Blog Archives

Post-Doc in Qualification of in silico-augmented clinical trial approach @ University of Bologna

Title: Qualification of in silico-augmented clinical trial approach to the efficacy assessment of new tuberculosis therapies in developing countries

Tutor: Prof Marco Viceconti – https://www.unibo.it/sitoweb/marco.viceconti/

Funding source: STriTuVaD project – https://cordis.europa.eu/project/rcn/212940_en.html

To apply: https://www.aricweb.unibo.it/BandiPubblicati/zz_Bandi_din.aspx?strid=961

Deadline: 9 January 2019, 12:00 (applications must be sent by post or delivered by hand)

Research Project

In the framework of the STRITUVAD project partner University of Catania is developing a sophisticated simulation of the human immune system that can predict how a patient will respond to the disease activation of the Mycobacterium Tuberculosis bacterium already present in his/her body in term of bacterial spread, as a function of the patient general immune condition, and to the inoculation of specific therapies. The project goal is to refine this model so that it can:

  1. predict with sufficient accuracy the change in bacterial load over time in individual patients treated with different therapies;
  2. generate a cohort of “virtual patients” that well represent the inter-subject variability of all determinants that affect the disease progression and the response to therapy;
  3. develop in collaboration with the University of Sheffield a Bayesian statistical model that combines observational results from a clinical trial to the in silico-predicted response on the virtual patients cohort into an in silico-augmented clinical trial aimed to shorted the duration and the number of physical patients enrolled;
  4. validate the results of the in silico augmented trial to those of a full sized standard clinical trial, so to produce sufficient evidences to qualify the in silico method for studies of future drugs.

Under the guidance of Prof Marco Viceconti, one of the top experts of in silico trials worldwide, the post holder, a post-doctoral researcher with documented experience in modelling and simulation in biomedicine, will conduct the research activities described above in close collaboration with the model developers in Catania, the statistical modelling experts in Sheffield, and the clinical trialists in New Delhi.

The research contract (Assegno di Ricerca), has an annual salary before taxes of € 26,174.00. While the initial contract is for 12 months, if successful the post holder contract will be extended until the end of the project, in July 2022.

The ideal candidate for this position holds a PhD in math, physics, or engineering, documented experience in modelling and simulation in biomedicine, excellent spoken and written English, and one or more of the following skills:

  • Familiarity with the mathematical modelling of the immune system
  • Familiarity with Bayesian statistics and Bayesian modelling
  • Previous experience with biomedical regulatory science
  • Previous experience with verification, validation, and uncertainty quantification of predictive models in biomedicine

If you are interested apply here: https://www.aricweb.unibo.it/BandiPubblicati/zz_Bandi_din.aspx?strid=961 or contact me by email for further information.

For original post see:
https://www.unibo.it/sitoweb/marco.viceconti/avvisi/fa93fd8b

Post-doc in Development of an open source software for the multiscale orchestration @ University of Bologna

Title: Development of an open source software for the multiscale orchestration of computational oncology simulations

Tutor: Prof Marco Viceconti – https://www.unibo.it/sitoweb/marco.viceconti/

Funding source: H2020 project PRIMAGE (SC1-PM-16-2017-826494)

To apply: https://www.aricweb.unibo.it/BandiPubblicati/zz_Bandi_din.aspx?strid=961

Deadline: 9 January 2019, 12:00 (applications must be sent by post or delivered by hand)

Research Project

In 2017 the European Commission called for proposals on the topic “In-silico trials for developing and assessing biomedical products”; one of the projects funded, PRIMAGE, which will start on December 1st, 2018, aims to develop in silico trials technologies to test the efficacy of new anti-tumour therapies. To predict the response of a new anti-cancer agent over a representative clinical population is a very complex endeavour, which requires a detailed model of the biochemical mechanism of action of the new drug on the cancer cells, another model that describe how this effect modulate the cell-to-cell and the cell-to-tissue interaction and signalling, and another model that can predict the overall growth of the tumour mass over time, its vascularisation, and its cellularity. As each of these models is defined at radically different space-time scales, their coupling is complex and involves an advanced orchestration to build a multiscale simulation.

This problem has been approached in different ways in the past by Prof Viceconti’s team and by other research groups, but all solutions so far have been not entirely satisfactory. The main problem is that the software stack to handle this orchestration becomes rapidly very large and complex (thus difficult to maintain), and strongly dependent on implementations of the models being orchestrated; as in most projects these are being developed in parallel, this create some serious difficulties.

