Alessandro Chiarini - Profile on Academia.edu (original) (raw)
Papers by Alessandro Chiarini
Partnership for Advanced Computing in Europe SHAPE pilot Monotricat SRL: Hull resistance simulations for an innovative hull using OpenFOAM
In the project we conduct a whole hull simulation of a ship, (including mesh generation of comple... more In the project we conduct a whole hull simulation of a ship, (including mesh generation of complex geometries, efficient solvers with various turbulent modelling and optimized parameters as well as visualization), along with a performance analysis for the simulation. This project makes it possible for Monotricat to take advantage of HPC-enabled simulation tools and potentially replace the traditional methods.
F1000Research, Jan 22, 2014
Results: The authors recently developed a web application for the management of ALS. Currently, t... more Results: The authors recently developed a web application for the management of ALS. Currently, the e-prototype is being validated in a small group of patients (Figures 2-3).
F1000Research, 2014
Results: The authors recently developed a web application for the management of ALS. Currently, t... more Results: The authors recently developed a web application for the management of ALS. Currently, the e-prototype is being validated in a small group of patients (Figures 2-3).
@neurIST - chronic disease management through integration of heterogeneous data and computer-interpretable guideline services
Studies in health technology and informatics, 2008
This paper presents an overview of computerised decision support for clinical practice. The conce... more This paper presents an overview of computerised decision support for clinical practice. The concept of computer-interpretable guidelines is introduced in the context of the @neurIST project, which aims at supporting the research and treatment of asymptomatic unruptured cerebral aneurysms by bringing together heterogeneous data, computing and complex processing services. The architecture is generic enough to adapt it to the treatment of other diseases beyond cerebral aneurysms. The paper reviews the generic requirements of the @neurIST system and presents the innovative work in distributing executable clinical guidelines.
The @neurIST project
Studies in health technology and informatics, 2008
Interface Focus, 2011
Cerebral aneurysms are a multi-factorial disease with severe consequences. A core part of the Eur... more Cerebral aneurysms are a multi-factorial disease with severe consequences. A core part of the European project @neurIST was the physical characterization of aneurysms to find candidate risk factors associated with aneurysm rupture. The project investigated measures based on morphological, haemodynamic and aneurysm wall structure analyses for more than 300 cases of ruptured and unruptured aneurysms, extracting descriptors suitable for statistical studies. This paper deals with the unique challenges associated with this task, and the implemented solutions. The consistency of results required by the subsequent statistical analyses, given the heterogeneous image data sources and multiple human operators, was met by a highly automated toolchain combined with training. A testimonial of the successful automation is the positive evaluation of the toolchain by over 260 clinicians during various hands-on workshops. The specification of the analyses required thorough investigations of modellin...
Enhancement of Peripheral Stents Reliability: Developing Interactive Procedure Planning by Means of Numerical Simulations and Clinical Software Development
Journal of Medical Devices, 2013
Around 20% of the population over 60-years-old have peripheral arterial disease. Symptoms can cau... more Around 20% of the population over 60-years-old have peripheral arterial disease. Symptoms can cause major lifestyle limitation through pain on walking (intermittent claudication). Progressive disease can also lead to critical limb ischemia, which is the major cause of amputation for adults. The implant of a stent is the endovascular therapy of election for the treatment of peripheral arterial disease. This, however, can increase the risk of fatigue fracture of the implanted device, under in vivo loading conditions. RT3S (real time simulations for safer vascular stenting) is a scientific project involving both universities and private companies, for a funded budget of more than $4.5 million (www.rt3s.eu). The project aims at providing physicians with interactive clinical software for an enhanced pre-operative planning of femoral artery stenting including a prediction of in vivo stent fracture risk, computed by means of numerical simulations. Software-developing companies developed an...
This paper presents the system architecture of the @neurIST project, which aims at supporting the... more This paper presents the system architecture of the @neurIST project, which aims at supporting the research and treatment of cerebral aneurysms by bringing together heterogeneous data, computing and complex processing services. The architecture is generic enough to adapt it to the treatment of other diseases beyond cerebral aneurysms. The paper describes the generic requirements of the system and presents the architecture, applications and middleware technologies used to realise the system and highlights the innovations in @neurIST.
