natl Cancer Inst 111(10):1023-1032

[6] Cao et al. An international pooled analysis of SBRT outcomes to oligometastatic spine and non-spine bone metastases. 2021, Radiother Oncol 164:98-103

[7] Cox et al. International spine radiosurgery consortium consensus guidelines for target volume definition in spinal stereotactic radiosurgery. 2012, Int J Radiat Oncol Biol Phys 83(5):e597-e602

[8] Nguyen et al. International multi-institutional patterns of contouring practice and clinical target volume recommendations for stereotactic body radiation therapy for non-spine bone metastases. 2022, Int J Radiat Oncol Biol Phys 112(2):351-360

Promotor, co-promotor, advisor : olivier.debeir@ulb.be, Bernardo.Innocenti@ulb.be, Zelda Paquier (zelda.paquier@hubruxelles.be), Fabian Kert (fabian.kert@hubruxelles.be)

Research Unit : LISA - BEAMS

Description

Background

Medical imaging scans are primarily diagnostic tools interpreted qualitatively by trained observers. However, it is evolving towards a more significant role in personalized healthcare, especially in oncology, by exploiting the quantitative information contained inside these digital images. Radiomics has emerged as a promising clinical tool in this context, as the extracted advanced quantitative features from the region of interest (ROI) could non-invasively provide information about the entire tumour region and the surrounding tissues.

Radiomics features, especially texture features that assess the heterogeneity of the ROI, are sensitive to imaging protocols, segmentation, image processing, etc. Testing those variations on patients is not always feasible (e.g. scanning the patient multiple times and in different centres), which explains the use of imaging phantoms instead. However, commercially available phantoms are usually homogeneous and not developed for texture analysis

Goals

The purpose of this work is to create an imaging phantom that mimics tumour heterogeneity. First, the student will have to develop the phantom based on real tumours using 3D printing. This step includes choosing the materials and designing the phantom in a modelling computer-aided design application. Then he will analyze the values of texture features from the phantom compared to real data.

Contact person

For more information please contact : *olivier.debeir@ulb.be, bernardo.innocenti@ulb.be, Zelda Paquier (zelda.paquier@hubruxelles.be), Fabian Kert (fabian.kert@hubruxelles.be) *

references

Lambin P, Leijenaar RTH, Deist TM, Peerlings J, De Jong EEC, Van Timmeren J, et al. Radiomics: The bridge between medical imaging and personalized medicine. Nat Rev Clin Oncol 2017;14:749–62. https://doi.org/10.1038/nrclinonc.2017.141.

Valladares A, Beyer T, Rausch I. Physical imaging phantoms for simulation of tumours heterogeneity in PET, CT and MRI: an overview of existing designs. Med Phys 2020. https://doi.org/10.1017/CBO9781107415324.004.

Li Y, Reyhan M, Zhang Y, Wang X, Zhou J, Zhang Y, et al. The impact of phantom design and material-dependence on repeatability and reproducibility of CT-based radiomics features. Med Phys 2022. https://doi.org/10.1002/mp.15491.

Promotor, co-promotor, advisor : olivier.debeir@ulb.be, egor.zindy@ulb.be,

Research Unit : LISA-CMMI

Description

Development of an AI supported annotation tool for high resolution digital pathology slides

Recent development in machine vision[Kirillov23] provides generic algorithm for image segmentation, this system is built on a general images corpus, but could be extended to domain specific images.

Context

The project is done in collaboration with researchers from the Center for Microscopy and Molecular Imaging (CMMI) of the ULB. The center is active in pre-clinical imaging from cell analysis to small animal imaging.

Objective

The aim of the research is to implement the state of the art in automatic image segmentation, to understand the limitations due to the change in image corpus and to specialise the algorithm in a specific domain.

The research will be carried out in direct collaboration with users, who will be able to provide their business expertise in return.

Prerequisite

• Python
• machine learning (DNN)
• Napari framework

Contact person

For more information please contact : olivier.debeir@ulb.be, egor.zindy@ulb.be

references

Kirillov23

Promotor, co-promotor, advisor : olivier.debeir@ulb.be, thierry.metens@ulb.be,

Research Unit : LISA-HUB

Description

Study of the flow of encephalic venous sinuses in the presence of stenosis (vascular narrowing) by MRI.

Based on a map of velocity vectors at different times of the cardiac cycle measured by 3T MRI via a 4DPCA sequence, the objective would be to use a hydrodynamic model that would allow an evaluation of pressures before and after stenosis.

The work would therefore consist of programming a code that calculates the pressures from the velocity vector field, based on a model adapted to non-laminar flows.

Context

The project is done in collaboration with the radiology department of Erasme hospital.

Prerequisite

• Python
• image processing

Contact person

For more information please contact : thierry.metens@ulb.be, olivier.debeir@ulb.be

Promotor, co-promotor, advisor : olivier.debeir@ulb.be, nicolas.pauly@ulb.be, Jennifer.dhont@bordet.be

Research Unit : LISA-HUB

Description

Data analysis of the first X patients treated on the MR LINAC

The project aims to solve an open issue in a certain domain of application.

Context

In radiotherapy, to goal is to deliver a high dose of ionizing radiation to the tumor, while minimizing the dose to nearby healthy tissue. High geometrical treatment accuracy is therefore crucial. However, anatomical changes - of different orders of magnitude and over different time scales - can occur throughout the patient’s body. Some examples are motion caused through patient breathing, cardiac motion, bowel movement or bladder filling, but also tumor progression or regression. Clear visualization of the internal anatomy of the patient right before and during treatment is therefore of substantial interest. The MR LINAC combines an external beam radiotherapy system with an on-board magnetic resonance imaging device. The latter enables excellent soft-tissue visualization, without any additional radiation dose to the patient. Both real-time 2D images as well as sparse 3D images at high resolution are possible.

At the radiotherapy department of Institut Jules Bordet, such an MR LINAC is currently being implemented in the clinic, and will be only the second MR LINAC in clinical use in Belgium

Objective

The purpose of this work is to perform an extensive evaluation of all data generated during the treatment of the first X patients treated on the newly installed MR LINAC. This data will consist of medical images, motion data, clinical data, treatment workflow parameters, radiotherapy treatment plans, … etc. The aim of this analysis is two-fold; (1) to validate and possibly optimize the clinical workflow and patient treatments and (2) to generate hypothesis for future research projects.

Prerequisite

• Strong interest in modern data science and programming is a must.

