PhD scholarship @Pompeu Fabra, Barcelona

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PhD Project D-Risc: Multiscale modelling & data mining for intervertebral disc degeneration risk prediction
(Pompeu Fabra University, Barcelona, Spain)

GRANT PROGRAMME: “LA CAIXA” DOCTORATE INPHINIT

35 PhD fellowships for early-stage researchers of any nationality to pursue their PhD studies in research centres accredited with the Spanish Seal of Excellence Severo Ochoa, María de Maeztu or Health Institute Carlos III. This frame is addressed exclusively to PhD research projects on STEM disciplines: life sciences and health, experimental sciences, physics, chemistry and mathematics.

More information

POSITION: “D-Risc: Multiscale modelling & data mining for intervertebral disc degeneration risk prediction“

Area and discipline: please choose 1 from the following list:

Area of knowledge

Physical Sciences, Mathematics and Engineering

Group of disciplines
Telecommunications, Electronics, Robotics, Biomedical Engineering, Automation Engineering, ICT

Discipline

Biomedical Engineering, ICT

Research project / Research Group description:

Research project and main focus of the research line of the research group in which the fellow would join

D-Risc aims to reveal critical interplays of crucial stimuli within the intervertebral disc (IVD) that might lead to IVD degeneration, based on morphological and physiological parameters. Different models at the organ, tissue and cellular levels will be used. Specifically, the project will combine multi-physics finite element models at the organ and tissue levels with agent-based and network models at the cell and molecular levels, to simulate the local regulation of IVD cells in multifactorial physical and biochemical micro-environments. Simulation results will be mined with patient-specific morphological, physical activity and life-style data. Depending on the identified multiscale paths that can lead to degeneration-related cell activity (i.e. catabolic shift of cell activity), personalised recommendations for prevention- and optimised conservative treatments will be established.

D-Risc will exploit the competencies of the Biomechanics and Mechanobiology (BMMB – http://biomech.es) lab of the BCN MedTech research unit at the Department of Information and Communication Technologies (DTIC) of the Universitat Pompeu Fabra (UPF), Barcelona. The project will be additionally implemented in cooperation with the medical image analysis and machine learning areas of BCN MedTech (http://bcn-medtech.upf.edu/).

UPF was established in 1990 as a public university with strong dedication to excellence in research and teaching. It is the 1st Spanish university in the world Top 200 (THE2020), the 11th (ranked 5th in Europe and 1st in Spain) under 50 years (THE18). It also ranked 5th in Europe and 1st in Spain (U-Multirank 2018) in teaching and research performance (U-Ranking, BBVA Foundation & Ivie, 2018), quality output (excellence rate), normalized impact and percentage of collaborative papers with foreign institutions. UPF is full member of the Big Data Value Association (BDVA). DTIC has since its creation emphasized scientific excellence and internationalisation as core aspects of its activities. It has an important track record of active participation in EU projects (a total of 66 FP7 projects and 10 other projects in non-FP7 program such as CIP, Ambient Assisted Living and the Lifelong Learning Program, and, up to now 44 H2020 projects). It is the Spanish university department with the largest number of ERC grants (9 FP7 and 9 H2020) and is part of the FET Flagship initiative “The Human Brain Project”. DTIC has been awarded the “María de Maeztu” excellence by the Spanish government for the quality and relevance of its pioneering scientific research.

BCN MedTech is the Barcelona Centre for New Medical Technologies at UPF. It focusses on biomedical integrative research, including mathematical and computational models, algorithms and systems for computer-aided diagnosis and treatment, and the translation thereof into relevant clinical problems and industrial products. It has a team of 60 full time researchers working on medical image and signal processing, computational simulation, computer-assisted surgery and biomedical electronics. Within BCN MedTech, the BMMB lab combines mechanistic and stochastic theoretical modelling with computational methods in biology and physics, to rationally explore the complex multiscale interactions between tissue multiphysics and biological processes, and to understand the bottom-up regulation of the functional biomechanics of organs in health and disease. The specific targets are cartilaginous (rheumatic disorders), bone (osteoporosis), arterial (atherosclerosis) and lung (emphysema) tissues. The project will combine this expertise with computational anatomy and manifold learning techniques for patient stratification, from the BCN MedTech medical image analysis and machine learning areas.

