Access profile

Given the multidisciplinary nature of the scientific field of the programme, there are a wide range of degrees that qualify applicants for admission. For the near future, the applicants considered most suitable for admission to the doctoral programme in Biomedical Engineering will be bachelor’s degree holders with a scientific and technological background who have completed a master's degree in Biomedical Engineering or one related to the scientific field of the programme. In addition to this academic background, it is considered important that applicants have certain personal characteristics—namely, an interest in the research projects carried out within the framework of the programme; critical and analytical skills; initiative and perseverance in their academic work; the ability to work in a team; and the ability to communicate effectively, both orally and in writing.

Output profile

Doctoral candidates who complete a doctoral degree will have acquired the following competencies, which are needed to carry out quality research (Royal Decree 99/2011, of 28 January, which regulates official doctoral studies):

a) A systematic understanding of the field of study and a mastery of the research skills and methods related to the field.
b) An ability to conceive, design or create, put into practice and adopt a substantial process of research or creation.
c) An ability to contribute to pushing back the frontiers of knowledge through original research.
d) A capacity for critical analysis and an ability to assess and summarise new and complex ideas.
e) An ability to communicate with the academic and scientific community and with society in general as regards their fields of knowledge in the manner and languages that are typical of the international scientific community to which they belong.
f) An ability to foster scientific, technological, social, artistic and cultural progress in academic and professional contexts within a knowledge-based society.

The award of a doctoral degree must equip the graduate for work in a variety of settings, especially those requiring creativity and innovation. Doctoral graduates must have at least acquired the personal skills needed to:

a) Develop in contexts in which there is little specific information.
b) Find the key questions that must be answered to solve a complex problem.
c) Design, create, develop and undertake original, innovative projects in their field.
d) Work as part of a team and independently in an international or multidisciplinary context.
e) Integrate knowledge, deal with complexity and make judgements with limited information.
f) Offer criticism on and intellectually defend solutions.

Finally, with respect to competencies, doctoral students must:
a) have acquired advanced knowledge at the frontier of their discipline and demonstrated, in the context of internationally recognised scientific research, a deep, detailed and well-grounded understanding of theoretical and practical issues and scientific methodology in one or more research fields;
b) have made an original and significant contribution to scientific research in their field of expertise that has been recognised as such by the international scientific community;
c) have demonstrated that they are capable of designing a research project that serves as a framework for carrying out a critical analysis and assessment of imprecise situations, in which they are able to apply their contributions, expertise and working method to synthesise new and complex ideas that yield a deeper knowledge of the research context in which they work;
d) have developed sufficient autonomy to set up, manage and lead innovative research teams and projects and scientific collaborations (both national and international) within their subject area, in multidisciplinary contexts and, where appropriate, with a substantial element of knowledge transfer;
e) have demonstrated that they are able to carry out their research activity in a socially responsible manner and with scientific integrity;
f) have demonstrated, within their specific scientific context, that they are able to make cultural, social or technological advances and promote innovation in all areas within a knowledge-based society;
g) have demonstrated that they are able to participate in scientific discussions at the international level in their field of expertise and disseminate the results of their research activity to audiences of all kinds.

Number of places

25

Duration of studies and dedication regime

Duration
The maximum period of study for full-time doctoral studies is three years, counted from the date of admission to the programme to the date of submission of the doctoral thesis. The academic committee of the doctoral programme may authorise a doctoral candidate to pursue doctoral studies on a part-time basis. In this case, the maximum period of study is five years, counting from the date of admission to the programme to the date of submission of the doctoral thesis. For calculating these periods, the date of admission is considered to be the date of the first enrolment for tutorials, and the date of submission the moment in which the Doctoral School officially deposits the doctoral thesis.

For full-time doctoral candidates, the minimum period of study is two years, counted from the date of an applicant's admission to the programme until the date on which the doctoral thesis is deposited; for part-time doctoral candidates it is four years. When there are justified grounds for doing so, and the thesis supervisor and academic tutor have given their authorisation, doctoral candidates may request that the academic committee of their doctoral programme exempt them from the minimum period of study requirement.

The calculation of periods of study will not include periods of absence due to illness, pregnancy or any other reason provided for in the regulations in force. Students who find themselves in any of these circumstances must notify the academic committee of the doctoral programme, which, where appropriate, must inform the Doctoral School. Doctoral candidates may also temporarily withdraw from the programme for up to one year, and this period may be extended for an additional year. Doctoral candidates who wish to interrupt their studies must submit a justified request to the academic committee of the doctoral programme, which will decide whether or not to approve the request. Each programme will establish conditions for readmission to doctoral studies.