In PRIMAGE we intend to tackle a completely different approach loosely inspired by the High Level Architecture approach standardised by IEEE Std 1516-2010, and popular especially in the context of defence research. We intend to develop a very simple and easy to maintain architecture that orchestrate the models by controlling their data flow, centralising in a database all intermediate data objects, so as to explore possible speed-up strategies based on pre-computation, interpolation, and surrogate modelling methods. The result will be an open source software tool that should make much easier for research groups around the world to design and deploy complex multiscale orchestrations, that execute efficiently and flexibly in different execution environments.

Under the guidance of Prof Marco Viceconti, one of the top experts of in silico trials and biomedical multiscale modelling worldwide, the post holder, a researcher with documented experience in software development in Python, will design and develop this orchestration framework, and use it to deploy a large scale multiscale simulation that orchestrate models developed by specialists at partners ANSYS, UNIVERSITY OF SARAGOZA, UNIVERSITY OF SHEFFIELD, and CHEMOTARGETS, which will be tested as in silico trial solution.

The research contract (Assegno di Ricerca), has an annual salary before taxes of € 26,174.00. While the initial contract is for 12 months, if successful the post holder contract will be extended until the end of the project, in November 2022.

The ideal candidate for this position holds a degree in computer science, math, physics, or engineering, documented experience in software development in Python, good spoken and written English, and one or more of the following skills:

  • Familiarity with computational science & engineering software development
  • Familiarity with computational biomedicine software development
  • Previous experience with model orchestration and/or multiscale modelling
  • Previous experience with database software development, NoSQL databases, blockchain public ledgers, surrogate modelling, and/or machine learning
  • Previous experience with Open Source projects management

If you are interested apply here: https://www.aricweb.unibo.it/BandiPubblicati/zz_Bandi_din.aspx?strid=961 or contact me by email for further information.

For the original post see:
https://www.unibo.it/sitoweb/marco.viceconti/avvisi/4c20aa93

Communication Officer in Dissemination, communication, and community engagement on in silico medicine @ University of Bologna

In the frame of the Strituvad project we are opening a new position for communication officer.  The position is initially for 12 months, but can be extended for additional two. The gross amount of the research contract (Assegno di Ricerca), contract is € 20.354,99 per annum. The amount is exempt of withholding tax and includes all statutory social security charges the Research Fellow is subject to.

The aim of this research contract is the creation of a community of practice around the emerging applications of the so-called in silico medicine, with particular reference to in silico trials, where modelling and simulation technologies are used for the certification of new drugs or medical devices. Under the guidance of Prof Marco Viceconti one of the top world-wide experts on in silico medicine, the researcher will create the content and manage web sites, social network accounts, e-newsletters, and online communities allowing all those interested in the topic who work in academia, industry, consulting or service firms or in regulatory agencies to exchange good practices on the use of modelling and simulation in medicine. The post is funded by the EU project STRITUVAD, which aims to develop in silico methods to reduce the cost of clinical trials for new therapies for tuberculosis in developing countries where this disease is endemic.

The ideal candidate should have:

  • A Master degree (Laurea Magistrale) or equivalent title in scientific disciplines or Communication Science
  • Excellent knowledge of English language (written and spoken)
  • Priority will be given to candidates with experience in Science Communication, dissemination of research results, networking and community building among scientists, production of press releases

If you are interested apply here: https://www.aricweb.unibo.it/BandiPubblicati/zz_Bandi_din.aspx?strid=961 or contact me by email for further information.The deadline is Thursday, January 10th, 2019 or contact me by email for further information.

For original post see:
https://www.unibo.it/sitoweb/marco.viceconti/avvisi/6dcf39bb

Call for Bids hosting ESB 2022

The ESB is inviting proposals for the organization of its annual congress in July 2022. If you are interested in hosting and organizing ESB2022, please read the ESB 2022 Bid rules for details.

Bids should be sent to prof. David Mitton (david.mitton@ifsttar.fr), Chair of the Meetings Committee. He can also be contacted for further information.

The deadline for submitting your bid for ESB2022 is 31st March 2019.