Job position description: role, responsibilities and skills required within the project/group.

D-Risc capitalizes on previous research at BCN MedTech, to assess the risk of disc degeneration (DD). Patient-specific IVD finite element (FE) models will be coupled to agent-based (AB)/network cell models, to predict catabolic shifts of cell activity in function of morphological, metabolic and mechanical factors. According to subsequent machine learning analyses, specific combination of factors will be identified as possible risks for DD.

Low back pain (LBP) affects up to 85% of people at some point in life. It is strongly related to DD, with phenotypes that cannot be explained solely by genetic factors as they also depend on mechanical loads.

In vivo or in-vitro studies investigated DD at the cell and tissue levels, but they are costly and limited in terms of parameterization, effective number of measurements and long-term observations. In contrast, computational modelling allows testing different boundary conditions (mechanical, biochemical, …) and numerous theoretical hypotheses over long timescales, at a relatively limited cost. 

Coupled to personalized organ models, multiscale models and simulations can indicate common patterns in specific groups of IVD, as well as critical combinations of cell stimuli and the effects thereof on DD observable features. In particular, the mining of model inputs together with simulated data can reveal such patterns and combinations.

The successful candidate will join the BCN MedTech team and will be co-supervised by faculties, experts in computational multiscale modelling and machine learning. (S)He will systematically analyze the 3D anatomy of 500 patient-specific IVD FE models, available at UPF, to define relevant groups of FE /AB multiscale simulations. Then, (s)he will use machine learning algorithms to build correlation models among personalized model inputs and predicted cell activity, to create a DD risk score model. 

D-Risc will involve key collaborations with population cohort infrastructures in UK and Finland.

PRINCIPAL INVESTIGATOR & CONTACT AT HOST

Dr Jérôme Noailly
Contact: jerome.noailly@upf.edu

Barcelona Centre for New Medical Technologies (BCN MedTech)

Department of Information and Communication Technologies

Universitat Pompeu Fabra, Barcelona, Spain

ADDITIONAL INFO

Press articles related with the work of the BCN MedTech BMMB team in disc degeneration:

CONTRACT CONDITIONS & ELEGIBILITY

The maximum total payment amount will be €122,592, as broken down below:

  • Three annual payments of €34,800 each one. Where applicable, the amounts corresponding to the Social Security contributions payable by the employer (in this case, the host institution), as well as any other compulsory fee, whether current or that may be provided for in a future legal framework, will be deducted from the yearly gross amount of €34,800 to be received by the fellow.
  • €3,564 per year, as an additional amount for conferences, courses, research stays, consumables, equipment, charges for the use of intellectual property, etc. This additional amount will be managed by the centre for the benefit of the fellow and must be justified separately.
  • ”la Caixa” Banking Foundation will award a prize of €7,500, which will be paid in the fourth year, should the fellow be able to deposit their thesis within 6 months after the third year of their fellowship has ended.
  • ”la Caixa” Banking Foundation will sign an agreement with the host institution, which will receive the fellowship payment directly. This must be wholly allocated to cover the amounts arising from Social Security contributions and other required corporate expenses payable by the employer, where applicable, as well as the fellow’s gross stipend and the additional amount.

Eligibility:

  • Experience: At the call deadline, applicants must be in the first four years (full-time equivalent research experience) of their research careers and not yet have been awarded a doctoral degree.
  • Studies pursued: At the time of recruitment, candidates must comply with one of the following options:
    • To have completed the studies that lead to an official university degree adapted to the European Higher Education Area awarding 300 ECTS credits, of which at least 60 ECTS credits must correspond to master level.
    • To have completed a degree in a university not adapted to the European Higher Education Area that gives access to doctoral studies. The verification of an equivalent level of studies to the ones mentioned above will be made by the university when the admission procedure starts.
  • Geographic mobility: For candidates applying to Spanish centres or units: Candidates must not have resided or have carried out their main activity (work, studies, etc.) in Spain for more than 12 months in the 3 years immediately prior to the call deadline.
  • Level of English: Candidates must have a demonstrable level of English (B2 or higher).