Extension
If full-time doctoral candidates have not applied to deposit their thesis by the end of the three-year period of study, the academic committee of the programme may authorise an extension of up to one year. In exceptional circumstances, a further one-year extension may be granted, subject to the conditions established by the corresponding doctoral programme. In the case of part-time doctoral candidates, an extension of two years may be authorised. In both cases, in exceptional circumstances a further one-year extension may be granted by the Doctoral School's Standing Committee, upon the submission of a reasoned application by the academic committee of the doctoral programme.

Dismissal from the doctoral programme
A doctoral candidate may be dismissed from a doctoral programme for the following reasons:

• The doctoral candidate submitting a justified application to withdraw from the programme.
• The maximum period of study and of extensions thereof ending.
• The doctoral candidate not having enrolled every academic year (unless he or she has been authorised to temporarily withdraw).
• The doctoral candidate failing two consecutive assessments.
• The doctoral candidate having disciplinary proceedings filed against him or her that rule that he or she must be dismissed from the UPC.

Dismissal from the programme implies that doctoral candidates cannot continue studying at the UPC and the closing of their academic record. This notwithstanding, they may apply to the academic committee of the programme for readmission and the committee must reevaluate them in accordance with the criteria established in the regulations.

Organization

• Jane Campos, Raimon

• Casals Gelpi, Alicia
• Ginebra Molins, Maria Pau
• Ginjaume Egido, Merce
• Jane Campos, Raimon
• Riu Costa, Pere Joan
• Tost Pardell, Dani

• Department of Automatic Control (PROMOTORA)
• Department of Computer Science
• Department of Electronic Engineering
• Department of Materials Science and Metallurgy
• Institute of Energy Technologies

Agreements with other institutions

• University of Zaragoza (https://estudios.unizar.es/estudio/ver-doct?id=7098): public inter-university agreement.
• Technical University of Madrid (http://www.upm.es/internacional/): exchange of professors, collaboration on content, student mobility. Launched in January 2005, open-ended.
Public

The research groups involved in the programme have a wide network of collaborations that enrich the student experience. Many doctoral students undertake periods of mobility thanks to these collaborations. The programme maintains well-established collaborations with various centres where doctoral students have completed research stays to work on their theses and obtain a European Doctorate mention.
The acceptance of students by collaborating centres is verified on their applications for mobility grants. Collaborating centres:
• MIT, USA
• Polytechnic University of Milan, Italy
• Oxford University
• Lund University
• Albert Ludwig University of Freiburg, Germany
• Kingston University, UK
• Polytechnic University of Turin, Italy
• University of Porto, Portugal
• Centre for Online Health, Australia
• University of Buenos Aires, Argentina
• Biomedical Engineering Research Centre (CREB), Barcelona
• Institute for Bioengineering of Catalonia (IBEC), Barcelona
• Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN)
• University of Ljubljana, Slovenia
• University of Michigan, USA
• National Institute for Research in Computer Science and Automation (INRIA), France
• Biomechanics Institute of Valencia, Polytechnic University of Valencia (IBV-UPV)
• Institute of Bioengineering, Miguel Hernandez University, Elche.
• Theoretical Chronobiology Unit, Free University of Brussels, Belgium
• Institute for Mechanics of Materials and Structures, Vienna University of Technology
• Faculty of Medicine, Department of Anatomy and Cell Biology, Technion – Israel Institute of Technology
• University of Valladolid
• Department of Bioengineering, Institute of Industrial Automation – CSIC, Madrid
• Trinity College, Dublin, Ireland
• KTH Royal Institute of Technology, Sweden
• Department of Medical Engineering and Biotechnology, University of Applied Sciences, Jena, Germany
• Galeazzi Orthopaedic Institute, Milan, Italy
• Instituto Tecnológico de Monterrey, Mexico
• Laboratory of Engineering of the Neuromuscular System and Motor Rehabilitation (ISiN), Polytechnic University of Turin, Italy
• University of Technology of Compiègne, France
• Faculty of Computing, Information Systems and Mathematics, Kingston University, UK
• LTSI, University of Rennes 1, France
• Pompeu Fabra University, Barcelona

Access profile

Given the multidisciplinary nature of the scientific field of the programme, there are a wide range of degrees that qualify applicants for admission. For the near future, the applicants considered most suitable for admission to the doctoral programme in Biomedical Engineering will be bachelor’s degree holders with a scientific and technological background who have completed a master's degree in Biomedical Engineering or one related to the scientific field of the programme. In addition to this academic background, it is considered important that applicants have certain personal characteristics—namely, an interest in the research projects carried out within the framework of the programme; critical and analytical skills; initiative and perseverance in their academic work; the ability to work in a team; and the ability to communicate effectively, both orally and in writing.