Contact person

For more information please contact : Jennifer.dhont@bordet.be, olivier.debeir@ulb.be, nicolas.pauly@ulb.be

Promotor, co-promotor, advisor : olivier.debeir@ulb.be, olivier.vanhove@hubruxelles.be,

Research Unit : LISA-HUB

Description

3D respiratory pattern detection and monitoring

The project aims to develop a 3D respiratory pattern recorder based on a 3D depth camera acquisition [VanHove23].

Context

The project is done in collaboration with the pneumology department of Erasme hospital.

Objective

• validate the qualitative and quantitative measures acquired

• develop a machine learning based system to detect specific respiratory patterns

• complete the device with connection to external devices (EEG, ECG, force platform ...)

Several aspects are tackled, some related to image acquisition and processing, others to hardware development, depending on the candidate(s), different options can be taken.

Prerequisite

• Python
• image processing
• Linux (the platform used is a Raspberry pi4)
• C (opt. depending on the hardware development)

Contact person

For more information please contact : olivier.vanhove@hubruxelles.be, olivier.debeir@ulb.be

references

VanHove23

Promotor, co-promotor, advisor : olivier.debeir@ulb.be, olivier.vanhove@hubruxelles.be,

Research Unit : LISA-HUB

Description

Project title

Development of a respiratory stress sensitivity test

Context

An asthmatic subject may be hypo-perceiving and not taking his or her treatment correctly. The development of such a test could make it possible to detect them and thus facilitate their treatment.

Other applications could obviously be made (hyper-perceptors, athletes, COPD).

The project is done in collaboration with the Erasme pneumology department.

Objective

The thesis will consist in acquiring a series of physiologic signals in a well defined setting. Example of constraints:

• Random increase in constant inspiratory load over 5 steps

• Load applied via a bi-directional valve (inspiratory/expiratory)

• Washout mechanism of the device so that there is no CO2 stagnation

• Measurement of exchanged volumes (sensor available)

• CO2 measurement (sensor available)

• Direct measurement of dyspnoea

• Coupling with an EMG of the parasternal muscles (in contact with the FSM)

Prerequisite

• C,
• C++,
• Python
• hardware/software interfaces

Contact person

For more information please contact : olivier.vanhove@hubruxelles.be, olivier.debeir@ulb.be

Promotor, co-promotor, advisor : bram.vanderborght@vub.be, Mohsen Omidi; Ilias El Makrini, Mohsen Omidi (Mohsen.Omidi@vub.be)

Research Unit : R&MM AND AIXC

Description

AR-Aided Interface for Human-Robot Collaboration

Promotors:

Bram Vanderborght (bram.vanderborght@vub.ac.be)

Research Groups:

Robotics & MultiBody Mechanics Research Group (R&MM)

Collaborative robots – Physical Human-Robot Interaction and AR Interface:

Human-robot collaboration is complex, involving coordination, communication, and understanding of task requirements. Challenges such as lack of effective communication, potential human errors, and safety concerns can hinder task execution. Traditional training methods may also be time-consuming and lack real-time feedback. Augmented Reality (AR) offers promising solutions by providing real-time visual cues, instructions, and feedback. AR-aided interfaces can improve coordination, communication, efficiency, and safety in human-robot collaboration. Benefits include enhanced coordination, improved efficiency, shortened training time, and enhanced safety. AR-aided interfaces can provide real-time visual representations of intentions, actions, and status information, allowing for better visualization of task execution in human-robot collaboration. These interfaces can also offer guidance through real-time instructions and feedback, improving the accuracy and efficiency of task performance in HRC scenarios. In this project you will investigate how to communicate with a cobot by an AR interface for doing a collaborative task.

Description MA2 thesis work:

During the thesis, the student will have to become familiar with controlling an Emika Franka robot arm and also, developing an AR-Aided interface for educating the collaborative task. The robotic system will be linked to the AR application where the task can be visualized.

The student will gain experience in:

• Human-robot interaction, Control, and navigation
• Working with HoloLens 2.0 and developing AR application by C#
• Using Unity3D to create Augmented Reality environments.

Number of possible students: 1

Assistant/PhD student that will guide the student:

Mohsen Omidi (Mohsen.Omidi@vub.be) Ilias El Makrini (Ilias.El.Makrini@vub.be)

Promotor, co-promotor, advisor : tom.verstraten@vub.be, - , Louis Flynn (lflynn@vub.be)

Research Unit : ROBOTICS & MULTIBODY MECHANICS RESEARCH GROUP

Description

See attached pdf or external link below for a detailed description of the project.

attached pdf document

Promotor, co-promotor, advisor : tom.verstraten@vub.be, - , Christopher van Vlerken (christopher.konstantin.van.vlerken@vub.be), Kevin Langlois (kevin.langlois@vub.be)

Research Unit : ROBOTICS & MULTIBODY MECHANICS RESEARCH GROUP (R&MM)

Description

See pdf for full description of the project.

Please contact the advisor before selecting this Master's thesis topic.

attached pdf document

Promotor, co-promotor, advisor : tom.verstraten@vub.be, - , Christopher van Vlerken (christopher.konstantin.van.vlerken@vub.be), Kevin Langlois (kevin.langlois@vub.be)

Research Unit : ROBOTICS & MULTIBODY MECHANICS RESEARCH GROUP (R&MM)

Description

See pdf for full description of the project.

Please contact the advisor before selecting this Master's thesis topic.

attached pdf document

Promotor, co-promotor, advisor : tom.verstraten@vub.be, - , Louis Flynn (Louis.Flynn@vub.be)

Research Unit : ROBOTICS & MULTIBODY MECHANICS RESEARCH GROUP (R&MM)

Description

See pdf for full description of the project. Please contact the advisor before selecting this Master's thesis topic.

attached pdf document

Promotor, co-promotor, advisor : tom.verstraten@vub.be, - , Louis Flynn (Louis.Flynn@vub.be)

Research Unit : ROBOTICS & MULTIBODY MECHANICS RESEARCH GROUP (R&MM)

Description

See pdf for full description of the project.

Please contact the advisor before selecting this Master's thesis topic.

attached pdf document

Promotor, co-promotor, advisor : tom.verstraten@vub.be, - , Felipe Ballen Moreno (felipe.ballen.moreno@vub.be), Kevin Langlois (kevin.langlois@vub.be)

Research Unit : ROBOTICS & MULTIBODY MECHANICS RESEARCH GROUP (R&MM)

Description

See pdf or external link below for a full description of the project. Please contact the advisor before selecting this Master's thesis topic.

attached pdf document

Promotor, co-promotor, advisor : tom.verstraten@vub.be, Ilias El Makrini (ilias.el.makrini@vub.be), Tom Turcksin (tom.turcksin@vub.be)

Research Unit : ROBOTICS & MULTIBODY MECHANICS RESEARCH GROUP (R&MM)

Description

See attached pdf or external link below for a full description of the thesis proposal.