APPLICATION & DEADLINES

How to apply: https://obrasociallacaixa.org/en/investigacion-y-becas/becas-de-la-caixa/doctorado-inphinit/incoming

Deadline: 4 February 2020

Important dates:

18 February 2020 – Deadline for submitting the language certificate.

16 April 2020 – Notification of the shortlist results.

27 and 28 May 2020 – Face-to-face interviews in Barcelona.

2 June 2020 – Publication of the final list of selected candidates.

From 2 to 30 June 2020 – Matching research centre – fellow.

Two PhD Positions at The City College of New York

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The Laboratory of Dr. Alessandra Carriero in the Department of Biomedical Engineering at The City College of New York, is offering two PhD Positions in the field of Bone Multiscale Mechanics and Mechanobiology, and Hearing Biomechanics.

Dr. Carriero’s research focuses on providing a comprehensive understanding of bone mechanics and adaptation in healthy, aging and disease so to aid in the development of new treatment strategies for bone frailty and deformities, and hearing loss.  Dr. Carriero’s lab uses mechanical engineering methods, material science approaches, high-resolution imaging, clinical data and biological analysis to reveal how mechanical forces influence bone growth, maintenance and function. Bone fragility is very common but yet not well understood. Understanding the mechanisms of bone failure and hearing loss in frailty has potential to make a significant positive impact on the quality of life of people worldwide, while delivering economic benefits to our society.

Position 1: This research will reveal the contribution of bone composition and structure to mechanical properties of bone along its multiscale hierarchy and specifically on its fracture toughness. The specific aims of this PhD project are to 1) investigate the fracture toughness properties of bone using high-resolution imaging acquisition and analysis for bone composition and structure while simultaneously fracturing bone in healthy, disease and treated bone; (2) assess local bone measurements with biomarkers and compare these to the structure/composition and mechanics of bone; (3) develop new multiscale modeling approaches to evaluate fracture resistance in brittle bones and treatments.


Position 2: This research will contribute to understanding of hearing loss in osteogenesis imperfecta (or brittle bone disease). The specific aims of this PhD project are to 1) develop novel high-resolution imaging acquisition analysis for cochlea micromechanics; (2) assess bone and soft tissue structure, composition and mechanics in mouse ears; (3) develop modeling approaches to evaluate cochlea mechanics in healthy, disease and treated conditions.

Both positions will be based at The City College of New York, where the students will be enrolled in the Doctorate Program in Biomedical Engineering, and research will be conducted in collaboration with other institutions in US and UK, particularly Hospital for Special Surgery, Northwestern University, Imperial College and the Diamond Light Source.

The successful candidate holds or will soon receive a Master’s or an equivalent Degree in Biomedical Engineering, Mechanical Engineering, Physics, Materials Science or Mathematics. A high motivation to work in a pioneering research environment at the interface between engineering, science and medicine is essential as well as the enthusiasm to work in an international and multidisciplinary team. Availability to travel internationally and work with animals is required. Good knowledge of English (oral and written) is essential. Experience in one or more of the following is desirable: biomedical research, mechanical testing, experimental testing of bone, imaging acquisition, imaging processing, computational modeling techniques.

We look forward to receiving your application including a motivation letter, CV, university transcripts and names and contact details of three references. Applications must be submitted to Dr. Carriero at acarriero@ccny.cuny.edu. The positions are available immediately and will last until filled.

For further information about the positions, please contact Dr. Alessandra Carriero at acarriero@ccny.cuny.edu.

Marie Sklodowska-Curie PhD Position

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Marie Curie PhD position in the EU ETN: Skin Tissue Integrity under Shear (STINTS)

Applications are invited for an Early Stage Researcher position in the Musculoskeletal Biomechanics Laboratory of the Department of Biomedical Engineering at the Faculty of Engineering of Tel Aviv University (TAU), Israel.

The topic of the PhD is the development and implementation of multiscale/multiphysics soft tissue models in non-diabetic and diabetic/obese persons, in the context of the individual risk for pressure ulcers or diabetic foot ulcers.