Access requirements

Applicants must hold a Spanish bachelor’s degree or equivalent and a Spanish master’s degree or equivalent, provided they have completed a minimum of 300 ECTS credits on the two degrees (Royal Decree 43/2015, of 2 February)

In addition, the following may apply:

• Holders of an official degree awarded by a university in Spain or any other country in the European Higher Education Area, pursuant to the provisions of Article 16 of Royal Decree 1393/2007, of 29 October, which establishes official university course regulations, who have completed a minimum of 300 ECTS credits on official university degrees, of which at least 60 must be at the master's degree level.
• Holders of an official Spanish bachelor’s degree comprising at least 300 credits, as provided for by EU regulations. Holder of degrees of this kind must complete bridging courses unless the curriculum of the bachelor’s degree in question included research training credits equivalent in value to those which would be earned on a master's degree.
• Holders of an official university qualification who, having passed the entrance examination for specialised medical training, have completed at least two years of a training course leading to an official degree in a health-sciences specialisation.
• Holders of a degree issued under a foreign education system. In these cases, homologation is not required, but the UPC must verify that the degree certifies a level of training equivalent to an official Spanish master's degree and qualifies the holder for admission to doctoral studies in the country where it was issued. Admission on this basis does not imply homologation of the foreign degree or its recognition for any purpose other than admission to doctoral studies.
• Holders of a Spanish doctoral qualification issued under previous university regulations.

Note 1: Doctoral studies entrance regulations for holders of an undergraduate degree awarded before the introduction of the EHEA (CG 47/02 2014)

Note 2: Governing Council Decision 64/2014, which approves the procedure and criteria for assessing the fulfilment of academic admission requirements for doctoral studies by holders of non-homologated foreign degrees (CG 25/03 2014)

Admission criteria and merits assessment

Criteria for admission to the programme include the following:

• Particular consideration will be given to personal contact with the student based on interviews, questionnaires or exercises aimed at assessing their suitability for the programme and motivation.
• Other factors, such as knowledge of languages and previous research experience, will also be considered.

Selection criteria and weighting
To give priority to applicants who meet all of the entry requirements, admission criteria will be weighted as follows:
• Academic record: 50%.
• Personal contact and interview: 25%.
• Motivation: 5%.
• Knowledge of languages: 10%.
• Experience and research: 10%.
The body responsible for admission of students is the Joint Programme Studies Committee for the doctoral degree in Biomedical Engineering of the Universitat Politècnica de Catalunya and the University of Zaragoza. In accordance with the collaboration agreement between the two universities, this committee may authorise the programme coordinators at each university to assume responsibility for the admission process.

Training complements

The academic committee for the programme may require that doctoral students pass specific bridging courses. In such cases, the committee will keep track of the bridging courses completed and establish appropriate criteria to limit their duration. Bridging courses will provide research training, but in no case may doctoral students be required to enrol for 60 or more ECTS credits. The natural pathway for entry to the doctoral programme is via the master’s degree in Biomedical Engineering. Graduates of this master’s degree are not required to take any bridging courses.

Depending on their academic background, students admitted from other master’s degrees may be required to take subjects from the master’s degree in Biomedical Engineering as bridging courses (less than 60 ECTS credits). In all cases, bridging courses will provide research training and will be proposed by the Studies Committee based on each student’s curriculum vitae.

As in the case of admission decisions, the body responsible for determining what bridging courses a student must take will be the Studies Committee for the joint doctoral programme in Biomedical Engineering of the Universitat Politècnica de Catalunya and the University of Zaragoza.

This decision will be based on the subjects the student took for their master's degree and the research area of their thesis. The Studies Committee for the programme will keep track of the bridging courses completed and establish criteria to limit their duration.
Depending on their previous academic training, students may be required to take some of the following subjects from the master’s degree in Biomedical Engineering:
• Fundamentals of Molecular and Cellular Biology
• Fundamentals of Biophysics
• Fundamentals of Physiology
• Fundamentals of Pathophysiology
• Fundamentals of Informatics and Communications
• Fundamentals of Mathematics
• Fundamentals of Physics
• Fundamentals of Circuit Theory, Electronics and Automatic Control
• Bioelectricity and Bioelectromagnetism
• Physiological Control Models and Systems
• Biomaterials
• Biomedical Devices
• Biomedical Imaging
• Biomedical Instrumentation
• Methods for Modelling and Simulation of Biosystems
• Biomedical Signals
• Statistical Analysis of Biomedical Data
• Advanced Analysis and Processing of Biomedical Signals
• Analysis and Visualisation of Medical Images in 2D and 3D
• Biomechanics
• Dosimetry of Ionising Radiations
• Clinical Engineering and Healthcare Models
•Tissue Engineering
• Hospital Engineering
• Microsystems and Nanobioengineering
• Development and Design of Biomedical Equipment and Systems
• Radiation and Human Health
• Medical Robotics
• Bioinformatics
• Fundamentals and Techniques of Instrumental Analysis
• Medical Informatics and Telemedicine
• Medical Radiophysics
• Wireless/FDTD/FEM Simulation Techniques for Biomedical Applications
Subjects from the master's degree linked to the programme have well-defined objectives, methodologies and assessment processes that will enable doctoral students to acquire the skills specified in the previous sections.

