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

Last update: 16/10/2021 04:47:07.

List of lodged theses

Last update: 16/10/2021 04:30:36.

List of defended theses by year

• KONKA, JOANNA MAGDALENA: 3D-Printed Biomimetic Bone
  
  Author: KONKA, JOANNA MAGDALENA
  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
  Reading date: 01/10/2021
  Thesis director: GINEBRA MOLINS, MARIA PAU | ESPAÑOL PONS, MONTSERRAT
  

  Committee:
       PRESIDENT: GONZÁLEZ FERNÁNDEZ, PÍO MANUEL
       SECRETARI: CANAL BARNILS, CRISTINA
       VOCAL: TAMIMI MARIÑO, FALEH AHMAD
  Thesis abstract: Over 2 million bone grafting procedures are performed each year. In the last years, synthetic calcium phosphates have drawn the attention of the researchers for their close similarity to the mineral phase of bone by offering exceptional bioactivity, osteoconductivity, and biocompatibility. Especially promising showed to be biomimetic calcium deficient hydroxyapatite (CDHA), which can be obtained through hydrolysis of a-tricalcium phosphate (a-TCP) at physiological temperature in a self-setting reaction. This has been exploited in calcium phosphate cements. Furthermore, this material can be fabricated by robocasting which offers great opportunities for patient-specific bone graft production by allowing control of external geometry and internal macroporosity of such obtained CDHA scaffolds. The present thesis is divided into two parts: (i) investigation of CDHA physicochemical changes after incubation in culture medium over long time periods, (ii) design and fabrication of 3D robocasted CDHA bone grafts to enhance their biological properties by two strategies, (a) the incorporation of ions and (b) the introduction of concave porosity in the printed filaments. Chapter 1 presents an overview of bone composition and biology, bone grafting strategies with their advantages and disadvantages, as well as puts forward strategies to enhance their biological performance. Chapter 2 investigates the physicochemical changes that undergoes CDHA after incubation in culture medium over extended time periods depending on the morphology of crystals (needle-like versus plate-like) and specific surface area (SSA). The study focuses on the structural changes such as crystallinity evolution, as well as the chemical ones in terms of local gradient of carbonation (confocal Raman microscopy mapping) and global ionic incorporation. Last but not least, differences in protein adsorption content and protein patterns (LC- MS/MS proteomics analysis) are put forward depending on the sample type. Overall, higher carbonation, ionic incorporation and protein adsorption capability and selectivity was observed for fine specimens of needle-like crystal morphology than coarse specimens of plate-like one. Chapter 3 and Chapter 4 explore two independent strategies to enhance biological properties of 3D printed CDHA. Chapter 3 explores incorporation of different ions (Sr, Mg, and Si) by soaking 3D CDHA in ionic solutions during the biomimetic setting at physiological temperatures. This easy strategy of chemical modification of scaffolds is evaluated by X-ray diffraction (XRD), scanning electron microscopy (SEM), inductively coupled plasma (ICP-OES), and fourier-transform infrared spectroscopy (FTIR). Furthermore, an ionic release study was performed and evaluated by ICP-OES. A comparison between scaffolds, before and after the release, was carried out by FTIR to obtain information about crystallinity and the evolution of the hydrated layer. Chapter 4 proposes the use of gelatin microspheres to introduce concave macropores into the robocasted filaments of 3D CDHA scaffolds. Neither the phase transformation responsible for the hardening of the scaffold nor the formation of characteristic network of needle-like hydroxyapatite crystals was affected by the addition of gelatin microspheres. The partial dissolution of the gelatin resulted in the creation of spherical pores throughout the filaments and exposed on the surface, increasing filament porosity from 0.2% to 67.9%. Moreover, the presence of retained gelatin proved to have a very significant effect on the mechanical properties, reducing the strength but simultaneously giving the scaffolds an elastic behavior, despite the high content of ceramic as a continuous phase. Notwithstanding the inherent difficulty of in vitro cultures with this highly reactive material, the presence of retained gelatin in the scaffolds was shown to favor the proliferation of MG-63 cells, as well as the spreading of hMSCs.
  