IEEE Transactions on Information Technology in Biomedicine, 2010
The increasing volume of data describing human disease processes and the growing complexity of un... more The increasing volume of data describing human disease processes and the growing complexity of understanding, managing, and sharing such data presents a huge challenge for clinicians and medical researchers. This paper presents the @neurIST system, which provides an infrastructure for biomedical research while aiding clinical care, by bringing together heterogeneous data and complex processing and computing services. Although @neurIST targets
Investigating the Influence of Haemodynamic Stimuli on Intracranial Aneurysm Inception
Annals of Biomedical Engineering, 2013
We propose a novel method to reconstruct the hypothetical geometry of the healthy vasculature pri... more We propose a novel method to reconstruct the hypothetical geometry of the healthy vasculature prior to intracranial aneurysm (IA) formation: a Frenet frame is calculated along the skeletonization of the arterial geometry; upstream and downstream boundaries of the aneurysmal segment are expressed in terms of the local Frenet frame basis vectors; the hypothetical healthy geometry is then reconstructed by propagating a closed curve along the skeleton using the local Frenet frames so that the upstream boundary is smoothly morphed into the downstream boundary. This methodology takes into account the tortuosity of the arterial vasculature and requires minimal user subjectivity. The method is applied to 22 clinical cases depicting IAs. Computational fluid dynamic simulations of the vasculature without IA are performed and the haemodynamic stimuli in the location of IA formation are examined. We observe that locally elevated wall shear stress (WSS) and gradient oscillatory number (GON) are highly correlated (20/22 for WSS and 19/22 for GON) with regions susceptible to sidewall IA formation whilst haemodynamic indices associated with the oscillation of the WSS vectors have much lower correlations.
2013 International Conference on Computer Medical Applications (ICCMA), 2013
We present a parallel implementation of an algorithm for the detection of colonic polyps from CT ... more We present a parallel implementation of an algorithm for the detection of colonic polyps from CT data sets. This implementation is designed specifically to take advantage of the computational power available on modern Graphics Processing Units (GPUs), which significantly reduces the execution time to streamline the workflow of clinicians examining the data. We provide details about the changes which were made to the existing algorithm to suit the new target hardware, and perform tests which demonstrate that the results are a very close match to the reference implementation while being computed in a fraction of the time. Computer aided diagnosis, GPU computing, Colon screening; I.
The Living Human Project: The Grand Challenge of European Biomechanics?
Computational Bioengineering, 2004
Langenbeck's Archives of Surgery, 2004
Background: All computer-aided surgery technologies assume that the surgeon knows the best positi... more Background: All computer-aided surgery technologies assume that the surgeon knows the best position for the implant components. However, there is indirect evidence that simple anatomical information may not be sufficient for the surgeon to decide size and position of the implant in a repeatable manner. Method: In the present study we estimated the variability in choosing the size and position of the components of a cementless total hip replacement (THR), using template-on-radiograph as well as computed tomography (CT)-based computer-aided planning. In addition, using a computer model, we assessed the sensitivity to such variability of implant fitting, location of the joint centre, skeletal range of motion, and resting length of major hip muscles. Using templates, surgeons selected the size with variability up to 2.5 mm for the stem and up to 4 mm for the socket. A similar variability was also observed when the CT-based planning program was used. Results: No major differences were found between surgeons. The standard deviation over repeated planning sessions of the selected position for each component, using the CT-based planning software, was found to be 3.9 mm and 8.9. Conclusion: On the basis of the computer simulation, this variability did not affect the selected biomechanical parameters in a drastic way, although some differences were observed, especially in the lever arm of the hip muscles.
Lecture Notes in Computer Science, 2014
In this paper we evaluate the performance of the OpenACC and Mint toolkits against C and CUDA imp... more In this paper we evaluate the performance of the OpenACC and Mint toolkits against C and CUDA implementations of the standard PolyBench test suite. Our analysis reveals that performance is similar in many cases, but that a certain set of code constructs impede the ability of Mint to generate optimal code. We then present some small improvements which we integrate into our own GPSME toolkit (which is derived from Mint) and show that our toolkit now out-performs OpenACC in the majority of tests.