Simpleware Software Release O-2018.12 Out

The latest version of Simpleware software is out now. It includes many exciting new features and performance improvements. New in Version O-2018.12

  • Improved Usability
  • Better Segmentation
  • Enhanced Dataset Processing

Synopsys will be running webinars on the new release January 16, 2019, and will also be hosting workshops in the UK on January23rd,2019, and in the U.S. on February 12, 2019. For more details visit this page or contact simpleware@synopsys.com.

ESBiomech Newsletter Autumn 2018

We are pleased to present our 2018 Autumn Newsletter with the latest ESB news, reports from ESB conference and honouring award winning researchers, and updates from our corporate members.

Please contact us with ideas of items you would like to see on our website and newsletter and these will be considered as the society continues to expand. If you do not wish to receive mailings including the newsletter and other updates from the European Society of Biomechanics you can update your settings in the membership section of the website here:

I hope you find the newsletter useful and informative.

Dieter Pahr – publication.chair@esbiomech.org

25th Congress of the European Society of Biomechanics

Featured

The 25th Congress of ESB will take place in Vienna, Austria from 7 – 10 July 2019.

ESB 2019 is jointly organized by Philipp THURNER (TU Wien), Dieter PAHR (TU Wien & KL Krems), and Christian HELLMICH (TU Wien). The congress itself will take place at the University of Vienna which is located in the centre of the city.

Prospective authors are encouraged to submit their latest research for capturing and discussing the science at the forefront of biomechanics in a mix of oral and poster presentations.

Abstracts have to be submitted online through the congress website by January 31, 2019. Further information is available here.

Further detailed information as well as information on sponsoring and exhibition can be found here.

We are looking forward to receiving your contributions and to welcoming you at ESB2019 in Vienna!

PhD Positions in Numerical study for Cardiovascular Stent @cimne

Scope:

The objective of the position is to develop a PhD work on the subject “Numerical study for Cardiovascular stent: design and analysis”. The aim of the work will be to analyze the expansion of the stent and the contact with the artery to simulate thrombectomy technique. The developments will have to be carried out within the Kratos framework.

Functions to be developed:

Participate in the development of the thrombectomy technique. This includes software developments and reporting.
Develop a PhD thesis on subjects related to thrombectomy technique.
Publish on subjects related to Biomedical Engineering area.
Develop within the framework of the Kratos project.

Education and training (required):

Formation: Master in Engineering or Mathematics
Basic Knowledge of programming (Python, C++).
Required Languages: English
Knowledge of FEM and Optimization Techniques

More Details

http://www.cimne.com/vnews/10569/vac-2018-28-%E2%80%93-phd-position-in-the-biomedical-engineering-department

 

Posdoc Position in characterization and modeling of elastic protein @ Université de Lyon (France)

Mechanical characterization and modeling of a synthetic elastic protein and its effects on the arterial function

A post-doctoral fellowship is available at the Center for Biomedical and Healthcare Engineering Mines Saint-Etienne – SAINBIOSE (INSERM-U1059) – Université de Lyon (France).

Scientific context: Elastin is the main elasticity provider for several soft tissues (such as dermis, arteries, pulmonary alveoli) in its fibrous form and a signaling molecule in cell/extracellular matrix interaction. Elastin-rich elastic fibers allow the large artery walls to transform the pulsatile blood flow ejected by the heart into a continuous blood flow in the peripheral arteries (Windkessel effect). Dysfunctions are highly correlated with diseases such as artery stenosis, aneurysm, hypertension or cardiac hypertrophy, which have strong repercussions on arterial biomechanics and can threaten the vessel integrity.
Setting aside surgery, there is currently no treatment for preventing, blocking or treating any loss of elasticity. It therefore appears, from a biomechanical point of view, that the introduction of an entity that provides elasticity within the arterial wall would be the most trivial action to stop arterial stiffening, but remains currently limited due to chemo-biological issues. The Arterylastic project, to which the thesis is linked, proposes to unlock this technological barrier using an original synthetic elastic protein (SEP) recently developed with a synthetic backbone devoted to skin engineering.

Academic context: As previously mentioned, the thesis takes place in a larger project named Arterylastic, funded by ANR, combining pluridisciplinary approaches of three laboratories in France: LBTI – the Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (UMR5305 CNRS/UCBL1 Lyon), HP2 –Hypoxie Physiopathologie Cardiovasculaire et Respiratoire (INSERM U1042 – University Grenoble Alpes) and Sainbiose (within the Center for Biomedical and Healthcare Engineering CISSAINBIOSE/INSERM U1059 – Mines Saint-Etienne). The PhD student will work at CIS, which also conducts major international research projects in the field of soft tissue biomechanics, in particular aortic aneurysms. He will collaborate with other researchers involved in ERC projects (https://www.mines-stetienne.fr/en/author/avril/, https://www.emse.fr/~badel/).

