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Quantum-optimal-control-inspired ansatz for variational quantum algorithms [article]

Alexandre Choquette, Agustin Di Paolo, Panagiotis Kl. Barkoutsos, David Sénéchal, Ivano Tavernelli, Alexandre Blais
2020 arXiv   pre-print
ACKNOWLEDGMENTS We thank David Poulin, Jonathan Gross and Alexandre Daoust for useful discussions.  ... 
arXiv:2008.01098v1 fatcat:wkhwflug7zchff46gr45yilun4

Numerical scaling analysis of the small-scale structure in turbulence [article]

Panagiotis Stinis, Alexandre J. Chorin
2005 arXiv   pre-print
We show how to use numerical methods within the framework of successive scaling to analyse the microstructure of turbulence, in particular to find inertial range exponents and structure functions. The methods are first calibrated on the Burgers problem and are then applied to the 3D Euler equations. Known properties of low order structure functions appear with a relatively small computational outlay; however, more sensitive properties cannot yet be resolved with this approach well enough to settle ongoing controversies.
arXiv:math/0509027v1 fatcat:7eshwgfr4nemjcwsvdymunuwbu

Endovascular Treatment of Intracranial Aneurysms

Antonis Adamou, Maria Alexandrou, Christian Roth, Achilles Chatziioannou, Panagiotis Papanagiotou
2021 Life  
Traditionally, surgical clipping was the only available treatment modality for intracranial aneurysms. However, in the last few decades, the endovascular therapy of intracranial aneurysms (IAs) has seen a tremendous evolution and development. From coiling to flow diversion and flow disruptor devices, endovascular treatment modalities have increased in number and received broader indications throughout the years. In this review article, the treatment modalities for the endovascular management of
more » ... IAs are presented, emphasizing newer devices and technologies.
doi:10.3390/life11040335 pmid:33920264 fatcat:msrnm6vmjfgmtn4njsozvctpt4

Variational Quantum Simulation of Ultrastrong Light-Matter Coupling [article]

Agustin Di Paolo, Panagiotis Kl. Barkoutsos, Ivano Tavernelli, Alexandre Blais
2019 arXiv   pre-print
We propose the simulation of quantum-optical systems in the ultrastrong-coupling regime using a variational quantum algorithm. More precisely, we introduce a short-depth variational form to prepare the groundstate of the multimode Dicke model on a quantum processor and present proof-of-principle results obtained via cloud access to an IBM device. We moreover provide an algorithm for characterizing the groundstate by Wigner state tomography. Our work is a first step towards digital quantum
more » ... tion of quantum-optical systems with potential applications to the spin-boson, Kondo and Jahn-Teller models.
arXiv:1909.08640v1 fatcat:vbtvgk6c5jhx7fyu7iogcspkb4

Shape-restrained modelling of protein-small molecule complexes with HADDOCK [article]

Panagiotis I Koukos, Manon F. Reau, Alexandre M.J.J. Bonvin
2021 bioRxiv   pre-print
Small molecule docking remains one of the most valuable computational techniques for the structure prediction of protein-small molecule complexes. It allows us to study the interactions between compounds and the protein receptors they target at atomic detail, in a timely and efficient manner. Here we present a new protocol in HADDOCK, our integrative modelling platform, which incorporates homology information for both receptor and compounds. It makes use of HADDOCK's unique ability to integrate
more » ... information in the simulation to drive it toward conformations which agree with the provided data. The focal point is the use of shape restraints derived from homologous compounds bound to the target receptors. We have developed two protocols: In the first, the shape is composed of fake atom beads based on the position of the heavy atoms of the homologous template compound, whereas in the second the shape is additionally annotated with pharmacophore data, for some or all beads. For both protocols, ambiguous distance restraints are subsequently defined between those beads and the heavy atoms of the ligand to be docked. We have benchmarked the performance of these protocols with a fully unbound version of the widely used DUD-E dataset. In this unbound docking scenario, our template/shape-based docking protocol reaches an overall success rate of 81% on 99 complexes, which is close to the best results reported for bound docking on the DUD-E dataset.
doi:10.1101/2021.06.10.447890 fatcat:ghqfdwiubzhtzggfsah2ukbqiu