Please contact the advisors for more information.

attached pdf document

Promotor, co-promotor, advisor : tom.verstraten@vub.be, - , Rossana Lovecchio

Research Unit : ROBOTICS & MULTIBODY MECHANICS RESEARCH GROUP (R&MM) @VUB

Description

Project title

Developing a multi-sensory framework to characterize skills

Context

In the manufacturing industry, expert operators perform tasks in different ways. This makes the transfer process of skills from an expert to a novice operator challenging. Therefore, there is a need to study and quantify different parameters in tasks performed by expert operators. Some important parameters are speed, applied force, body posture, and eye movement, which can be tracked by using various sets of sensors.

Objective

The goal is to have a better understanding of the implicit skills of highly experienced operators by studying their behavior with a multi-sensory system.

Methods

The master thesis student will work on: • Identifying relevant parameters from previous studies and documentation that differentiate experts from novices. • Implementation of a sensory system to track parameters (i.e. through eye-tracking technologies, i.e. Hololens, hand tracking, i.e. MANUS glove, force sensors, etc.) potentially for three use cases • Analyzing data captured by the sensory system through feature selection, feature extraction, or other methodologies to capture the abilities of expert workers compared to novices.

Prerequisite

*MATLAB

Contact person

PhD/Postdoc that will guide the student: Rossana Lovecchio (rossana.lovecchio@vub.be) Hoang-Long Cao (hoang.long.cao@vub.be)

attached pdf document

Promotor, co-promotor, advisor : bram.vanderborght@vub.be, - , Kevin Langlois

Research Unit : ROBOTICS (R&MM)

Description

Recent technological advancements have enabled the creation of portable, low-cost, and unobtrusive sensors with tremendous potential to alter the clinical practice of rehabilitation. The application of wearable sensors to movement tracking has emerged as a promising paradigm to enhance the care provided to patients with neurological or musculoskeletal conditions. The challenge is that these sensors are currently poorly integrated in wearable devices and can cause discomfort to the user. Additionally, the quality of the data has to be improved to extract relevant therapeutic information and actionable data. A possible solution is to introduce the sensors directly in elastic fabrics. This can be done via screen printing, the same technique used to create images on T-shirts. There are many different sensors that can be integrated into such fabrics, such as near-infrared spectroscopy (NIRS) and electromyography (EMG). The first step in your thesis will be to set a list of desired outcomes and expectations and to analyse which sensor modalities will provide the best solution. One of the objectives is to achieve good skin to electrode contact and integrate the right mix of sensors. After doing so, you will develop basic machine learning algorithms to translate the raw data from your wearable sensor into relevant therapeutic information, such as, classification of motions performed by the wearer, maximal grip force, range of motion, level of fatigue, etc. Finally, you will evaluate your design on a test audience. During this project, you will be able to investigate the whole process from sensor design, fabrication to testing in a human-robot interface. Interested? Do not hesitate to contact us for more information. Prerequisites: C++, Python, Matlab Advisors: Kevin Langlois, Ellen Roels, Joris De Winter Promotor: Bram Vanderborght For more information please contact : kevin.langlois@vub.be

attached pdf document

Promotor, co-promotor, advisor : pierre.lambert@ulb.be, Benoit HAUT, Clément RIGAUT

Research Unit : TIPS

Description

Project title

Nose-to-Brain drug delivery for neurological disorders: classification of nasal anatomy for personalised medicine

Context

Personalized medicine is an ensemble of techniques aiming to adapt medical treatments to each patient. For example, in the context of nose-to-brain delivery (i.e. administrating neurological drugs via the nose), personalised medicine could improve the outcome of the treatment. Indeed, the drug has to reach a precise region of the nose, the olfactory area, to be effective. But accessing this zone is challenging and requires strategies adapted to the patient’s nasal anatomy.

Objective

This thesis aims to classify the anatomies of the patients into families. To this end, the results of spray deposition in nasal replicas, Computational Fluid Dynamics simulations and other measurements based directly on the CT scan can be exploited. The goal is to be able to advise appropriate procedures and administration for each patient with minimal measurements.

Methods

First, the appropriation data reduction and clustering methods will be used to give a first idea of the parameters influencing drug deposition in the cavities. Then, a predictive model will be developed and tested to generalise the findings. Finally, general recommendations will be drawn to guide health practioners to choose the best approach for each case.

Prerequisite

Multivariate statistics Knowledge of a programming language

Contact person

Clément Rigaut (clement.rigaut@ulb.be)

references

[1] J. A. Keeler, A. Patki, C. R. Woodard, and D. O. Frank-Ito, ‘A Computational Study of Nasal Spray Deposition Pattern in Four Ethnic Groups’, Journal of Aerosol Medicine and Pulmonary Drug Delivery, vol. 29, no. 2, Art. no. 2, Apr. 2016, doi: 10.1089/jamp.2014.1205. [1] W. Keustermans, T. Huysmans, B. Schmelzer, J. Sijbers, and J. JJ. Dirckx, ‘The effect of nasal shape on the thermal conditioning of inhaled air: Using clinical tomographic data to build a large-scale statistical shape model’, Computers in Biology and Medicine, vol. 117, p. 103600, Feb. 2020, doi: 10.1016/j.compbiomed.2020.103600.

attached pdf document

Promotor, co-promotor, advisor : pierre.lambert@ulb.be, Benoit HAUT, Gilles DECROLY

Research Unit : TIPS

Description

Project title

Solar cooking on the Solbosch campus

Context

Cooking with fossil fuels or wood raises a series of concerns in terms of energy supply and its environmental impact, energy of greenhouse gas, and public health (emission of particulate matter or NO2, promoting asthma as recently reported by TNO 2022 R12249). Solar cooking offers an alternative in sunny regions and for domestic use. However, recent initiatives back solar cooking for collective restaurants (the restaurant Le Présage at Aix-Marseille University or bakery and grains torrefaction at https://neoloco.fr, Normandy).