Objectives: The objective is to restore (or at least improve) arterial function and mechanical properties under conditions of elastic fibers injury. The objective will be reached if the SEP is correctly integrated into elastic fibers and if the SEP restores arterial wall elasticity and/or physiological parameters in relevant animal models. In this thesis, we will evaluate the mechanical behavior of the cross-linked SEP and of arterial samples from treated mouse models and a numerical model will be developed from experimental data to better predict treatment parameters.
The main tasks will be:
1. Experimental tests will be carried out for characterizing the macroscopic mechanical properties of the SEP and of arteries treated with the SEP. The cross-linked SEP will be characterized using tensile tests with a customized device. Mechanical parameters of treated arteries will be assessed by measuring pressure-diameter curves from mouse arteries tested in a customized tension-inflation test.
2. A multiscale numerical model of the mechanical behavior of arteries will be elaborated, taking into account their microstructural composition and morphology (bilayer, specific contributions of elastin, collagen, smooth muscle cells, possible proteoglycans) and including the effects of possible grafting of the SEP to the arterial wall. The model will be tested for arteries with competent elastic fibers, for arteries with damaged elastin and induced-tissue remodelling, and for arteries treated with the SEP.
3. The experimental results obtained at task 1 will be used to evaluate and calibrate the prediction ability of the numerical model developed in task 2. Sensitivity analysis permitting to find the optimal treatment conditions with the SEP for different types of therapeutic targets will be addressed.

Candidate profile: Candidates with strong skills in mechanics (modeling and experimental) and biomechanics are expected. Motivation and interest in bioengineering applications is recommended.

How to apply: Send CV, cover letter and letters of recommendation to claire.morin@emse.fr and avril@emse.fr.

PhD Positions in Failure Criterion for Implanted Bone Screws @KLKREMS

The Karl Landsteiner University of Health Sciences (KL) is part of an academic and research community located at the Campus Krems, and includes a network of comprising teaching hospitals in St. Pölten, Krems and Tulln. The university offers degree programs in Human Medicine, Psychotherapy, Counselling Sciences and Psychology and are tailored to the requirements of the Bologna model, opening the door to new, cutting-edge health professions. KL is committed to raising its profile in specific areas of biomedicine, biomedical engineering, and biopsychosocial sciences by entering into strategic academic and research partnerships with other institutions.

Starting at November 2018, the department of anatomy and biomechanics (division of biomechanics, Prof. Pahr, Dr. Reisinger) offers a research position, which is limited to the duration of three years:

Research Assistant m/f (Pre Doc, 30 h)

Your responsibilities:

  • Participation in the funded research project “A morphology based failure criterion for implanted bone screws”
  • In more detail: using of micro CT imaging, biomechanical testing, continuum mechanics, and 3d- printing
  • Programming of evaluation- and analysis scripts
  • Assistance in teaching in the fields of mathematics, physics, informatics and biomedical engineering
  • Engagement in other research projects

Your profile:

  • Degree in civil or mechanical engineering, biomedical engineering, technical physics, or similar fields
  • Basic knowledge in programming, biomechanics, imaging (CT), experimental material
  • characterization
  • Good English skills
  • The willingness to support teaching, experience is of advantage
  • Self-responsible and reliable working approach
  • Interest on scientific working and writing a dissertation
  • Friendly and team oriented personality

Your perspective:

  • You can expect a challenging job in an internationally recognized and highly motivated team
  • Achieve the academic degree of a PhD (Dr. techn.), issued from the TU Vienna.

The Karl Landsteiner University of Health Sciences is dedicated to achieving a balanced mix of male and female academic and non-academic staff. Consequently, applications from female candidates are particularly welcome.

The minimum gross salary for this position is € 2.112,40 (30 h).

Applications should include a motivation letter, curriculum vitae, and credentials and should be mailed by 17.10.2018 to Ms. Christina Schwaiger of the Karl Landsteiner University of Health Sciences, Dr.-Karl- Dorrek-Straße 30, 3500 Krems, Austria (bewerbung@kl.ac.at).