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1. Implementation of matrix compression in the coupling of JOREK to realistic 3D conducting wall structures

Author

Cipolletta, Federico, Schwarz, Nina, Hoelzl, Matthias, Ventre, Salvatore, Isernia, Nicola, Rubinacci, Guglielmo, Soba, Alejandro, Mantsinen, Mervi Johanna, and Team, the JOREK

Subjects
Physics - Plasma Physics
Abstract

JOREK is an advanced non-linear simulation code for studying MHD instabilities in magnetically confined fusion plasmas and their control and/or mitigation. A free-boundary and resistive wall extension was introduced via coupling to the STARWALL and CARIDDI codes, both able to provide dense response matrices describing the electromagnetic interactions between plasma and conducting structures. For detailed CAD representations of the conducting structures and high resolutions for the plasma region, memory and computing time limitations restrict the possibility of simulating the ITER tokamak. In the present work, the Singular Value Decomposition provided by routines from the ScaLAPACK library has been successfully applied to compress some of the dense response matrices and thus optimize memory usage. This is demonstrated for simulations of Tearing Mode and Vertical Displacement Event instabilities. An outlook to future applications on large production cases and further extensions of the method are discussed., Comment: 19 pages, 9 figures, firstly presented at the 4th Fusion HPC Workshop in November 2023, submitted to Plasma Physics and Controlled Fusion in April 2024, First Revision after referee report in July 2024

Published
2024

5. Synthesis of resonant modes in electromagnetics

Author

Tamburrino, Antonello, Forestiere, Carlo, Miano, Giovanni, Rubinacci, Guglielmo, and Ventre, Salvatore

Subjects
Physics - Optics, Physics - Classical Physics
Abstract

Resonant modes determine the response of electromagnetic devices, including dielectric and plasmonic resonators. Relying on the degrees of freedom that metamaterials provide, this contribution shows how to design, at will, the resonant modes of a dielectric object placed in an unbounded space. Specifically, the proposed method returns in analytical form the spatial distribution of the dielectric susceptibility tensor for which the object exhibits resonances at prescribed frequencies and spatial distribution of the polarization. Together with the synthesis of the material, two key concepts are introduced: the controlled tunability of the resonant modes and the number of essential modes, i.e. the number of modes that uniquely characterize the spatial distribution of the dielectric susceptibility. Moreover, this approach can be applied to design the resonant modes of any system where the constitutive relationship is linear and local.

Published
2023

7. Top researchers in andrology: a bibliometric and demographic analysis of the last 7 years

Author

Simone Tammaro, Davide Arcaniolo, Lorenzo Spirito, Francesco Bottone, Carmelo Quattrone, Marco Stizzo, Marco Terribile, Raffaele Balsamo, Luigi Napolitano, Felice Crocetto, Lorenzo Romano, Michelangelo Olivetta, Arturo Lecce, Andrea Rubinacci, Giampiero Della Rosa, Salvatore Papi, Paola Coppola, Marco De Sio, and Celeste Manfredi

Subjects
andrology, bibliometric, demographic, researcher, sexual medicine, Medicine (General), R5-920
Abstract

The aim of this study is to perform a bibliometric and demographic analysis of the 10 most productive researchers over the past 7 years in relation to the selection of key topics in andrology. We conducted a bibliometric analysis in December 2023, using Scopus Researcher Discovery. Seven major andrological topics were identified: erectile dysfunction (T1), premature ejaculation (T2), male infertility (T3), Peyronie’s disease (T4), male hypogonadism (T5), priapism (T6), and low sexual desire (T7). A total of 10 researchers per topic were identified (51 unique authors). Most were urologists (65%) or endocrinologists (23%). Most authors belonged to centers in the USA (35.7%) and Italy (32.9%). The majority of authors were male (77.1%) and over 40 years old (83.3% of authors of known age). The mean (standard deviation (SD)) H-index of the 10 top researchers was 42.6 (24.6), ranging from 6 to 119. Male infertility was the topic with the most articles (1110) written by the top 10 researchers and the most cited (20,585). Erectile dysfunction was the second topic for articles (678) and third for citations after male hypogonadism (6046 vs. 11,384). The mean (SD) impact factor of the journals in which the andrological articles were published varied from 3.5 (0.53) for premature ejaculation to 5.33 (1.85) for hypogonadism.