Objective

The goal is to design and model a prototype of solar oven which could be used on the Solbosch campus by the collective restaurants (e.g. Turbean). A (possibly downscaled) model will be built, scientifically characterized and benchmarked with existing solutions, and finally gastronomically tested. The context will be also integrated in the engineering design process: how should such an oven be operated in Brussels, also known for its rainy days? Which yearly fraction of meals could be solar-cooked? What about safety issues?

Methods

Literature review (models, designs, usages), understanding the SOlbosch context, thermal and sun tracking model, design and fabrication, characterization, tests. The topic must be treated scientifically, and follow a design methology.

Prerequisite

Mechanics (to build it and understand the daily and yearly sun trajectory), physics and thermic (to model it), digital fabrication skills (to build it in the Fablab), control and Arduino electronics (to implement sun tracking).

Contact person

For more information please contact : Gilles Decroly (gilles.decroly@ulb.be)

references

[1] https://lytefire.com/en [2] Solar cookers with and without thermal storage—A review https://doi.org/10.1016/j.rser.2008.08.018 [3] Design and experimental characterization of a solar cooker with a prismatic cooking chamber and adjustable panel reflectors https://doi.org/10.1016/j.renene.2022.11.083 [4] Climatoligical data in Ixelles, https://www.meteo.be/resources/climatology/climateCity/pdf/climateINS210099120_fr.pdf

attached pdf document

Promotor, co-promotor, advisor : pierre.lambert@ulb.be, - , Loïc AMEZ-DROZ, Mateo TUNON DE LARA

Research Unit : TIPS

Description

Project title

Soft microrobotics: towards a new set up to characterize active soft materials for voxel actuators

Context

Soft microrobotics use active soft materials to generate motion and forces exploited as soft actuators. “Soft” means here a deformable polymer and “active” means responsive to an external stimulus (light, heat) to generate a mechanical output (force and displacement). Such a material can be 3D printed with at the 10-100μm scale thanks to a two photon polymerization machine available in ULB. We recently demonstrated [1] the production of “active voxels”, ie 50μm x 50μm x 50μm cubes designed to exhibit bending, contraction, twist or shear deformation. The next step is now to characterize the mechanical performance of such actuators (force-displacement characteristics and response time).

Many data are already available

Objective

Design, build, calibrate and exploit an original experimental set up to measure the force-displacement characteristics of the “voxel-actuators”, inspired from atomic force microscopy and MEMS force sensors in silicon, but to be produced in the lab with glass microstructures, which will be strained when contacting the active voxel. The strain of these “springs-like” glass structures can be measured optically on different ways: with a camera, making use of a reflected beam (AFM inspired solution), or by patterning a waveguide and a Bragg grating in the glass structure to measure its strain with the so-called Bragg wavelength shift.

Methods

Design a suitable compliant glass structure [2], to be embedded in a comprehensive set up enabling the voxel heating, imaging its motion, contacting it with the glass sensor thanks to positioning stages along the required degrees of freedom. Produce this glass structure with our FemtoPrint machine. Apply the develop set up to characterize polymer active voxels, and extract the parameters for a relevant materials model.

Prerequisite

Mechanics, materials, physics. Interested in mechanical design and experimental work.

Contact person

For more information please contact : loic.amez-droz@ulb.be, Mateo.Tunon.De.Lara.Ramos@ulb.be

references

[1] A Voxel-Based Approach for the Generation of Advanced Kinematics at the Microscale, https://doi.org/10.1002/aisy.202200394 [2] Compliant Mechanisms, https://www.wiley.com/en-us/Compliant+Mechanisms-p-9780471384786

attached pdf document

Promotor, co-promotor, advisor : pierre.lambert@ulb.be, Thomas LESSINNES, Loïc AMEZ-DROZ

Research Unit : TIPS

Description

Project title

Soft microrobotics: bistable mechanism in glass

Context

Soft microrobotics use elastic deformation of materials to generate a specific displacement (bending, elongation, twist…) upon the application of an input stimulus such as air pressure in pneumatic fluidic actuator, light or heat in polymeric transduction. When the stimulus is removed, the displacement comes back to zero. It is therefore of the utmost importance to make use of bistable systems, which only switch from one stable state to another one upon application of the input stimulus, while conserving their position in absence of any stimulus. This also paves the way to multi-stability [1] (more than two stable states), and to defining motion sequences in the structural design of the soft actuator. Bistable structures can also be used as threshold-based force sensor, or recently in endoscopic biopsy capsules [2].

Objective

Model different bistable scenario and implement them first with upscaled PLA-3D printed models, second with true scale glass prototypes. Characterize them to validate the models. Provide a state of the art on the use of bi- and multi-stable mechanism in microrobotics.

Methods

Literature review. Matlab and FEM implementation of reference models [3-5]. Produce upscaled models and true scale prototypes. Characterize them (force-displacement.

Prerequisite

Mechanics and mathematics. Interested in a combined theoretical and experimental work.

Contact person

For more information please contact : loic.amez-droz@ulb.be

references

[1] Inflatable Origami: Multimodal Deformation via Multistability (2022), https://doi.org/10.1002/adfm.202201891 [2] Design of a Microbiota Sampling Capsule using 3D-Printed Bistable Mechanism (2018) 10.1109/EMBC.2018.8513141 [3] An analytical analysis of a compressed bistable buckled beam (1998) https://doi.org/10.1016/S0924-4247(98)00097-1 [4] Analytical modeling for rapid design of bistable buckled beams (2019) https://doi.org/10.1016/j.taml.2019.04.006 [5] A centrally-clamped parallel-beam bistable MEMS mechanism (2001) https://doi.org/10.1109/MEMSYS.2001.906551

attached pdf document

Promotor, co-promotor, advisor : pierre.lambert@ulb.be, - , Mateo TUNON DE LARA, Loïc AMEZ-DROZ

Research Unit : TIPS

Description

Project title

Optimization of Bragg grating instrumented compliant structures

Context

Femtosecond laser [1] can interact with glass to create optical waveguide and Bragg gratings, but also to micromachine glass parts in 3D at the microscale [2]. Optical Bragg gratings can also be used in combination with Surface Plasmon Resonance to provide a wide spectrum of biosensors [3]. In the TIPs department, we are developing compliant glass mechanisms, instrumented with Bragg gratings to provide strain measurement.

Objective

The goal of this master thesis is to optimize current designs by (1) improving the connection between the compliant glass mechanisme and an external optical fibre to limit the optical losses; (2) by optimizing the Bragg grating location in the compliant mechanism to maximize the optical signal output by Bragg reflection.