EPHA2, EPHA4, and EPHA7 Expression in Triple-Negative Breast Cancer

Ilias Nikas, Constantinos Giaginis, Kalliopi Petrouska, Paraskevi Alexandrou, Artemis Michail, Panagiotis Sarantis, Gerasimos Tsourouflis, Eugene Danas, Alexandros Pergaris, Panagiotis K. Politis, Lydia Nakopoulou, Stamatios Theocharis
2022 Diagnostics  
Ongoing research continues to elucidate the complex role of ephrin receptors (EPHs) and their ligands (ephrins) in breast cancer pathogenesis, with their varying expression patterns implied to have an important impact on patients' outcome. The current study aims to investigate the clinical significance of EPHA2, EPHA4, and EPHA7 expression in triple-negative breast cancer (TNBC) cases. EPHA2, EPHA4, and EPHA7 protein expression was assessed immunohistochemically on formalin-fixed and
more » ... bedded (FFPE) TNBC tissue sections from 52 TNBC patients and correlated with key clinicopathologic parameters and patients' survival data (overall survival (OS); disease-free survival (DFS)). EPHA2, EPHA4, and EPHA7 expression was further examined in TNBC cell lines. EPHA2 overexpression was observed in 26 (50%) of the TNBC cases, who exhibited a shorter OS and DFS than their low-expression counterparts, with EPHA2 representing an independent prognostic factor for OS and DFS (p = 0.0041 and p = 0.0232, respectively). EPHA4 overexpression was associated with lymph node metastasis in TNBC patients (p = 0.0546). Alterations in EPHA2, EPHA4, and EPHA7 expression levels were also noted in the examined TNBC cell lines. Our study stresses that EPHA2 expression constitutes a potential prognostic factor for TNBC patients. Given the limited treatment options and poorer outcome that accompany the TNBC subtype, EPHA2 could also pose as a target for novel, more personalized, and effective therapeutic approaches for those patients.
doi:10.3390/diagnostics12020366 pmid:35204461 pmcid:PMC8871500 fatcat:2t47fwaotjevnfoxed3xwlzyz4

Problem reduction, renormalization, and memory

Alexandre Chorin, Panagiotis Stinis
2006 Communications in Applied Mathematics and Computational Science  
doi:10.2140/camcos.2006.1.1 fatcat:ulqtkum3cbgttpe2fjo3okbccm

High Pregnane X Receptor (PXR) Expression Is Correlated with Poor Prognosis in Invasive Breast Carcinoma

Stamatios Theocharis, Constantinos Giaginis, Stefania Gourzi, Paraskevi Alexandrou, Gerasimos Tsourouflis, Panagiotis Sarantis, Eugene Danas, Artemis Michail, Nikolaos Tsoukalas, Alexandros Pergaris, Panagiotis K. Politis, Lydia Nakopoulou
2021 Diagnostics  
Pregnane X Receptor (PXR) is involved in human cancer, either by directly affecting carcinogenesis or by inducing drug-drug interactions and chemotherapy resistance. The clinical significance of PXR expression in invasive breast carcinoma was evaluated in the present study. PXR protein expression was assessed immunohistochemically on formalin fixed paraffin-embedded breast invasive carcinoma tissue sections, obtained from 148 patients, and was correlated with clinicopathological parameters,
more » ... cular phenotypes, tumor cells' proliferative capacity, and overall disease-free patients' survival. Additionally, the expression of PXR was examined on human breast carcinoma cell lines of different histological grade, hormonal status, and metastatic potential. PXR positivity was noted in 79 (53.4%) and high PXR expression in 48 (32.4%), out of 148 breast carcinoma cases. High PXR expression was positively associated with nuclear grade (p = 0.0112) and histological grade of differentiation (p = 0.0305), as well as with tumor cells' proliferative capacity (p = 0.0051), and negatively with luminal A subtype (p = 0.0295). Associations between high PXR expression, estrogen, and progesterone receptor negative status were also recorded (p = 0.0314 and p = 0.0208, respectively). High PXR expression was associated with shorter overall patients' survival times (log-rank test, p = 0.0009). In multivariate analysis, high PXR expression was identified as an independent prognostic factor of overall patients' survival (Cox-regression analysis, p = 0.0082). PXR expression alterations were also noted in breast cancer cell lines of different hormonal status. The present data supported evidence that PXR was related to a more aggressive invasive breast carcinoma phenotype, being a strong and independent poor prognosticator.
doi:10.3390/diagnostics11111946 pmid:34829293 pmcid:PMC8624096 fatcat:e7ltz6fr5vegfb65fdgcviepwi