In any case, depending on a student’s academic background, the Studies Committee may make adaptations with respect to the bridging courses required.
Taking into account the doctoral student activity report, the Studies Committee for the programme may propose measures that complement those specified in these regulations, and which result in doctoral students who do not meet the specified requirements being excluded from the programme.

Enrolment period for new doctoral students

The enrolment period for new doctoral students will be in September.

More information at the registration section for new doctoral students

Enrolment period

After the first year, the enrolment period for doctoral students will run from September to mid-October.

More information at the general registration section

Procedure for the preparation and defense of the research plan

Doctoral candidates must submit a research plan, which will be included in their doctoral student activity report, before the end of the first year. The plan may be improved over the course of the doctoral degree. It must be endorsed by the tutor and the supervisor, and it must include the method that is to be followed and the aims of the research.

At least one of these annual assessments will include a public presentation and defence of the research plan and work done before a committee composed of three doctoral degree holders, which will be conducted in the manner determined by each academic committee. The examination committee awards a Pass or Fail mark. A Pass mark is a prerequisite for continuing on the doctoral programme. Doctoral candidates awarded a Fail mark must submit a new research plan for assessment by the academic committee of the doctoral programme within six months.

The committee assesses the research plan every year, in addition to all of the other activities in the doctoral student activity report. Doctoral candidates who are awarded two consecutive Fail marks for the research plan will be obliged to definitely withdraw from the programme.

If they change the subject of their thesis, they must submit a new research plan.

Formation activities

Activity: Tutorial.
Hours: 288.
Type: compulsory.

Activity: Complementary courses taught by visiting professors.
Hours: 18.
Type: optional.

Activity: Seminars on very specific research topics and lectures given by visiting professors or researchers.
Hours: 3.
Type: optional.

Activity: Workshops on the use of scientific tools in biomedical engineering.
Hours: 3.
Type: optional.

Activity: International mobility.
Hours: 480.
Type: optional.

Activity: Training in information skills.
Hours: 1.5.
Type: optional.

Activity: Research methodology.
Hours: 12.
Type: optional.

Activity: Innovation and creativity.
Hours: 8.
Type: optional.

Activity: Language and communication skills.
Hours: 18.
Type: optional.

Activity: Assessment based on doctoral student activity report (DAD) and research plan.
Hours: 4.
Type: compulsory.

Procedure for assignment of tutor and thesis director

The academic committee of the doctoral programme assigns a thesis supervisor to each doctoral candidate when they are admitted or enrol for the first time, taking account of the thesis supervision commitment referred to in the admission decision.

The thesis supervisor will ensure that training activities carried out by the doctoral candidate are coherent and suitable, and that the topic of the candidate’s doctoral thesis will have an impact and make a novel contribution to knowledge in the relevant field. The thesis supervisor will also guide the doctoral candidate in planning the thesis and, if necessary, tailoring it to any other projects or activities undertaken. The thesis supervisor will generally be a UPC professor or researcher who holds a doctoral degree and has documented research experience. This includes PhD-holding staff at associated schools (as determined by the Governing Council) and UPC-affiliated research institutes (in accordance with corresponding collaboration and affiliation agreements). When thesis supervisors are UPC staff members, they also act as the doctoral candidate’s tutor.

PhD holders who do not meet these criteria (as a result of their contractual relationship or the nature of the institution to which they are attached) must be approved by the UPC Doctoral School's Standing Committee in order to participate in a doctoral programme as researchers with documented research experience.

The academic committee of the doctoral programme may approve the appointment of a PhD-holding expert who is not a UPC staff member as a candidate’s thesis supervisor. In such cases, the prior authorisation of the UPC Doctoral School's Standing Committee is required. A UPC staff member who holds a doctoral degree and has documented research experience must also be proposed to act as a co-supervisor, or as the doctoral candidate’s tutor if one has not been assigned.

A thesis supervisor may step down from this role if there are justified reasons (recognised as valid by the committee) for doing so. If this occurs, the academic committee of the doctoral programme will assign the doctoral candidate a new thesis supervisor.

Provided there are justified reasons for doing so, and after hearing any relevant input from the doctoral candidate, the academic committee of the doctoral programme may assign a new thesis supervisor at any time during the period of doctoral study.

If there are academic reasons for doing so (an interdisciplinary topic, joint or international programmes, etc.) and the academic committee of the programme gives its approval, an additional thesis supervisor may be assigned. Supervisors and co-supervisors have the same responsibilities and academic recognition.

The maximum number of supervisors of a doctoral thesis is two: a supervisor and a co-supervisor.