Methods

Literature review. Optomechanical design. Optical path measurements with a digital holographic microscope. Design, fabrication and characterisation of an original instrumented compliant glass structure.

Prerequisite

Mechanical design. Optics. Photonics. Interest in an experimental work.

Contact person

For more information please contact : mateo.tunon.de.lara.ramos@ulb.be , loic.amez-droz@ulb.be

references

[1] Bellouard, Y., et al. "The femtoprint project." Journal of Laser Micro/Nanoengineering 7.1 (2012): 1-10. [2] A. Chafai. A Volume-Tuning Capillary Gripper That Enhances Handling Capabilities and Enables Testing of Micro-Components (2022) [3] Hill, Ryan T. "Plasmonic biosensors." Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology 7.2 (2015): 152-168.

attached pdf document

Promotor, co-promotor, advisor : benoit.scheid@ulb.be, - , Omer Atasi

Research Unit : TRANSFERS, INTERFACES AND PROCESSES (TIPS)

Description

Project title

Numerical study of the interfacial rheology of soap films.

Context

A soap film is a thin film of water held together by a monolayer of soap molecules, the surfactants. The stability of these soap films is of paramount importance in the formulation of liquid foams, whether they are explicitly desired as shaving foams, or whether they are formed on dishes and laundry. The stability of foams depends largely on the rheology of the surfactant monolayers (forces that the surfactants can withstand).

Objective

Numerous methods of measuring these properties have been developed, but these techniques are very limited in frequency and probe the resistance of surfactants only over long times of the order of a second. In this thesis, we will focus on the rupture of a soap film which shrinks in a few milliseconds in order to probe the interfacial rheology over very short times.

Methods

This study will rely on direct numerical simulations to understand the influence of physicochemistry on the non-equilibrium reorganization/rheology of a soap film. This numerical work will be confronted with experimental results obtained in collaboration with the Institut Jean Le Rond d'Alembert (Paris) in order to potentially develop a new technique to measure the fast interfacial rheology.

Prerequisite

• C,
• C++,
• Python

Contact person

For more information please contact : Benoit.Scheid@ulb.be

references

https://www.researchgate.net/publication/342018827LifetimeofSurfaceBubblesinSurfactant_Solutions

Promotor, co-promotor, advisor : benoit.scheid@ulb.be, Francis Corazza,

Research Unit : TRANSFERS, INTERFACES AND PROCESSES (TIPS)

Description

Project title

Improvement of an intra-utero rate-of-hemoglobin diagnostic of a fetus during echography using microfluidic technology.

Context

Measuring the rate of hemoglobin in the blood of a fetus is performed by an intro-utero test during echography. If this rate is too low, the fetus is in danger and a surgical procedure is necessary. The accuracy of the test strongly relies on the underlying theoretical model, based on assumptions that could be invalidated in some conditions.

Objective

The goal of the master thesis will then consist in contributing to the understanding of the conditions for which the hemoglobin test should be improved.

Methods

The work will consist in mimicking in-vitro the blood flow of a fetus using microfluidics technology. Once the model adjusted with in-vitro measurements, it will be tested in-vivo and assessments as compared to existing tests will be made with the aim to eventually improve the accuracy of the diagnostic. The in-vitro measurements will be made at the TIPs-microfluidics lab at ULB-Solbosh, while the in-vivo measurements will be performed at the Hemato-oncology department at ULB-Brugmann in collaboration with Prof. F. Corazza.

Contact person

For more information please contact : Benoit.Scheid@ulb.be

Promotor, co-promotor, advisor : benoit.scheid@ulb.be, - ,

Research Unit : TRANSFERS, INTERFACES AND PROCESSES (TIPS)

Description

Project title

Oil-free encapsulation using microfluidic antibubbles

Context

An emerging breakthrough in microfluidics is the formation of antibubbles (= a drop inside a bubble in a liquid). Antibubbles turn out to be a potential new elementary component in microfluidics (beside bubbles and droplets) with unequalled properties, combining those of bubbles and droplets, such as “flash” release of a disperse phase into a continuous one or contact-free all-aqueous emulsification (in the context of CO2 sequestration or protein encapsulation). Nevertheless, despite the current knowledge on antibubble dynamics two limitations prevent the antibubble to be used at the scale of a microfluidic process: the limited lifetime and the automated production in microfluidics.

Objective

The master thesis will contribute to produce and manipulate micro-antibubbles by designing dedicated micronozzles using the nanoscribe 3D printer.

Methods

Experimental, numerical and theoretical methods will be used.

Prerequisite

• C,
• C++,
• Python

Contact person

For more information please contact : Benoit.Scheid@ulb.be

references

https://www.researchgate.net/publication/333383348Controllingthelifetimeof_antibubbles

Promotor, co-promotor, advisor : benoit.scheid@ulb.be, - , Robin Debuysschère

Research Unit : TRANSFERS, INTERFACES AND PROCESSES (TIPS)

Description

Project title

Microfluidic continuous crystallisation of a pharmaceutical compound: influence of the flow

Context

In the frame of a research effort to continuously produce a pharmaceutical ingredient of interest, we focus in this student project on the crystallization process in flow, and in particular on the influence of the shear stress on the nucleation rate, offering an additional degree of freedom for the fine control of the crystal size and size distribution.

Contact person

For more information please contact : Benoit.Scheid@ulb.be

Promotor, co-promotor, advisor : benoit.haut@ulb.be, Pierre Lambert, Laura Deruyver

Research Unit : TRANSFERS, INTERFACES AND PROCESSES (WWW.TIPS-ULB.BE)

Description

Permeation of nose-to-brain drugs through the olfactory mucosa.

Nose-to-brain drug delivery is a promising way to deliver drugs to the brain. For this purpose, the drug formulation injected in the nose must permeate through the olfactory mucosa before following the olfactory nerve to the brain. This permeation step is crucial to an achieve effective amount of drug in the brain. This thesis is the follow-up of a previous work that allowed to develop the first iterations of in-vitro permeation experiments and a computer code simulating drug permeation.

The first part of the thesis aims to measure the permeation of an anti-Parkinson drug formulation through a cell layer cultivated from a cell line commonly used for evaluating nasal drugs. The second part of the thesis aims to develop a code that simulates the diffusion of the drug through the mucus and cell layers of the olfactory mucosa. Finally, the results obtained via the code will be used to explain the experimental observations and to optimize the formulation of the drugs.