Partnership for Advanced Computing in Europe SHAPE pilot Monotricat SRL: Hull resistance simulations for an innovative hull using OpenFOAM
In the project we conduct a whole hull simulation of a ship, (including mesh generation of comple... more In the project we conduct a whole hull simulation of a ship, (including mesh generation of complex geometries, efficient solvers with various turbulent modelling and optimized parameters as well as visualization), along with a performance analysis for the simulation. This project makes it possible for Monotricat to take advantage of HPC-enabled simulation tools and potentially replace the traditional methods.
F1000Research, Jan 22, 2014
Results: The authors recently developed a web application for the management of ALS. Currently, t... more Results: The authors recently developed a web application for the management of ALS. Currently, the e-prototype is being validated in a small group of patients (Figures 2-3).
F1000Research, 2014
Results: The authors recently developed a web application for the management of ALS. Currently, t... more Results: The authors recently developed a web application for the management of ALS. Currently, the e-prototype is being validated in a small group of patients (Figures 2-3).
@neurIST - chronic disease management through integration of heterogeneous data and computer-interpretable guideline services
Studies in health technology and informatics, 2008
This paper presents an overview of computerised decision support for clinical practice. The conce... more This paper presents an overview of computerised decision support for clinical practice. The concept of computer-interpretable guidelines is introduced in the context of the @neurIST project, which aims at supporting the research and treatment of asymptomatic unruptured cerebral aneurysms by bringing together heterogeneous data, computing and complex processing services. The architecture is generic enough to adapt it to the treatment of other diseases beyond cerebral aneurysms. The paper reviews the generic requirements of the @neurIST system and presents the innovative work in distributing executable clinical guidelines.
The @neurIST project
Studies in health technology and informatics, 2008
Interface Focus, 2011
Cerebral aneurysms are a multi-factorial disease with severe consequences. A core part of the Eur... more Cerebral aneurysms are a multi-factorial disease with severe consequences. A core part of the European project @neurIST was the physical characterization of aneurysms to find candidate risk factors associated with aneurysm rupture. The project investigated measures based on morphological, haemodynamic and aneurysm wall structure analyses for more than 300 cases of ruptured and unruptured aneurysms, extracting descriptors suitable for statistical studies. This paper deals with the unique challenges associated with this task, and the implemented solutions. The consistency of results required by the subsequent statistical analyses, given the heterogeneous image data sources and multiple human operators, was met by a highly automated toolchain combined with training. A testimonial of the successful automation is the positive evaluation of the toolchain by over 260 clinicians during various hands-on workshops. The specification of the analyses required thorough investigations of modellin...
Enhancement of Peripheral Stents Reliability: Developing Interactive Procedure Planning by Means of Numerical Simulations and Clinical Software Development
Journal of Medical Devices, 2013
Around 20% of the population over 60-years-old have peripheral arterial disease. Symptoms can cau... more Around 20% of the population over 60-years-old have peripheral arterial disease. Symptoms can cause major lifestyle limitation through pain on walking (intermittent claudication). Progressive disease can also lead to critical limb ischemia, which is the major cause of amputation for adults. The implant of a stent is the endovascular therapy of election for the treatment of peripheral arterial disease. This, however, can increase the risk of fatigue fracture of the implanted device, under in vivo loading conditions. RT3S (real time simulations for safer vascular stenting) is a scientific project involving both universities and private companies, for a funded budget of more than $4.5 million (www.rt3s.eu). The project aims at providing physicians with interactive clinical software for an enhanced pre-operative planning of femoral artery stenting including a prediction of in vivo stent fracture risk, computed by means of numerical simulations. Software-developing companies developed an...
This paper presents the system architecture of the @neurIST project, which aims at supporting the... more This paper presents the system architecture of the @neurIST project, which aims at supporting the research and treatment of cerebral aneurysms by bringing together heterogeneous data, computing and complex processing services. The architecture is generic enough to adapt it to the treatment of other diseases beyond cerebral aneurysms. The paper describes the generic requirements of the system and presents the architecture, applications and middleware technologies used to realise the system and highlights the innovations in @neurIST.