• LÓPEZ DEL RÍO, ÁNGELA: Data preprocessing and quality diagnosis in deep learning-based in silico bioactivity prediction
  
  Author: LÓPEZ DEL RÍO, ÁNGELA
  Thesis link: http://hdl.handle.net/10803/672385
  Programme: DOCTORAL DEGREE IN BIOMEDICAL ENGINEERING
  Department: Department of Automatic Control (ESAII)
  Mode: Article-based thesis
  Reading date: 23/06/2021
  Thesis director: PERERA LLUNA, ALEXANDRE
  

  Committee:
       PRESIDENT: MARCO COLÁS, SANTIAGO
       SECRETARI: GIBERT OLIVERAS, CARINA
       VOCAL: PUJADAS ANGUIANO, GERARD
  Thesis abstract: Drug discovery is a time and resource consuming process involving the identification of a target and the exploration of suitable drug candidates for it. To streamline drug discovery, computational techniques help identifying molecular candidates with desirable properties by modeling their interactions with the target. These techniques are in constant improvement thanks to the development of algorithms, the increasing computational power and the growth of public molecular databases. Specifically, machine learning approaches provide predictive models on biochemical properties and target-ligand binding activity. Deep learning is a machine learning approach that automatically extracts multiple levels of representations of the data. Within the last ten years, deep learning has outperformed classical prediction models in most domains, including drug discovery. Common use cases encompass molecular property prediction, de novo compound generation, protein secondary structure prediction and target-compound binding prediction. However, studies point out the reported performance of deep learning bioactivity prediction models could be a consequence of data bias rather than generalization capability. Efforts are being put in addressing this problem, but it is still present in the state of the art, rewarding novelty over critical assessment. Moreover, the flexibility of deep learning derives in a lack of consensus on how to represent the input spaces, making it difficult to compare models in a common benchmark. Bioactivity data has limited availability because of its associated costs and is often imbalanced, hampering the model learning process. The diagnosis of these problems is not straightforward, since deep learning models are considered black boxes, hindering their adoption as the de facto solution in computer-aided drug discovery. The present thesis aims to improve deep learning models for computational drug discovery, focusing in the input representation, the data bias control, the data imbalance correction and the model diagnosis. First, this thesis assesses the effect that different validation strategies have on binding classification models, aiming to find the most realistic performance estimates. The strategy based on clustering molecules to avoid having similar compounds in training and test sets showed to be the most similar to a prospective validation, and thus, more consistent than random cross-validation (over-optimistic) or than an external test set from other database (over-pessimistic).Second, this thesis focuses on the sequential inputs padding. Padding is necessary to establish a common sequence length by adding zeros to each sequence. These are usually added at the end of the sequence, without formal justification behind it. Here, classical and novel padding strategies were compared in an enzyme classification task. Results showed that the padding position has an effect in the performance of deep learning models, so it should be tuned as an additional hyperparameter.Third, this thesis studies the effect of data imbalance in protein-compound activity classification models and its mitigation through resampling techniques. The model performance was assessed for different combinations of oversampling the minority class and clustering. Results showed that the proportion of actives predicted by the model was explained by the actual data balance in the test set. Data clustering, followed by data resampling in training and validation sets, stood as the best performing strategy without altering the test set.To accomplish the three points above, this thesis provides a systematic way to diagnose deep learning models, identifying the factors that govern the model predictions and performance. Specifically, explanatory linear models enabled informed, quantitative decisions regarding input preprocessing. This ultimately leads to more consistent deep learning target-compound binding prediction models.
  