Tasks : • Literature review/state of the art • Culture of the cells and drug diffusion experiments • Computational code development to explain the experimental results 

Promotor, co-promotor, advisor : benoit.haut@ulb.be, Pierre Lambert, Clément Rigaut

Research Unit : TRANSFERS, INTERFACES AND PROCESSES (WWW.TIPS-ULB.BE)

Description

Influence of the nasal cycle on nose-to-brain delivery.

Nose-to-brain drug delivery is a promising way to deliver drugs. To this end, the airflow generated by a spray must convey the drug particles through the nose and deposit them in the so-called olfactory area. However, the mucosa of the nose swell and decrease periodically on a daily basis (this is called the “nasal cycle”). This swelling is asymmetric and can impact the deposition of the spray. To date, no studies were dedicated to this effect. This thesis would then be of great interest for nose-to-brain delivery.

This thesis aims to compare drug delivery in the nasal cavity during each step of the nasal cycle. To this end, 3D-printed replicas of the nasal cast of a health subject (called nasal casts) will be created. These casts will then be used for in-vitro experiments to map the delivery in the nose. The final goal of this project is to optimize nose-to-brain drugs and draw administration guidelines for health practitioners and patients.

Tasks : • Literature review/state of the art • Drug deposition tests in nasal casts • Recommendation for optimal drug administration depending on the nasal cycle parameters

Promotor, co-promotor, advisor : benoit.haut@ulb.be, Benjamin Sobac (Université de Pau et des Pays de l'Adour), Omer Atasi

Research Unit : TRANSFERS, INTERFACES AND PROCESSES (WWW.TIPS-ULB.BE)

Description

Evaporation of complex binary solutions.

Solvent evaporation is a unit operation widely used in industry to concentrate a solute, to separate the components of a solution, or to dry colloidal suspensions. These processes are key unit operations in the cosmetics and pharmaceutical industries, as well as in other fields such as environmental engineering or public health. Recently, the study of airborne aerosols has received attention because they are a vector of disease transmission. The evaporation of airborne aerosols, emitted during speaking or coughing, determines how long an aerosol will stay suspended before falling to the ground. This suspension time is therefore a key parameter to predict and control, in order to reduce the transmission of diseases by air.

In this Master thesis, we propose to study, by mathematical modeling and numerical simulation, the evaporation of drops in one or several complex situations, which can, for example, be linked to the evaporation of a small drop saliva containing non-volatile material (virus, mucins, etc.). The objective will be to identify the phenomena governing the evaporation of this drop, by posing equations describing them, setting up a method of numerical simulation of these equations, and by analyzing the results obtained in order to shed new light on the underlying phenomena, for example within the framework of the characterization of the propagation of an aerosol emitted by a human.

Promotor, co-promotor, advisor : benoit.haut@ulb.be, Benjamin Sobac, Laboratoire des Fluides Complexes et leurs Réservoirs, CNRS, Université de Pau et des Pays de l’Adour, Charlotte Van Engeland

Research Unit : TRANSFERS, INTERFACES AND PROCESSES (WWW.TIPS-ULB.BE)

Description

Experimental and theoretical study of the impregnation of a porous medium by a volatile liquid.

The impregnation of a porous medium by a fluid is a very common process in nature (e.g. percolation of rainwater to reach groundwater) and in many industrial processes, such as surface water filtration or satellite electronic component cooling systems. It is a complex process, because it involves many coupled phenomena (capillarity, gravity, and evaporation if the fluid is volatile).

The objective of this Master thesis is, by experiments and modelling, to acquire a better understanding of the phenomena governing the impregnation of a porous medium by a fluid of a large volatility (example of application related to the environment: cryogenic hydrogen storage). In this case, it is expected that the evaporation of the fluid, concomitant with the impregnation of the porous medium, will significantly influence the process (by cooling the gas-liquid interface, which increases its surface tension, and by transforming a significant part of the liquid matter into vapor). The experimental part will implement optical diagnostic techniques on laboratory model porous media, while the theoretical part will aim to develop simple models, highlighting the key dimensionless numbers characterizing the process.

Promotor, co-promotor, advisor : benoit.haut@ulb.be, - , Rami Taheri

Research Unit : TRANSFERS, INTERFACES AND PROCESSES (WWW.TIPS-ULB.BE)

Description

Analysis and processing of clinical reference data in cardiac output estimation.

To assess the heart's ability to supply organs with oxygen and nutrients, clinicians rely on the measurement of the cardiac output (CO); a hemodynamic parameter defined as the volume of blood pumped by the heart in one minute. This clinical parameter is essential in the evaluation of the cardiovascular status of a patient and in the orientation of therapy. There are two reference techniques for measuring cardiac output in patients at rest and undergoing exercise testing: right heart catheterization (RHC) and echocardiography. In parallel, other physiological measurements are taken for the same patients via techniques such as ergospirometry or ECG. In this master thesis, these clinical data will be provided, for numerous patients, by the Erasme Hospital and the Italian Auxological Institute San Luca Hospital in Milan.

Aim of the thesis: • To create a database containing all the clinical data provided for given patients and to label them; • Based on the identification of physiological clusters in the data, to establish trends in the value of cardiac output according to these groups; • To extract data of interest from an open access database "MIMIC II”; • To automate the digital extraction of pressure curves from clinical paper files.

Promotor, co-promotor, advisor : francois.horlin@ulb.be, Jean-François Determe, Evert Pocoma Copa

Research Unit : ULB - WIRELESS

Description

MOTIVATION

There is considerable interest in developing reliable and cost-effective technologies enabling healthy living. When people are active (walk, run, spring, etc.), their limbs follow repetitive instantaneous speed patterns containing unique discriminative features useful for healthcare applications, such as assisted living (fall detection, activity classification), intensive training (running monitoring), and bio- medical applications (illness detection, rehabilitation).

Motion capture (MoCap) and Kinect sensors have been often considered for such applications. They provide 3D-position of skeleton joints that can be used to analyze the movement of limbs. However, MoCap sensors require expensive equipment and laborious/tedious calibrations processes. Kinect cameras suffer from low light conditions and are subject to privacy concerns. On the contrary, mm- wave radars are less invasive and provide clear representation of the movements (see the instantaneous speeds in the figure above). In addition, radars powered by Artificial Intelligence (AI) algorithms are used more and more in several domains.

Therefore, the goal of the master thesis is to build a radar capable of capturing the frequency variations known as micro-Doppler due to the motions of the limbs. This is done by performing a time-frequency analysis of the received signal. By inspecting the resulting Doppler spectrum and applying AI- algorithms, the gait parameters will be estimated and abnormal patterns will be detected.