Published
2024
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8. Mapache: a flexible pipeline to map ancient DNA

Author

Neuenschwander, Samuel, Dávalos, Diana I. Cruz, Anchieri, Lucas, da Mota, Bárbara Sousa, Bozzi, Davide, Rubinacci, Simone, Delaneau, Olivier, Rasmussen, Simon, and Malaspinas, Anna-Sapfo

Subjects
Quantitative Biology - Genomics
Abstract

Summary: Mapping ancient DNA to a reference genome is challenging as it involves numerous steps, is time-consuming and has to be repeated within a study to assess the quality of extracts and libraries; as a result, the mapping needs to be automatized to handle large amounts of data in a reproducible way. We present mapache, a flexible, robust, and scalable pipeline to map, quantify and impute ancient and present-day DNA in a reproducible way. Mapache is implemented in the workflow manager Snakemake and is optimized for low-space consumption, allowing to efficiently (re)map large data sets such as reference panels and multiple extracts and libraries., Comment: Availability: Mapache is freely available on GitHub (https://github.com/sneuensc/mapache). Supplementary information: An extensive manual is provided at https://github.com/sneuensc/mapache/wiki

Published
2022
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10. Practical Model for the Calculation of Lateral Electromagnetic Loads in Tokamaks at Asymmetric Vertical Displacement Events (AVDEs)

Author

Sergey Sadakov, Fabio Villone, Daniel Iglesias, Luis Maqueda, Jesus Almenara-Rescalvo, Guglielmo Rubinacci, and Salvatore Ventre

Subjects
tokamak, asymmetric, vertical, parametric, model, balance, Physics, QC1-999, Plasma physics. Ionized gases, QC717.6-718.8
Abstract

This paper describes a new practical numerical model for the calculation of lateral electromagnetic (EM) loads in tokamaks during asymmetric vertical displacement events (AVDEs). The model combines key features of two recently reported trial models while avoiding their drawbacks. Their common basic feature is the superposition of two patterns of halo current: one perfectly symmetric and another perfectly anti-symmetric. This model combines the following features that have not been combined before (a) a helically distorted halo layer wrapping around core plasma, and (b) halo-to-wall interception belts slipping along plasma-facing walls. This combination almost doubles the lateral net forces. An AVDE creates significant lateral net moments. Being relatively modest at VDEs, the lateral moments become a dominant component of EM loads at AVDEs. The model carefully tracks the balance of net EM loads (zero total for the tokamak), as a necessary condition for the consequent numerical simulation of the tokamak’s dynamic response. This balance is needed as well for the development of tokamak monitoring algorithms and simulators. In order to decouple from the current uncertainties in the interpretation and simulation of AVDE physics, the model does not simulate AVDE evolution but uses it as an input assumption based on the existing interpretation and simulation of AVDE physics. This means the model is to be used in a manner of parametric study, at widely varied input assumptions on AVDE evolution and severity. Parametric results will fill a library of ready-for-use waveforms of asymmetric EM loads (distributed and total) at tokamak structures and coils, so that the physics community may point to specific variants for subsequent engineering analysis. This article presents the first practical contribution to this AVDE library.

Published
2024
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11. Assessing the impact of post-mortem damage and contamination on imputation performance in ancient DNA

Author

Antonio Garrido Marques, Simone Rubinacci, Anna-Sapfo Malaspinas, Olivier Delaneau, and Bárbara Sousa da Mota

Subjects
Medicine, Science
Abstract

Abstract Low-coverage imputation is becoming ever more present in ancient DNA (aDNA) studies. Imputation pipelines commonly used for present-day genomes have been shown to yield accurate results when applied to ancient genomes. However, post-mortem damage (PMD), in the form of C-to-T substitutions at the reads termini, and contamination with DNA from closely related species can potentially affect imputation performance in aDNA. In this study, we evaluated imputation performance (i) when using a genotype caller designed for aDNA, ATLAS, compared to bcftools, and (ii) when contamination is present. We evaluated imputation performance with principal component analyses and by calculating imputation error rates. With a particular focus on differently imputed sites, we found that using ATLAS prior to imputation substantially improved imputed genotypes for a very damaged ancient genome (42% PMD). Trimming the ends of the sequencing reads led to similar improvements in imputation accuracy. For the remaining genomes, ATLAS brought limited gains. Finally, to examine the effect of contamination on imputation, we added various amounts of reads from two present-day genomes to a previously downsampled high-coverage ancient genome. We observed that imputation accuracy drastically decreased for contamination rates above 5%. In conclusion, we recommend (i) accounting for PMD by either trimming sequencing reads or using a genotype caller such as ATLAS before imputing highly damaged genomes and (ii) only imputing genomes containing up to 5% of contamination.