Other institutions in the STINTS network include Eindhoven University of Technology (Prof. Cees Oomens) and Université Grenoble Alpes (Prof. Yohan Payan): https://cordis.europa.eu/project/rcn/218412/factsheet/es

The link to the advertisement for this position with further details about TAU, the STINTS European Training Network (ETN), and personal requirements/eligibility criteria can be found here: https://euraxess.ec.europa.eu/jobs/378983

 Informal enquiries are encouraged and should be directed to: Prof. Amit Gefen (gefen@tauex.tau.ac.il)

 Closing date for applications: 8th November 2019. The position is available now, with a start date expected to be as soon as is practical.

POSTDOCTORAL FELLOW in PARIS

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Project information:

The “Birdsong for Human(e) voices” project is funded by the CRI and is led by Dr. Pauline Provini. More information on the project: https://projects.cri-paris.org/projects/tY6OqgWS/summary

Job Description Summary:

We are searching for a highly motivated, independent, multidisciplinary postdoctoral researcher to be part of a team focusing on understanding the biomechanics of birdsong. The postdoctoral researcher will play a substantive role in planning and conducting research by using quantitative modelling methods. In close collaboration with the Principal Investigator, the postdoctoral researcher will

  • Participate to the collection of experimental data (multiple X-ray and light high-speed videos, Particle Image Velocimetry data, acoustic data, etc.) of different species of birds during vocalization.
  • Fluid dynamics analysis (CFD model) of bird vocalization.
  • Aero-acoustic modelling of birdsong based on experimental data collected by the team.
  • Draft and publish scientific papers derived from the data.
  • Attend annual scientific meetings to present research derived from the project research.
  • Actively participate to meetings, seminars, and CRI life in general.

Minimum Qualifications:

PhD qualification with relevant research experience in biomechanics (e.g. engineering, modelling) or a closely related field.

Additional positive qualifications:

Specific expertise in one or more of the targeted experimental techniques (PIV, XROMM, and acoustic recordings), experience with live animals, and knowledge of the functional morphology of vertebrates are considered as additional positive elements for the candidate. An interdisciplinary background is highly appreciated.

Typical Hiring Range: Full-Time job ±2200 Euro/month (net) according to the INSERM salary scale.

Location: Centre de Recherche Interdisciplinaire, 8bis Rue Charles V, 75004 Paris France.

Institution information:

The Center for Research and Interdisciplinarity (CRI) experiments and spreads new ways of learning, teaching, conducting research and mobilizing collective intelligence in life, learning and digital sciences. The CRI promotes scientists who thrive in dynamic environments, are inspired and motivated by daily interactions with diverse peers, work best in teams and comfortably mix disciplines, rearranging, straddling field boundaries and wish to explore uncharted domains.

Job Open/Close Date: Fall 2020/ Summer 2022.

Required Documents

To apply for the position, please send the following documents to Pauline.provini@cri-paris.org:

  1. Curriculum Vitae
    1. Cover letter summarizing research interests, professional experience, and career goals.
    1. Names and Contact Information for References

Please have 2 recommendations forwarded directly to Dr. Pauline Provini email address by those individuals providing the references. These should not come from the applicant.

Review of applications will begin on September 15th and continue until the position is filled.

Research Assistant m/f (30 h) Project PrintMyBone @ KL Krems, Austria

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The Karl Landsteiner University of Health Sciences (KL) offers a research position for three year (starting Dec. 2019) in the Department of Anatomy and Biomechanics (Division Biomechanics, Head: Univ.-Prof. Dieter Pahr):

Your responsibilities:

  • Participation in the research project “PrintMyBone – 3D printing of artificial bones from clinical CT data”.
  • In particular: use of FDM and SLA printing processes, extension of these printing processes (keywords: “composite materials” and “non-planar slicing”) as well as characterization of 3D printed parts (mechanical testing, micro-CT imaging). The goal is to create 3D printed structures that mimic the mechanical properties of human bones and can be used for precise, repeatable tests for the development of medical devices or for training purposes.
  • Submission of research applications, participation in third-party funded projects
  • Supervision of students and participation in teaching

Your profile:

  • Master degree in biomedical engineering, mechanical or civil engineering, technical physics, material sciences or similar fields
  • handicraft skills and enjoyment of manual laboratory work
  • Basic knowledge of image processing and programming
  • Interest in 3D printing and scientific work
  • Reliable and independent way of working
  • Friendly and team oriented personality

Your Perspektive:

You can expect a challenging job in a highly motivated team with the possibility to achieve the academic degree of a PhD (Dr. techn.)