OBJECTIVES

• Model typical and abnormal human gaits when walking • Understand the radar principles, implement the Doppler spectrum estimation • Validate the algorithms experimentally with a radar platform • Compare the results to other technologies such as Kinect • Apply gait parameter estimation and anomaly classification algorithms

CONTACT

François Horlin, francois.horlin@ulb.be Jean-François Derterme, jean-francois.determe@ulb.be

Solbosch campus, building U, level. 3, OPERA department

attached pdf document

Promotor, co-promotor, advisor : michel.kinnaert@ulb.be, - , Maxime Bussios

Research Unit : ULB-SAAS

Description

Degradation detection and localization in battery packs

Context

Renewable energies and electric transportation are the cornerstones for developing a sustainable future society. Energy storage is fundamental in this context, in order to store surplus of energy and use it when the wind does not blow or the sun does not shine, or to produce vehicles that do not pollute the environment when they are on the roads. Among the possibilities, lithium-ion batteries are the technology of choice given their high energy capacity and efficiency. However in contrast with other battery technologies, the benefits of lithium-ion batteries come at the price of careful monitoring requirements. Indeed, faulty cells in a battery pack can have catastrophic consequences including fire.

Objective

The objective of this thesis is to develop a monitoring system that is able to detect and localize the degraded or weak cells within a pack on the basis of available voltage, current and temperature measurements. Both synthetic data obtained from a realistic battery pack simulator, and real data recorded on a 4-cell battery pack will be exploited to determine features that can be extracted from the measurements, or from combinations of measurements, and that exhibit pack malfunction. Next, appropriate classification tools will be investigated in order to decide on the healthy or degraded state of the pack and to localize the degraded cell/cells by processing the features extracted from the measurements. Various degradation levels and types will be considered in order to characterize the sensitivity to each fault.

Methods

The student should 1. perform a bibliographic search on fault/degradation diagnosis for battery packs, 2. generate synthetic data for heathy pack operation and for various degradation types and levels, 3. Use measurements and/or appropriate functions of the measurements to generate features that exhibit faulty/degraded behaviour, 4. Develop a classification method that decides on the pack state by processing the features extracted from regular measurements.

Contact person

For more information please contact : Michel Kinnaert (Michel.Kinnaert@ulb.be and Maxime Bussios (Maxime.Bussios@ulb.be)

attached pdf document

Promotor, co-promotor, advisor : michel.kinnaert@ulb.be, Laurent Catoire,

Research Unit : ULB-SAAS

Description

Design of new didactic devices for teaching of control engineering

Context

The framework of the project is the teaching of control system theory to future engineers. The goal consists in designing new modular, evolving, and open-source solutions to provide a better, more practical learning experience to the student. A set of didactic devices is under development including a self-balancing robot, a fluid mixer,…. The aim of this project consists in modifying/designing new features involving mechanical, electrical, as well as software parts, in order to end up with a fully functional device that can be used both for teaching labs and for demos.

Objective

*selection of the sensors/actuators *design of the signal conditioning / acquisition stages *design of the experimental setup (SolidWorks, 3D printer …) *design of the power supply & cable management *implementation of a control strategy (Arduino/C programming or Matlab/data-acquisition board) *setup of some didactic experiments & their related teaching materials

Requested skills

*quick & autonomous learner in a dynamic environment *team player, creativity *basic knowledge in control theory, digital signal processing, electronics

Contact person

For more information please contact : Laurent Catoire (Laurent.Catoire@ulb.be) and Michel Kinnaert (Michel.Kinnaert@ulb.be)

attached pdf document

Promotor, co-promotor, advisor : adrian.munteanu@vub.be, Nastaran Nourbakhsh Kaashki,

Research Unit : VUB - ETRO

Description

Object Tracking on Low-cost Edge Devices

Object tracking is the algorithm tracking the movement of an object. In other words, it is the task of estimating or predicting the positions and other relevant information of moving objects in a video. It is expected that the student will report over the state-of-the-art object tracking methods and the ones compatible with the performance of common EdgeAI devices will be developed and tested.

Background

• Programming skills (Python/C++)
• Experience with computer vision and image processing techniques
• Experience with deep-learning-based methods is a plus.
• The student must sign an NDA before starting the project.

Contact person

If you are interested, please send your resume and transcript to nknourba@etrovub.be (Dr. Nastaran Nourbakhsh), and adrian.munteanu@vub.be (Prof. Adrian Munteanu)

Promotor, co-promotor, advisor : adrian.munteanu@vub.be, Nastaran Nourbakhsh Kaashki,

Research Unit : VUB - ETRO

Description

Object pose estimation on embedded devices

State-of-the-art object pose estimations are mainly developed for powerful devices with high-end GPUs. In this research, the student will explore the state-of-the-art methods for 6DoF pose estimation which can run on low-cost embedded systems such as Nvidia Jetson nano. A concise report of such methods and their comparison is expected as the outcome of this research.

This work will be done in collaboration with ABB.

Background

• Programming skills (Python/C++)
• Experience with computer vision and image processing techniques
• Experience with deep-learning-based methods is a plus.
• The student must sign an NDA before starting the project.

Contact Person

If you are interested, please send your resume and transcript to nknourba@etrovub.be (Dr. Nastaran Nourbakhsh), and adrian.munteanu@vub.be (Prof. Adrian Munteanu)

Promotor, co-promotor, advisor : adrian.munteanu@vub.be, Nastaran Nourbakhsh Kaashki,

Research Unit : VUB - ETRO

Description

Seat-occupancy detection system and breathing rate monitoring

Radar has evolved from automotive applications such as driver assistance systems, safety and driver alert systems, and autonomous driving systems to low-cost solutions, penetrating industrial and consumer market segments. Radar has been used for perimeter intrusion detection systems, gesture recognition, human-machine interfaces, outdoor positioning and localization, and indoor people counting ​[1]​​ [2]​.
In this project, a radar-based method for human detection and breath rate monitoring is developed. A report over the state-of-the-art methods for radar-based human detection methods is expected.

[1] A. Lazaro, M. Lazaro, R. Villarino and D. Girbau, "Seat-occupancy detection system and breathing rate monitoring based on a low-cost mm-Wave radar at 60 GHz," IEEE Access, vol. 9, pp. 115403-115414, 2021.
[2] M. Stephan and A. Santra, "Radar-based human target detection using deep residual u-net for smart home applications," in 18th IEEE international conference on machine learning and applications, IEEE, 2019.

This work will be done in collaboration with ABB.