IEEE Transactions on Information Technology in Biomedicine, 2010
The increasing volume of data describing human disease processes and the growing complexity of un... more The increasing volume of data describing human disease processes and the growing complexity of understanding, managing, and sharing such data presents a huge challenge for clinicians and medical researchers. This paper presents the @neurIST system, which provides an infrastructure for biomedical research while aiding clinical care, by bringing together heterogeneous data and complex processing and computing services. Although @neurIST targets
Investigating the Influence of Haemodynamic Stimuli on Intracranial Aneurysm Inception
Annals of Biomedical Engineering, 2013
We propose a novel method to reconstruct the hypothetical geometry of the healthy vasculature pri... more We propose a novel method to reconstruct the hypothetical geometry of the healthy vasculature prior to intracranial aneurysm (IA) formation: a Frenet frame is calculated along the skeletonization of the arterial geometry; upstream and downstream boundaries of the aneurysmal segment are expressed in terms of the local Frenet frame basis vectors; the hypothetical healthy geometry is then reconstructed by propagating a closed curve along the skeleton using the local Frenet frames so that the upstream boundary is smoothly morphed into the downstream boundary. This methodology takes into account the tortuosity of the arterial vasculature and requires minimal user subjectivity. The method is applied to 22 clinical cases depicting IAs. Computational fluid dynamic simulations of the vasculature without IA are performed and the haemodynamic stimuli in the location of IA formation are examined. We observe that locally elevated wall shear stress (WSS) and gradient oscillatory number (GON) are highly correlated (20/22 for WSS and 19/22 for GON) with regions susceptible to sidewall IA formation whilst haemodynamic indices associated with the oscillation of the WSS vectors have much lower correlations.
2013 International Conference on Computer Medical Applications (ICCMA), 2013
We present a parallel implementation of an algorithm for the detection of colonic polyps from CT ... more We present a parallel implementation of an algorithm for the detection of colonic polyps from CT data sets. This implementation is designed specifically to take advantage of the computational power available on modern Graphics Processing Units (GPUs), which significantly reduces the execution time to streamline the workflow of clinicians examining the data. We provide details about the changes which were made to the existing algorithm to suit the new target hardware, and perform tests which demonstrate that the results are a very close match to the reference implementation while being computed in a fraction of the time. Computer aided diagnosis, GPU computing, Colon screening; I.
The Living Human Project: The Grand Challenge of European Biomechanics?
Computational Bioengineering, 2004
Langenbeck's Archives of Surgery, 2004
Background: All computer-aided surgery technologies assume that the surgeon knows the best positi... more Background: All computer-aided surgery technologies assume that the surgeon knows the best position for the implant components. However, there is indirect evidence that simple anatomical information may not be sufficient for the surgeon to decide size and position of the implant in a repeatable manner. Method: In the present study we estimated the variability in choosing the size and position of the components of a cementless total hip replacement (THR), using template-on-radiograph as well as computed tomography (CT)-based computer-aided planning. In addition, using a computer model, we assessed the sensitivity to such variability of implant fitting, location of the joint centre, skeletal range of motion, and resting length of major hip muscles. Using templates, surgeons selected the size with variability up to 2.5 mm for the stem and up to 4 mm for the socket. A similar variability was also observed when the CT-based planning program was used. Results: No major differences were found between surgeons. The standard deviation over repeated planning sessions of the selected position for each component, using the CT-based planning software, was found to be 3.9 mm and 8.9. Conclusion: On the basis of the computer simulation, this variability did not affect the selected biomechanical parameters in a drastic way, although some differences were observed, especially in the lever arm of the hip muscles.
Lecture Notes in Computer Science, 2014
In this paper we evaluate the performance of the OpenACC and Mint toolkits against C and CUDA imp... more In this paper we evaluate the performance of the OpenACC and Mint toolkits against C and CUDA implementations of the standard PolyBench test suite. Our analysis reveals that performance is similar in many cases, but that a certain set of code constructs impede the ability of Mint to generate optimal code. We then present some small improvements which we integrate into our own GPSME toolkit (which is derived from Mint) and show that our toolkit now out-performs OpenACC in the majority of tests.