People with disabilities who meet the required qualification criteria are expressly invited to apply and are given special consideration. The minimum classification is € 2,100 gross per month.

Applications should include a motivation letter, curriculum vitae, and credentials and should be mailed by 17 of November 2019 to Ms. Christina Schwaiger of the Karl Landsteiner University of Health Sciences, Dr.-Karl-Dorrek-Straße 30, 3500 Krems, Austria (bewerbung@kl.ac.at).

Vacancy Editor @ Taylor & Francis: Computer Methods in Biomechanics and Biomedical Engineering

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Would you like to be the Editor of Computer Methods in Biomechanics and Biomedical Engineering (CMBBE)?

We are looking for a new Editor/Editorial Team to lead the editorial board of CMBBE. Applicants should have an academic background in biomechanics and biomedical engineering, specifically a high level of multidisciplinary knowledge across the fields of computational biomechanics, biomedical applications and numerical methods, as well as the passion to drive the journal forward. 

The successful candidate(s) will be responsible for editorial oversight and decision-making on submissions. They will have authority to accept articles following successful peer review and will ensure that reviewers and authors adhere to the Journal’s Code of Publishing Ethics. For more information on the role of a journal editor, please click here.

Becoming the editor of a journal is a rewarding and fulfilling experience where you will extend your own networks, promote the research that you are passionate about, increase visibility of your own research and be recognized as a leading figure within the academic community. 

Interested in applying? Here are the skills and attributes we would be looking for in a successful applicant:

·       Someone who is active in the community with strong personal networks

  • Confidence to engage with authors and researchers to solicit the highest quality submissions
  • Strong organizational skills to ensure that submissions are handled in a timely manner
  • The ability to foster positive working relationships with colleagues in the Editorial Board
  • This position may be available as a co-editorship – please note your interest in this in your application.

Submitting your Application

If you would like to apply for the position please forward your CV to Ishtiaque Shams, Portfolio Manager, at Ishtiaque.Shams@tandf.co.uk. 

Deadline for application is 31 October 2019.CMBBE is a leading Journal in the field with the aim to provide a means of communicating the advances being made in the area of computational biomechanics and biomedical engineering with the emphasis being placed on biomechanics. For more formation about the Journal please click here.

Call for Bids hosting ESB 2023

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The ESB invites proposals for the organization of its annual congress in 2023. If you would like to host and organize the 2023 ESB congress and wish to prepare and submit a bid, please read the conference rules.

Interested members can contact or send a proposal/bid to Prof. David Mitton, Chair of the Meetings Committee (david.mitton(at)ifsttar.fr),

The deadline for bid submission (first step) to organize the ESB 2023 is 15 December 2019.

2nd ESB Webinar Announced: OpenSim

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Jumping into Musculoskeletal Modeling with OpenSim

We are delighted to announce the second webinar of the ESB Webinar Series which will introduce the OpenSim Software. The webinar will take place on October 16th 2019 at 18:00 CEST.

OpenSim is a freely-available, open-source musculoskeletal simulation software for visualizing and simulating movement. Musculoskeletal modeling and simulation are powerful tools to help understand the complex interactions between the neuromuscular and skeletal systems during movement.

This webinar aims to:

  • Introduce the main capabilities of OpenSim, including new features from the latest release of the software
  • Demonstrate a typical pipeline of creating and visualizing a muscle-driven simulation starting with motion capture data of a subject jumping

By the end of this tutorial, attendees will learn some of the core capabilities of OpenSim, including how to:

  • Load and visualize motion capture data
  • Load and explore a musculoskeletal model
  • Visualize a motion
  • Create a dynamic simulation.

The webinar will be conducted by Dr. Jennifer Hicks. Dr. Hicks is Associate Director the National Center for Simulation in Rehabilitation Research, an NIH-funded center at Stanford University that brings state-of-the-art engineering tools to rehabilitation scientists. In addition, she is the Research and Development Manager of the OpenSim software project, guiding the project’s development team and serving as the voice of the software user/researcher.