Mechanical Recanalization With Flow Restoration in Acute Ischemic Stroke

Christian Roth, Wolfgang Reith, Silke Walter, Stefanie Behnke, Michael Kettner, Julio Viera, Umut Yilmaz, Maria Alexandrou, Maria Politi, Panagiotis Kostopoulos, Heiko Körner, Christoph Krick (+3 others)
2013 JACC: Cardiovascular Interventions  
Objectives This study sought to assess the feasibility and safety of a recently described technique of mechanical recanalization with the help of a stent-like device. Background In the special group of acute stroke patients with an intracranial large vessel occlusion, intravenous tissue-type plasminogen activator on its own leads to a good clinical outcome (mRS Յ2) in only 15% to 25% of cases. The aforementioned technique of mechanical recanalization showed very promising clinical results.
more » ... ds Forty patients presenting within 6 h from stroke symptom onset were enrolled. Mechanical recanalization was performed using a Solitaire FR revascularization device. The primary endpoint of the study was the clinical outcome rated with the help of the modified Rankin Scale (mRS) after 90 days. Results Twenty-four patients (60%) showed a good clinical outcome (mRS Յ2) at 90 days. One symptomatic hemorrhage was detected on follow-up computed tomography. The death rate was 12.5% (5 patients). Successful recanalization (Thrombolysis In Cerebral Infarction score Ն2b) of the target vessel was achieved in 95% of the patients with a mean of 1.8 runs with the device. Conclusions The ReFlow (Mechanical Recanalization With Flow Restoration in Acute Ischemic Stroke) study shows that mechanical recanalization with flow restoration is highly effective in stroke patients with a large intracranial vessel occlusion presenting within 4.5 h after symptom onset. (Mechanical Recanalization With Flow Restoration in Acute Ischemic Stroke [ReFlow]; NCT01210729) (J Am Coll Cardiol Intv 2013;6:386 -91)
doi:10.1016/j.jcin.2012.11.013 pmid:23523460 fatcat:sabcqwwsqbd65hmazo2vyaiplq

MENSADB: A Thorough Structural Analysis of Membrane Protein Dimers [article]

Pedro Matos-Filipe, António J. Preto, Panagiotis I. Koukos, Joana Mourão, Alexandre M.J.J. Bonvin, Irina S. Moreira
2019 arXiv   pre-print
Alexandre M.J.J. Bonvin and P. Koukos acknowledge funding from the Dutch Foundation for Scientific Research (NWO) (TOP-PUNT grant 718.015.001). Figure 1 -Overall representation of MENSAdb.  ... 
arXiv:1902.02321v1 fatcat:n4ekobjs3zb6fbicbvj2yjb23a

Defining distance restraints in HADDOCK

Alexandre M. J. J. Bonvin, Ezgi Karaca, Panagiotis L. Kastritis, João P. G. L. M. Rodrigues
2018 Nature Protocols  
doi:10.1038/s41596-018-0017-6 pmid:29942005 fatcat:tw3jhwylfjbqrc7ym3ptvnafja

Challenges and opportunities at the intersection of model reduction and uncertainty quantification

David Barajas-Solano, Alexandre Tartakovsky, Panagiotis Stinis, Xiu Yang
2017 figshare.com  
Barajas-Solano, Panos Stinis, Xiu Yang, Alexandre M. TartakovskyPacific Northwest National LaboratoryAddressing Question 1b.  ... 
doi:10.6084/m9.figshare.5318104 fatcat:dloda2zb2fdcxnxj2ab4n7f6um