Published
2024
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12. Static surface mode expansion for the full-wave scattering from penetrable objects

Author

Forestiere, Carlo, Gravina, Giovanni, Miano, Giovanni, Rubinacci, Guglielmo, and Tamburrino, Antonello

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics, Physics - Computational Physics
Abstract

We introduce the longitudinal and transverse static surface modes and use them to solve the full-wave electromagnetic scattering problem from penetrable objects. The longitudinal static modes are the eigenmodes with zero surface curl of the electrostatic integral operator that gives the tangential component of the electric field, as a function of the surface charge density. The transverse static modes are the eigenmodes with zero surface divergence of the magnetostatic integral operator that returns the tangential component of the vector potential, as a function of the surface current distribution. The static modes only depend on the shape of the object, thus, the same static basis can be used regardless of the frequency of operation and of the material constituting the object. We expand the unknown surface currents of the Poggio-Miller-Chang-Harrington-Wu-Tsai surface integral equations in terms of the static surface modes and solve them using the Galerkin-projection scheme. The static modes expansion allows the regularization of the singular integral operators and yields a drastic reduction of the number of unknowns compared to a discretization based on sub-domain basis functions. The introduced expansion significantly reduces the cpu-time required for the numerical solution of the scattering problem from particle arrays.

Published
2022
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13. Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy

Author

Parikh, Victoria N, Ioannidis, Alexander G, Jimenez-Morales, David, Gorzynski, John E, De Jong, Hannah N, Liu, Xiran, Roque, Jonasel, Cepeda-Espinoza, Victoria P, Osoegawa, Kazutoyo, Hughes, Chris, Sutton, Shirley C, Youlton, Nathan, Joshi, Ruchi, Amar, David, Tanigawa, Yosuke, Russo, Douglas, Wong, Justin, Lauzon, Jessie T, Edelson, Jacob, Mas Montserrat, Daniel, Kwon, Yongchan, Rubinacci, Simone, Delaneau, Olivier, Cappello, Lorenzo, Kim, Jaehee, Shoura, Massa J, Raja, Archana N, Watson, Nathaniel, Hammond, Nathan, Spiteri, Elizabeth, Mallempati, Kalyan C, Montero-Martín, Gonzalo, Christle, Jeffrey, Kim, Jennifer, Kirillova, Anna, Seo, Kinya, Huang, Yong, Zhao, Chunli, Moreno-Grau, Sonia, Hershman, Steven G, Dalton, Karen P, Zhen, Jimmy, Kamm, Jack, Bhatt, Karan D, Isakova, Alina, Morri, Maurizio, Ranganath, Thanmayi, Blish, Catherine A, Rogers, Angela J, Nadeau, Kari, Yang, Samuel, Blomkalns, Andra, O’Hara, Ruth, Neff, Norma F, DeBoever, Christopher, Szalma, Sándor, Wheeler, Matthew T, Gates, Christian M, Farh, Kyle, Schroth, Gary P, Febbo, Phil, deSouza, Francis, Cornejo, Omar E, Fernandez-Vina, Marcelo, Kistler, Amy, Palacios, Julia A, Pinsky, Benjamin A, Bustamante, Carlos D, Rivas, Manuel A, and Ashley, Euan A

Subjects
Biological Sciences, Genetics, Pneumonia & Influenza, Lung, Prevention, Human Genome, Clinical Research, Infectious Diseases, Infection, Good Health and Well Being, COVID-19, Genome, Viral, Genome-Wide Association Study, Humans, Pandemics, SARS-CoV-2
Abstract

The SARS-CoV-2 pandemic has differentially impacted populations across race and ethnicity. A multi-omic approach represents a powerful tool to examine risk across multi-ancestry genomes. We leverage a pandemic tracking strategy in which we sequence viral and host genomes and transcriptomes from nasopharyngeal swabs of 1049 individuals (736 SARS-CoV-2 positive and 313 SARS-CoV-2 negative) and integrate them with digital phenotypes from electronic health records from a diverse catchment area in Northern California. Genome-wide association disaggregated by admixture mapping reveals novel COVID-19-severity-associated regions containing previously reported markers of neurologic, pulmonary and viral disease susceptibility. Phylodynamic tracking of consensus viral genomes reveals no association with disease severity or inferred ancestry. Summary data from multiomic investigation reveals metagenomic and HLA associations with severe COVID-19. The wealth of data available from residual nasopharyngeal swabs in combination with clinical data abstracted automatically at scale highlights a powerful strategy for pandemic tracking, and reveals distinct epidemiologic, genetic, and biological associations for those at the highest risk.