The seminar will last 45 minutes followed by 15 minutes of Q/A from the audience. You will have the chance to ask your questions which will be addressed by the speaker at the end of the webinar. However, it would be great if you could send your question in advance while filling the registration form or by sending to Ehsan.soodmand@charite.de and/or rodrigo.romarowski@grupposandonato.it  before the start of the webinar.

Click here to register for the webinar.

October 16th 2019 18:00 CEST

Live on ESB YouTube Channel – Please Subscribe! (https://www.youtube.com/esbiomech )

Looking forward to your attendance.

ESB Student Committee

Fully funded PhD studentship @Nottingham

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The link to the position advertisement is  http://jobs.nottingham.ac.uk/ENG1305 .

Applications are invited for an exciting fully-funded PhD studentship in the Bioengineering Research Group, Faculty of Engineering at the University of Nottingham.

Research area. The research topic focuses on developing solutions that enable in-natura markerless motion capture for biomechanical modelling in Biomedical and Sports Engineering. Specifically, it addresses the fundamental research problem of reconstruction of person-specific human pose, kinematics, and surface geometry to enhance our understanding of the non-linear behaviour of human motion, musculoskeletal injury and disease and enable modelling of soft-tissue dynamics. Open problems in human-object interaction and tracking will also be explored.

The project. The candidate is expected to develop a fast and robust method for inferring and tracking 3D shapes of deformable objects, humans in particular. The method will be mainly based on visual sensing. Inertial and force sensors will be used as complementary sensing. The method can use either or both of model-based and learning-based approaches, such as CNN based segmentation, geometric CNNs, or convolutional kernel filter based tracking. The candidate will have access to a newly established state-of-the-art integrated motion capture laboratory.

The candidate. The ideal candidate will have;

  1. a first or upper second class honours or Masters degree in Electrical and Electronic Engineering, Physics, Computer Science or other relevant and equivalent degree from a quality recognised institution.
  2. a solid background in mathematics and excellent analytical and numerical skills, as well as problem solving skills
  3. strong background in 3D computer vision, pose estimation, shape reconstruction, structure from motion, segmentation, or object detection.
  4. experience in image or video processing and digital signal processing.
  5. strong programming skills in Matlab, C/C++, or Python. Previous hands-on experience with deep learning platforms and agile software development as well as experience of working within industry will be an advantage.
  6. very good written and communication skills and fluency in English.
  7. a driven, independent professional and self-reliant work attitude within a fast-paced & collaborative environment.

Informal enquiries about the project may be addressed to Dr Ami Drory. Please (i) insert your cover letter, CV and copies of academic transcripts into a single pdf file. (ii) Name the file with your name as ”firstName_lastName_phd”. (iii) e-mail to: Ami.Drory@nottingham.ac.uk, with [3D shape reconstruction PhD application – lastName] as the email subject.

Application instructions. Formal applications are to be made via http://www.nottingham.ac.uk/pgstudy/apply/applyonline.aspx

Closing date for applications. Review of applications will commence on 15 October 2019 and remain open until filled. A start date is expected to be as soon as practical thereafter.

The University. The University of Nottingham is a world-class University consistently ranked among the world’s top 100 universities. It is a Russell Group university and a member of Universitas 21 (U21), the global network of research-intensive universities. The University is ranked eighth in the UK on ‘research power’ in the latest REF rankings. The Faculty of Engineering is ranked in the top 10 in the UK with more than 98 per cent of its research ranked of international quality, with 85 per cent graded as ‘world-leading’ or ‘internationally excellent’.

The university was awarded the University of the Year for both International and Sports in the 2019 Guide. With award-winning campuses, University Park is The University of Nottingham’s largest campus at 300 acres. The campus is widely regarded as one of the largest and most attractive in the UK. Set in extensive greenery and around a lake, University Park campus has consistently won a Green Flag Award for its green and environmentally friendly spaces every year since 2003. The University of Nottingham was ranked the World’s second greenest university in 2019 (GreenMetric). The brand new £40 million David Ross Sports Village is now open, offering an inspirational and accessible sports provision for all.