Background

• Programming skills (Python/C++)
• Experience with computer vision and image processing techniques
• Experience with deep-learning-based methods is a plus.
• The student must sign an NDA before starting the project.

Contact Person

If you are interested, please send your resume and transcript to nknourba@etrovub.be (Dr. Nastaran Nourbakhsh), and adrian.munteanu@vub.be (Prof. Adrian Munteanu)

Promotor, co-promotor, advisor : yves.rolain@vub.be, John.Lataire@vub.be, Andy.Keymolen@vub.be and Antoine.Marchal@vub.be

Research Unit : VUB/ELEC

Description

Did the patient get better? Determine the health condition of patients in intensive care by using data-driven modelling.

When patients end up in intensive care, they are often subjected to artificial ventilation. In this case, it is important to be able to monitor the states of the patients' lungs, especially in the case of a lung disease (such as COVID). In this thesis, we propose to use Respiratory Oscillometry (RO) to track the evolution of the state of the lungs. RO uses data-driven modelling techniques to identify the lung impedance by applying small pressure oscillations (i.e. excitations) onto the breathing or ventilation. Information about the respiratory mechanics can be extracted out of this impedance, including the resistance (R) and elastance (E) of the lung. At the ELEC department we implemented a novel RO protocol, using a customized multisine excitation signal, in two professional mechanical ventilator devices. After extensive testing and the regulatory approval, a clinical trial is going to be executed in the months June, July and august of 2023. This will give us a lot of data with a lot of potentially interestinginformation to discover. The goal of the thesis is to identify statistically relevant parameter changes over multiple measurements of the same patient. The following subtasks can be identified: - Data cleaning: before the flow and pressure measurements can be processed, they need to be cleaned. This includes removal of transients, removal of breathing artefacts (e.g. coughing). - Signal processing: Before a parametric model can be estimated, a quality check needs to be performed. - Data driven modelling: a parametric model will need to be estimated, starting from a first order model. Next, implement techniques to identify time varying behaviour of the model parameters. - Statistics: Ensure that the time-variations are statistically relevant. - Automate the data processing to execute the analysis of multiple patients efficiently

The student will be able to start on an existing code base

For more information please contact: John.Lataire@vub.be, Andy.Keymolen@vub.be or Antoine.Marchal@vub.be

attached pdf document

Promotor, co-promotor, advisor : yves.rolain@vub.be, John.lataire@vub.be, john.lataire@vub.be, kevin.langlois@vub.be

Research Unit : VUB/ELEC

Description

A robotically aided method for characterization of the mechanical behavior of patients

With the appearance of robotic assistance in rehabilitation there is a need to automatically extract information on the biomechanic state of the patient. Robots are being prepared to help physiotherapists to repeat simple motions, for the patients to learn basic tasks again. The advantage of the robot is that it never gets tired. The challenge is that the robot needs to be configured to take over the actions of a human manipulator. In this process, it is important that the robot can 'feel' the patient, not only for security reasons, but also to determine the amount of help that the patient requires to move, and to detect the allowable range of motion. By using data-driven modeling, possibly combined with machine learning, the goal of this thesis is to characterise the patient's dynamic mechanical behaviour by using robotic manipulators. The challenges will lie in designing informative experiments such that the mechanical properties of the human's joints can be extracted from the data. Possibly, equivalent mechanical models of the human will be set up, describing him/her as an interconnection of (mechanical) impedances, such as inertial, damping and stiffness elements, to be identified from the experimental data. Interested? Do not hesitate to contact us for more information.

Prerequisites: C++, Python, Matlab

Advisors: John Lataire, Kevin Langlois, Joris De Winter, Greet Van de Perre Promotor: John Lataire, Greet Van de Perre

For more information please contact : john.lataire@vub.be kevin.langlois@vub.be

attached pdf document

Promotor, co-promotor, advisor : yves.rolain@vub.be, John.Lataire@vub.be, Antoine.Marchal@vub.be

Research Unit : VUB/ELEC

Description

Build a breathing simulator using Generative AI In pneumology, it is of interest to use system identification on the human respiratory system to inform medical practitioners on the patient’s state of health. This is achieved by having a machine such as a ventilator hooked to the patient and exciting his/her respiratory system with a specific excitation. However, it can be proven that patient activity, such as breathing, distorts the data and prevents accurate parametric identification. There is thus a need to model human breathing, seen as a stochastic process. In this thesis you will explore how generative AI can contribute to modelling human breathing. The goal is to compare your results with a Gaussian Process approach and outperform it. To this end, you will explore using various techniques such as Diffusion Models, GANs, VAE or other methods. You will have to gather your dataset based on equipment available at the ELEC department, namely the DemcAir ventilator manufactured by Demcon Macawi. In a first step, you will use simulated data from the Gaussian Process approach.

For more information please contact : John.Lataire@vub.be and/or Antoine.Marchal@vub.be

attached pdf document

Promotor, co-promotor, advisor : yves.rolain@vub.be, John.Lataire@vub.be, greet.van.de.perre@vub.be, Thierry.Rene.Hubert@vub.be

Research Unit : VUB/ELEC AND BRUBOTICS

Description

Project title

The project aims to solve an open issue in a certain domain of application.

Data-driven modelling and control of flexible Cobots

Cobots are robots that are specifically designed to collaborate with humans. Safety is an important point of attention for this type of robots. Traditional industrial robots are designed with a high stiffness, which makes it possible to accurately calculate the state of the end-effector using the knowledge of the joint angles and speeds. However, this results in heavy robots with high inertia, which can lead to serious injuries in the case of an impact between the robot and a human. When the manipulator is designed with a lower stiffness, and thus allowing the structure to deflect, a considerable drop in mass can be reached. Given the combination of their lightweightness and flexible aspect, flexible link robots are interesting for applications in human-robot collaboration. However, flexible links come with an additional challenge to control them. The dynamic behaviour of the robot becomes very dependent on the load to be manipulated.

Cobots have been designed (and will be further optimised) by the Robotics and multibody mechanics group of the VUB. Will you take the challenge to use data-driven modelling to describe the dynamic behaviour of these robots, and to help design optimal control strategies to obtain accurate end effector tracking?

Interested? Do not hesitate to contact us for more information.

Promotors: John Lataire, Greet Van de Perre John.Lataire@vub.be, greet.van.de.perre@vub.be

Advisors: John Lataire, Greet Van de Perre, Thierry Hubert (Thierry.Rene.Hubert@vub.be)

attached pdf document