• NOLLA COLOMER, CARME: Anàlisi de patrons funcional i estructurals en la regulació del calci en les cèl·lules cardíaques
  
  Author: NOLLA COLOMER, CARME
  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: Temporary seizure
  Reading date: 28/05/2021
  Thesis director: BENITEZ IGLESIAS, RAUL | MADSEN, LEIF HOVE
  

  Committee:
       PRESIDENT: MARTI BONMATI, JOAN
       SECRETARI: RODELLAR BENEDE, JOSE JULIAN
       VOCAL: GUERRA RAMOS, JOSÉ MARÍA
  Thesis abstract: In 2019 the data published by the World Health Organization showed that the cardiac ischemia is the first cause of death worldwide. These diseases are caused by irregularities of the contractile mechanism¿s function, starting from the cellular level till the organ dysfunction. To further understand the origin of these dysfunctions the thesis will focus on the molecular and cellular level. The small changes of the physiology at that level can lead to an anomalous cardiac electrophysiology.The previous studies suggest that there is a relation between the cardiac arrhythmia and the increase of global spontaneous calcium activity in cells. Ryanodine receptors have the major role in the calcium regulation. They release the calcium stored in the sarcoplasmic reticulum into the cytosol, then the calcium attaches to the actin and myosin to produce the mechanicalcontraction of the cell. The irregularities have been also related with an hyperphosphorylation of the ryanodine receptor channels, which increases the open probability of those.A large amount of data is generated in the biology and physiology laboratories, these have to be characterized, clustered and analysed to extract the meaning of the observed divergences. Thus, an interdisciplinary thesis has been developed in order to obtain experimental data with a confocal microscope in the laboratory and then creating new image processing tools in order to have an interpretable analysis of the experimental data.The main objective of the project is to characterize the spontaneous calcium activity through image processing tools and to observe its variations under different physiological conditions, such as the hiperphosphorylation of the ryanodine receptor channels or under cardiac arrhythmia conditions. The aim is to see how the modifications in the calcium activity affect to the propagation along the cell and report how the variations may lead to electric and contractile dysfunctions, and so, cause arrhythmias.To reach this goals the thesis is divided into three main sections or hypothesis:1. Experimental data acquisition, define the best image acquisition method in order to develop the studies of calcium images and proposal of methods to detect subcellular structures and spontaneous calcium events.2. Study of the calcium events substructure and the involved ryanodine receptor clusters. Comparison of the calcium activity properties of the cells at the basal level and under conditions of hyperphosphorylation or arrhythmia.3. Study of the physiological modifications in the calcium activity through different phosphorylation pathways.The results explain the ryanodine receptor clusters distribution through the cells, allow to have the localization of the channels and the calcium activity simultaneously and show relevant details such as, the increase in the duration of the events or the increase in the volume of calcium released when more ryanodine receptor clusters are co-activated. These modifications lead to have bigger events and, thus, more potentially dangerous because can depolarize the neighbouring cells. The parameters reflect the relationship between the phosphorylation of the ryanodine receptors and the spontaneous calcium release in the arrhythmogenesis process.
  

Last update: 16/10/2021 05:11:51.

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

• ALESANCO IGLESIA, ALVARO
• ALMEIDA, RUTE
  
• ALTANKOV, GEORGE PETROV
• BAILON, RAQUEL
• BALDASSARRI, SANDRA
• BURDÍO PINILLA, FERNANDO
• CALVO CALZADA, BEGOÑA
• DOBLARE CASTELLANO, MANUEL
• FALCO BOUDET, JORGE
• GARCIA AZNAR, JOSE MANUEL
• GARCIA MOROS, JOSE
• GIL MUR, XAVIER
• GRACIA VILLA, LUIS
• LACROIX, DAMIEN
• LAGUNA LASAOSA, PABLO
• LLEIDA SOLANO, EDUARDO
• MAINARDI, LUCA
• MARTINEZ CORTES, JUAN PABLO
• MARTINEZ MONTIEL, JOSE MARIA
• MARTINEZ RUIZ, IGNACIO
• MATEOS TIMONEDA, MIGUEL ANGEL
  
• MINGUEZ ZAFRA, JAVIER
• NOAILLY, JEROME
• OLMOS GASSO, SALVADOR
• ORRITE URUÑUELA, CARLOS
• PLANELL ESTANY, JOSEP A.
• PUEYO PAULES, ESTHER
• SANZ MOLINA, ALFREDO