For theses carried out under a cotutelle agreement or as part of an Industrial Doctorate, if necessary and if the agreement foresees it this maximum number of supervisors may not apply. This notwithstanding, the maximum number of supervisors belonging to the UPC is two.

More information at the PhD theses section

Permanence

The academic committee of the programme may authorise an extension of up to one year for full-time doctoral candidates who have not applied to deposit their thesis by the end of the three-year period of study, in the terms outlined in the Academic Regulations for Doctoral Studies of the Universitat Politècnica de Catalunya. In the case of part-time candidates, an extension of two years may be authorised. In both cases, in exceptional circumstances a further one-year extension may be granted by the Doctoral School's Standing Committee, upon the submission of a reasoned application by the academic committee of the doctoral programme.

A doctoral candidate may be dismissed from a doctoral programme for the following reasons:

• The doctoral candidate submitting a justified application to withdraw from the programme.
• The maximum period of study and of extensions thereof ending.
• The doctoral candidate not having enrolled every academic year (unless he or she has been authorised to temporarily withdraw).
• The doctoral candidate failing two consecutive assessments.
• The doctoral candidate having disciplinary proceedings filed against him or her that rule that he or she must be dismissed from the UPC.

Dismissal from the programme implies that doctoral candidates cannot continue studying at the UPC and the closing of their academic record. This notwithstanding, they may apply to the academic committee of the programme for readmission and the committee must reevaluate them in accordance with the criteria established in the regulations.

International Mention

The doctoral degree certificate may include International Doctorate mention. In this case, the doctoral candidate must meet the following requirements:

a) During the period of study leading to the award of the doctoral degree, the doctoral candidate must have spent at least three months at a respected higher education institution or research centre outside Spain to complete courses or do research work. The stays and activities carried out must be endorsed by the thesis supervisor and authorised by the academic committee of the programme. The candidate must provide a certifying document issued by the person responsible for the research group of the body or bodies where the stay or activity was completed. This information will be added to the doctoral student’s activity report.
b) Part of the thesis (at least the summary and conclusions) must be written and presented in one of the languages commonly used for science communication in the relevant field of knowledge, which must not be an official language of Spain. This rule does not apply to stays and reports in Spanish or to experts from Spanish-speaking countries.
c) At least two PhD-holding experts belonging to a higher education institution or research centre outside Spain must have issued officially certified reports on the thesis.
d) The thesis examination committee must have included at least one PhD-holding expert from a higher education or research institution outside Spain who was not responsible for the candidate’s stay abroad (point a) above).
e) The thesis defence must have taken place on UPC premises or, in the case of joint programmes, at the location specified in the collaboration agreement.

List of authorized thesis for defense

• ORDOÑO FERNÁNDEZ, JESÚS: Lactate: unraveling the regenerative potential for cardiac tissue engineering
  