Published
2022

16. Exploring the Multifactorial Landscape of Penile Cancer: A Comprehensive Analysis of Risk Factors

Author

Ugo Amicuzi, Marco Grillo, Marco Stizzo, Michelangelo Olivetta, Simone Tammaro, Luigi Napolitano, Pasquale Reccia, Luigi De Luca, Andrea Rubinacci, Giampiero Della Rosa, Arturo Lecce, Paola Coppola, Salvatore Papi, Francesco Trama, Lorenzo Romano, Carmine Sciorio, Lorenzo Spirito, Felice Crocetto, Celeste Manfredi, Francesco Del Giudice, Matteo Ferro, Bernardo Rocco, Octavian Sabin Tataru, Raffaele Balsamo, Giuseppe Lucarelli, Dario Del Biondo, and Biagio Barone

Subjects
penile cancer, risk factors, epidemiology, human papillomavirus, circumcision, early detection, Medicine (General), R5-920
Abstract

Penile cancer, while rare, is a critical public health issue due to its profound impact on patients and the complexities of its management. The disease’s multifactorial etiology includes risk factors such as HPV infection, poor hygiene, smoking, genetic predispositions, and socioeconomic determinants. This article provides a comprehensive review and analysis of these diverse risk factors, aiming to enhance understanding of the disease’s underlying causes. By elucidating these factors, the article seeks to inform and improve prevention strategies, early detection methods, and therapeutic interventions. A nuanced grasp of the multifactorial nature of penile cancer can enable healthcare professionals to develop more effective approaches to reducing incidence rates and improving patient outcomes.

Published
2024
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17. Cognitive Targeted Prostate Biopsy Alone for Diagnosing Clinically Significant Prostate Cancer in Selected Biopsy-Naïve Patients: Results from a Retrospective Pilot Study

Author

Michelangelo Olivetta, Celeste Manfredi, Lorenzo Spirito, Carmelo Quattrone, Francesco Bottone, Marco Stizzo, Ugo Amicuzi, Arturo Lecce, Andrea Rubinacci, Lorenzo Romano, Giampiero Della Rosa, Salvatore Papi, Simone Tammaro, Paola Coppola, Davide Arcaniolo, Ferdinando Fusco, and Marco De Sio

Subjects
clinically significant prostate cancer, transrectal prostate biopsy, cognitive targeted prostate biopsy, Medicine (General), R5-920
Abstract

(1) Background: To identify a particular setting of biopsy-naïve patients in which it would be reasonable to offer only cognitive targeted prostate biopsy (PBx) with a transrectal approach. (2) Methods: We designed an observational retrospective pilot study. Patients with a prostatic specific antigen (PSA) level > 10 ng/mL, either a normal or suspicious digital rectal examination (DRE), and a lesion with a PI-RADS score ≥ 4 in the postero-medial or postero-lateral peripheral zone were included. All patients underwent a transrectal PBx, including both systematic and targeted samples. The detection rate of clinically significant prostate cancer (csPCa) (Gleason Score ≥ 7) was chosen as the primary outcome. We described the detection rate of csPCa in systematic PBx, targeted PBx, and overall PBx. (3) A total of 92 patients were included. Prostate cancer was detected in 84 patients (91.30%) with combined biopsies. A csPCa was diagnosed in all positive cases (100%) with combined biopsies. Systematic PBxs were positive in 80 patients (86.96%), while targeted PBxs were positive in 84 men (91.30%). Targeted PBx alone would have allowed the diagnosis of csPCa in all positive cases; systematic PBx alone would have missed the diagnosis of 8/84 (9.52%) csPCa cases (4 negative patients and 4 not csPCa) (p = 0.011). (4) Conclusions: Cognitive targeted PBx with a transrectal approach could be offered alone to diagnose csPCa in biopsy-naïve patients with PSA ≥ 10 ng/mL, either normal or suspicious DRE, and a lesion with PI-RADS score ≥ 4 in the postero-medial or postero-lateral peripheral zone.