Structural biology in the clouds: The WeNMR-EOSC Ecosystem [article]

Rodrigo Vargas Honorato, Panagiotis I. Koukos, Brian Jiménez-García, Andrei Tsaregorodtsev, Marco Verlato, Andrea Giachetti, Antonio Rosato, Alexandre M.J.J. Bonvin
2021 arXiv   pre-print
Structural biology aims at characterizing the structural and dynamic properties of biological macromolecules at atomic details. Gaining insight into three dimensional structures of biomolecules and their interactions is critical for understanding the vast majority of cellular processes, with direct applications in health and food sciences. Since 2010, the WeNMR project (www.wenmr.eu) has implemented numerous web-based services to facilitate the use of advanced computational tools by researchers
more » ... in the field, using the high throughput computing infrastructure provided by EGI. These services have been further developed in subsequent initiatives under H2020 projects and are now operating as Thematic Services in the European Open Science Cloud (EOSC) portal (www.eosc-portal.eu), sending >12 millions of jobs and using around 4000 CPU-years per year. Here we review 10 years of successful e-infrastructure solutions serving a large worldwide community of over 23,000 users to date, providing them with user-friendly, web-based solutions that run complex workflows in structural biology. The current set of active WeNMR portals are described, together with the complex backend machinery that allows distributed computing resources to be harvested efficiently.
arXiv:2107.01056v1 fatcat:a5v7mp6bxrcg7i7xfo2zonba7y

A Membrane Protein Complex Docking Benchmark

Panagiotis I. Koukos, Inge Faro, Charlotte W. van Noort, Alexandre M.J.J. Bonvin
2018 Journal of Molecular Biology  
We report the first membrane protein-protein docking benchmark consisting of 37 targets of diverse functions and folds. The structures were chosen based on a set of parameters such as the availability of unbound structures, the modeling difficulty and their uniqueness. They have been cleaned and consistently numbered to facilitate their use in docking. Using this benchmark, we establish the baseline performance of HADDOCK, without any specific optimization for membrane proteins, for two
more » ... s: true interface-driven docking and ab initio docking. Despite the fact that HADDOCK has been developed for soluble complexes, it shows promising docking performance for membrane systems, but there is clearly room for further optimization. The resulting set of docking decoys, together with analysis scripts, is made freely available. These can serve as a basis for the optimization of membrane complex-specific scoring functions.
doi:10.1016/j.jmb.2018.11.005 pmid:30414967 fatcat:frfwtqrrcfannimqkiui7lix74

Gemstones of Greece: Geology and Crystallizing Environments

Panagiotis Voudouris, Constantinos Mavrogonatos, Ian Graham, Gaston Giuliani, Alexandre Tarantola, Vasilios Melfos, Stefanos Karampelas, Athanasios Katerinopoulos, Andreas Magganas
2019 Minerals  
In the Hellenides Orogen, minerals of various gem quality occur in various rock types from mainly four tectono-metamorphic units, the Rhodope, Pelagonian, and the Attico-Cycladic massifs, and the Phyllites-Quartzites unit of Crete Island. In crystalline rocks, gemstones are related to both regional metamorphic-metasomatic processes (e.g., gem corundums, Mn-andalusite, thulite/clinothulite, spessartine, titanite, jadeite), and to the formation of late alpine-type fissures, such as, for example,
more » ... uartz, albite, adularia and titanite. The Tertiary (and Mesozoic) magmatic-hydrothermal environments provide gem-quality sapphire, beryl, garnet, vesuvianite, epidote, fluorite, and SiO2 varieties. The supergene oxidation zone of the Lavrion deposit hosts gem-quality smithsonite and azurite. Coloration in the studied material is either due to various chromophore trace elements present in the crystal structure, or due to inclusions of other mineral phases. Future modern exploration methods combined with gemological investigations (such as treatment and faceting of selected stones), are necessary in order to obtain a better knowledge of the gemstone potential of Greece for its possible exploitation.
doi:10.3390/min9080461 fatcat:3gx5rv3f6jhpriduq66jjs77qm
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