  Author: ORDOÑO FERNÁNDEZ, JESÚS
  Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
  Programme: DOCTORAL DEGREE IN BIOMEDICAL ENGINEERING
  Department: (CEM)
  Mode: Temporary seizure
  Deposit date: 29/09/2020
  Reading date: pending
  Reading time: pending
  Reading place: pending
  Thesis director: ENGEL LOPEZ, ELISABET | PEREZ AMODIO, SOLEDAD GRACIELA
  Committee:
       PRESIDENT: SEMINO MARGRETT, CARLOS EDUARDO
       SECRETARI: CANAL BARNILS, CRISTINA
       VOCAL: MORONI, LORENZO
  Thesis abstract: The increasing prevalence of cardiovascular diseases and their high health and socioeconomic impact on the world population urge the development of efficient new therapies for the reestablishment of the cardiac function. The heart has a very limited regenerative ability, and so lost cardiomyocytes cannot be replaced, thus causing permanent damage. These cells undergo different metabolic changes during development crucial for their maturation and adult function. During fetal development, proliferating cardiac cells reside in a low oxygen environment with high concentrations of lactate. After birth, cardiomyocytes cease their proliferating activity and shift their metabolism to fatty acid oxidation. Alterations of cardiac metabolism have also been associated with multiple disease states and pathological hypertrophy. Here in this work, we evaluated the response of cardiac cells to the presence of exogenous lactate, thus mimicking the metabolic microenvironment of early developmental stages.Lactate-exposed mouse primary cardiomyocytes and human iPSC-derived cardiomyocytes quickly acquired a characteristic dedifferentiated phenotype, with enhanced proliferative activity as determined by the expression of cell cycle (Ki67) and cytokinesis (AurB) effectors. We characterized lactate-induced cardiomyocyte dedifferentiation through RNA-sequencing and gene expression analysis and identified increased expression of BMP10 (involved in embryonic cardiomyocyte proliferation and stemness), LIN28 (a master regulator of stem cell fate and metabolism) and other genes associated to regulation of the stem cell fate (P63, TCIM or GATA4). On the other hand, we saw a downregulation of cardiac maturation genes related to lipid metabolism (DGKK) or electrical impulse regulation (GRIK1). Bottom-up analysis suggested the activation of hypoxia signaling pathways, indicating that, indeed, lactate may be a key player of hypoxic regenerative responses in the heart.Cardiomyocytes, however, are only 30-40% of the total population of cardiac cells. The majority of non-myocyte cells are comprised of cardiac fibroblasts and endothelial cells, whose interactions with cardiomyocytes highly contribute to heart repair and tissue homeostasis. Our results showed that lactate did not affect cardiac fibroblast proliferation, collagen production, migration or myofibroblast activation, which are detrimental factors for an effective cardiac regeneration. Lactate showed to reduce the expression of inflammatory cytokines involved in heart failure and cardiomyocyte apoptosis (Fas, Fractalkine or IL-12p40) and promote the production of healing and pro-regenerative signals (IL-13 and SDF-1a). In addition, endothelial precursor cells demonstrated their ability to use lactate as an effective energy source for survival and proliferation, even equivalent to the utilization of glucose. Taken together, the synergistic lactate response of the main cardiac cell types could enhance heart regeneration by supporting the growth and survival of new cardiomyocytes to repopulate the ischemic injury.Additionally, cardiac tissue constructs and ex vivo neonatal heart culture showed a more immature electromechanical behavior, with prolonged cardiac functions and improved proliferation as well as tissue integrity when culture media was supplemented with lactate. Thus, we explored the use of lactate-releasing cardiac scaffolds using different biomaterials, such as PLA, PLGA, alginate or conductive polymers, and different fabrication techniques, such as electrospinning; considering the fundamental aspects of cardiac scaffolds (anisotropy, flexibility and conductivity). These scaffolds proved to be an attractive and simple approach for a cardiac regenerative therapy.Altogether, the use of lactate as a metabolic modulator for the in situ activation of endogenous cardiac regenerative programs may revolutionize the design of new therapies for the treatment and regeneration of the failing heart.
  

Last update: 24/10/2020 05:09:06.

List of lodged theses

• FEBRER NAFRÍA, MIRIAM: Optimal control prediction of assisted walking using torque-driven models
  
  Author: FEBRER NAFRÍA, MIRIAM
  Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
  Programme: DOCTORAL DEGREE IN BIOMEDICAL ENGINEERING
  Department: Department of Mechanical Engineering (EM)
  Mode: Temporary seizure
  Deposit date: 22/10/2020
  Reading date: pending
  Reading time: pending
  Reading place: pending
  Thesis director: FONT LLAGUNES, JOSEP MARIA | FREGLY, BENJAMIN J.
  Committee:
       PRESIDENT: TAVARES DA SILVA, MIGUEL
       SECRETARI: BARJAU CONDOMINES, ANA
       VOCAL: GONZÁLEZ VARELA, FRANCISCO JAVIER
  Thesis abstract: Walking impairment after spinal cord injury leads to a decreased quality of life, other serious health conditions, and substantial health care costs. Consequently, gait restoration is a high priority among spinal cord-injured (SCI) subjects; and it can be partially achieved using active orthoses or exoskeletons, together with some type of external support for balance (e.g., crutches or a walker). Customisation of active orthoses control algorithms to maximise the walking ability of each patient is currently done through trial-and-error methods, making it difficult if not impossible to identify the best active control parameters for any particular patient. An objective simulation-based method that accounts for patient-specific needs would lead to a patient-tailored assistive device development process. Multibody system dynamics has been used for many years for the biomechanical analysis and simulation of human motion. Moreover, optimal control is being used to predict novel human motions, while methods to develop patient-specific neuromusculoskeletal models are currently being investigated. There are published studies that show the potential that subject-specific simulations have to improve rehabilitation treatments and assistive device adaptation to specific subjects. However, researchers have not yet fully demonstrated the effectiveness of these methods using a larger number of patients and a wider variety of treatments.In this thesis, we have investigated the use of optimal control formulations to predict crutch-orthosis-assisted walking using torque-driven multibody dynamic models. The main objective has been to develop a simulation tool to predict crutch-orthosis-assisted walking that could serve in the future as a basis to support the design and control of an active knee-ankle-foot orthosis. The approach used involved development of a subject-specific torque-driven model based on a current available model in OpenSim, into which orthoses and crutches were incorporated. The foot-ground and crutch-ground interactions have been modelled with compliant contact models using visco-elastic force models. The different optimal control problems have been solved using a direct and simultaneous collocation method using the optimal control software GPOPS-II.First, eight different optimal control formulations to track normal and crutch-assisted walking motions were developed and compared. Then, foot- and crutch- ground contact models were developed and calibrated to obtain dynamically consistent full walking cycles using an optimal tracking problem. Moreover, an optimal control framework for predictive simulations of normal and crutch-assisted walking patterns was implemented. Normal walking cycles were predicted using different optimality criteria, and results were analysed and compared. Crutch-assisted walking cycles were also predicted using different optimality criteria, following different walking patterns (four-point, two-point and swing-through), and at different walking speeds. Finally, predictive simulations of crutch-orthosis-assisted walking of a healthy subject and an SCI subject using a real assistive robotic orthosis were performed, and results were evaluated against experimental data. These simulations represent a step forward toward developing a predictive tool for the personalisation of active orthoses to specific SCI subjects, which could maximise the walking ability of each patient.
  

Last update: 24/10/2020 05:08:01.

List of defended theses by year

• IGLESIAS FERNÁNDEZ, JELISA MARIA: Enrichment of virtual screening results using induced-fit techniques
  
  Author: IGLESIAS FERNÁNDEZ, JELISA MARIA
  Thesis link: http://hdl.handle.net/10803/668826
  Programme: DOCTORAL DEGREE IN BIOMEDICAL ENGINEERING
  Department: Department of Automatic Control (ESAII)
  Mode: Normal
  Reading date: 16/01/2020
  Thesis director: GUALLAR TASIES, VÍCTOR | ESTRADA COLLADO, JORGE
  

  Committee:
       PRESIDENT: FERNÁNDEZ RECIO, JUAN
       SECRETARI: GELPI BUCHACA, JOSE LUIS
       VOCAL: CORTÉS MASTRAL, JUAN
  Thesis abstract: This thesis explains the design, development, test on the benchmarking dataset DUD-e and the application to an industrial virtual screening project of the PELE VS platform.The most common and quick tools used on virtual screening campaigns do not take into account the induced-fit effect, although there are some methodologies capable of reproducing this effect they are either time consuming or very limited on which transformations the protein may undergo. In this thesis with the development of the PELE VS platform we aim at using the simulation software PELE (Protein Energy Landscape Exploration) to account for the induced-fit effect.The PELE software uses a monte carlo algorithm coupled with an energy minimization step to explore the ligand conformations and model the protein. This approach allows the program to account for both big conformational changes and small local changes of the protein and to perform a good conformational search of the ligand, which coupled can account for the induced-fit effect with only a quick simulation.PELE has been traditionally, and successfully, used in the enzyme engineering field where only a few compounds per protein are usually tested and studied. In order to apply the program to the virtual screening field, where thousands of compounds are tested in silico, the first step was to automatize the whole procedure of preparing, launching and analyzing the simulations. Thus, during this thesis the PELE VS platform has been developed altogether with other auxiliary tools.Once the platform was developed, we wanted to test the behaviour of PELE on a well known benchmarking dataset, thus we tried our methodology on the DUD-e dataset. Since this dataset is formed by more than 100 proteins, we chose a few proteins for eachof the families present in the dataset, reducing the number of proteins to 21 systems. Then, we tried to use a general protocol for all the chosen proteins in order to improve the results of currently used scoring functions in the field. After studying the simulations and trying several protocols on this subset we we observed that every protein (or at least family) that we want to study needs an specific simulation protocol in order to correctly reproduce the induced-fit effect and improve the results of the most used scoring function: glide from schrodinger.Finally we applied the platform and our previous hypothesis to an industrial virtual screening campaign, as part of the collaborative Retos project: Silicoderm. In this case we worked with only one protein and several compounds and we confirmed the need for a tailored simulation protocol for the receptor in order to improve results.
  

• PICART ARMADA, SERGIO: Statistical Normalisation of Network Propagation Methods for Computational Biology
  
  Author: PICART ARMADA, SERGIO
  Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
  Programme: DOCTORAL DEGREE IN BIOMEDICAL ENGINEERING
  Department: Department of Automatic Control (ESAII)
  Mode: Article-based thesis
  Reading date: 23/07/2020
  Thesis director: PERERA LLUNA, ALEXANDRE
  

  Committee:
       PRESIDENT: VALENCIA HERRERA, ALFONSO
       SECRETARI: TOST PARDELL, DANIELA
       VOCAL: CASTELO VALDUEZA, JUAN ROBERTO
  Thesis abstract: The advent of high-throughput technologies and their decreasing cost have fostered the creation of a rich ecosystem of public database resources. In an era of affordable data acquisition, the core challenge has shifted to improve data interpretation, in order to understand normal and disease states. To that end, leveraging the current contextual knowledge in the form of annotations and biological networks is a powerful data amplifier to elucidate novel hypotheses.Label propagation and diffusion are the linchpin of the state of the art in network algorithms. In its simplest form, label propagation predicts the labels of a given node (for instance a gene, protein or metabolite) using those of its interactors. More elaborated approaches propagate beyond direct interactors, with robust performance in many computational biology domains.It has been pointed out that the topological structure of biological networks can bias propagation algorithms. Poorly known entities are overlooked and harder to link to experimental findings, which in turn keeps them barely annotated. Some efforts try to break this circularity by statistically normalising the topological bias, but the properties of the bias and the real benefit of its removal are yet to be carefully examined.This thesis covers two blocks. First, a characterisation of the bias in diffusion-based algorithms, with the implementation of statistical normalisations. Second, the application of such normalisation in classical computational biology problems: pathway analysis for metabolomics data and target gene prediction for drug development. In the first block, the presence of the bias is confirmed and linked to the network topology, albeit dependent on which nodes have labels. Equivalences are proven between diffusion processes with variations on their definitions, thus easing its choice. Closed forms on the first and second statistical moments of the null distributions of the diffusion scores are provided and linked to the spectral features of the network. The normalisation can be detrimental if the bias favours nodes with positive labels. An ad-hoc study of the data and the expected properties of the findings is recommended for an optimal choice. To that end, this thesis contributes the diffuStats software package, easing the computation and benchmark of several normalised and unnormalised diffusion scores.The second block starts with pathway analysis for metabolomics data. This choice is driven by the relative lack of computational solutions for metabolomics, whose output still requires an effortful interpretation. Here, a knowledge graph is conceived to connect the metabolites to the biological pathways through intermediate entities, like reactions and enzymes. Given the metabolites of interest, a propagation process is run to prioritise a relevant sub-network, suitable for manual inspection. The statistical normalisation is required due to the network design and properties. The usefulness of this approach is proven not only regarding pathway findings, but also examining the metabolites and reactions within the suggested sub-networks. The knowledge network construction and the propagation algorithm are distributed in the FELLA software package.The second practical application is the prediction of plausible gene targets in disease. Besides benchmarking the effect of the statistical normalisation, particular care is put into obtaining meaningful performance estimates for practical drug development. Target data is usually known at the protein complex level, which leads to performance over-estimation if ignored. Here, this effect is corrected in a varied comparison of prioritisation algorithms, networks, performance metrics and diseases. The results support that the statistical normalisation has a small but negative impact. After correcting for the protein complex structure, network-based algorithms are still deemed useful for drug discovery.
  

Last update: 24/10/2020 05:07:30.

Research groups

• B2SLab-Bioinformatics and Biomedical Signals Laboratory
• BBT-Biomaterials, Biomechanics and Tissue Engineering
• BIOSPIN-Biomedical Signal Processing and Interpretation
• DRM-Dosimetry and Medical Radiation Physics
• GIE-Engineering Informatics Group
• GREC-Knowledge Engineering Research Group
• GRINS-Intelligent Robots and Systems
• GRUP ISI-Instrumentation, Sensors and Interfaces Group
• IEB-Electronic and Biomedical Instrumentation
• InSup-Surface Interaction in Bioengineering and Materials Science Research Group
• VIS-Artificial Vision and Intelligent Systems

Teachers

• Amat Girbau, Josep
• Aranda Lopez, Joan
• Ayala Vallespi, Maria Dolors
• Aymerich Martinez, F. Xavier
• Benitez Iglesias, Raul
• Bragos Bardia, Ramon
• Caminal Magrans, Pere
• Canal Barnils, Cristina
• Casals Gelpi, Alicia
• Casas Piedrafita, Jaime Oscar
• Duch Guillen, M. Amor
• Engel Lopez, Elisabet
• Español Pons, Montserrat
• Fernandez Chimeno, Mireya
• Font Llagunes, Josep Maria
• Frigola Bourlon, Manel
• Garcia Gonzalez, Miquel A.
• Ginebra Molins, Maria Pau
• Ginjaume Egido, Merce
• Giraldo Giraldo, Beatriz F.
• Gomis Roman, Pedro
• Jane Campos, Raimon
• Manero Planella, Jose M.
• Mañanas Villanueva, Miguel Angel
• Mas Moruno, Carlos
• Millan Garcia Varela, Maria Sagrario
• Montseny Masip, Eduard
• Nescolarde Selva, Lexa Digna
• Oñate Ibañez de Navarra, Eugenio
• Pallàs Areny, Ramon
• Perera Lluna, Alexandre
• Pla Garcia, Nuria
• Ramos Castro, Juan Jose
• Riu Costa, Pere Joan
• Rodellar Benede, Jose
• Rodriguez Rius, Daniel
• Rosell Ferrer, Javier
• Sobrevilla Frison, Pilar
• Torres Cebrian, Abel
• Tost Pardell, Dani
• Vallverdu Ferrer, Maria Montserrat
• Vigo Anglada, Marc