Published
2024
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19. Humoral and cell-mediated immune responses in HIV-vertically infected young patients after three doses of the BNT162b2 mRNA SARS-CoV-2 vaccine

Author

Claudia Vanetti, Marta Stracuzzi, Elisa Crivellaro, Federica Ciciliano, Micaela Garziano, Claudio Fenizia, Mara Biasin, Valeria Rubinacci, Antonella Amendola, Elisabetta Tanzi, Gian Vincenzo Zuccotti, Mario Clerici, Vania Giacomet, and Daria Trabattoni

Subjects
PLWH, SARS-CoV-2 vaccine efficacy, immunocompromised subjects, COVID-19 SIV individuals, immune response, Immunologic diseases. Allergy, RC581-607
Abstract

BackgroundData on the efficacy of three SARS-CoV-2 mRNA BNT162b2 vaccine doses and the role of previous SARS-CoV-2-infection in enhancing vaccine immunogenicity in HIV-vertically-infected people living with HIV (PLWH) are limited, as is the duration of vaccine-induced responses.MethodsSARS-CoV-2 plasma neutralizing activity (NA) against the European (B.1), Delta (B.1.617.2) and Omicron (B.1.1.529) variants and cell-mediated immunity (CMI) were analyzed in 29 ART-treated young PLWH (mean age 27.9 years) and 30 healthy controls (HC) who received three BNT162b2 vaccine doses. Individuals were stratified based on the presence/absence of previous SARS-CoV-2 infection (infected and vaccinated -SIV-; uninfected and vaccinated -SV-). Analyses were performed before vaccination (T0), 25 days from the second dose (T1), the day the third dose was administered (T2), and 3 months after the third dose (T3).ResultsIn PLWH: i) NA against all variants was higher in SIV compared to SV at T2 and was increased at T3; ii) switched-memory plasmablasts were augmented in SIV alone at T2 and T3; iii) a SARS-CoV-2 specific T cell memory was generated; iv) IFN-γ-secreting CD4+ and CD8+ T lymphocytes were boosted at T3 mainly in SV. CMI magnitude was reduced in PLWH compared to HC. Notably, after the third dose of vaccine viremia was unmodified, but CD4 T cell counts were reduced>20% in 3/29 PHLW.ConclusionA third dose of BNT162b2 vaccine induces strong humoral and CMI responses in young ART-treated PLWH independently from a previous SARS-CoV-2 natural infection. The lower magnitude of CMI responses should be considered when planning mRNA vaccine booster doses in PLWH.

Published
2024
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20. Resonance frequency and radiative Q-factor of plasmonic and dielectric modes of small objects

Author

Forestiere, Carlo, Miano, Giovanni, and Rubinacci, Guglielmo

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics, Physics - Optics
Abstract

The electromagnetic scattering resonances of a non-magnetic object much smaller than the incident wavelength in vacuum can be either described by the electroquasistatic approximation of the Maxwell's equations if its permittivity is negative, or by the magnetoquasistatic approximation if its permittivity is positive and sufficiently high. Nevertheless, these two approximations fail to correctly account for the frequency shift and the radiative broadening of the resonances when the size of the object becomes comparable to the wavelength of operation. In this manuscript, the radiation corrections to the electroquasistatic and magnetoquasistatic resonances of arbitrarily-shaped objects are derived, which only depend on the quasistatic current modes. Then, closed form expressions of the frequency-shift and the radiative Q-factor of both plasmonic and dielectric modes of small objects are introduced, where the dependencies on the material and the size of the object are factorized. In particular, it is shown that the radiative Q-factor explicitly depends on the multipolar components of the quasistatic modes.

Published
2020
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21. Use of a spoof plasmon to optimize the coupling of infrared radiation to Josephson Junction fluxon oscillations

Author

Tagliacozzo, A., De Nicola, S., Montemurro, D., Campagnano, G., Petrarca, C., Forestiere, C., Rubinacci, G., Tafuri, F., and Pepe, G. P.

Subjects
Condensed Matter - Superconductivity
Abstract

We show that Infrared radiation impinging onto a 1-d array of grooves drilled in the superconductor electrode of a long overlap junction can improve matching between fluxon oscillations at THz frequencies and a spoof plasmon of comparable wavelength. This example proves that metamaterials can be very helpful in integrating superconductive and subwavelength optical circuits with optimized matching bridging the gap between infrared and microwave radiation.

Published
2020
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22. Imputation of ancient human genomes

Author

Sousa da Mota, Bárbara, Rubinacci, Simone, Cruz Dávalos, Diana Ivette, G. Amorim, Carlos Eduardo, Sikora, Martin, Johannsen, Niels N., Szmyt, Marzena H., Włodarczak, Piotr, Szczepanek, Anita, Przybyła, Marcin M., Schroeder, Hannes, Allentoft, Morten E., Willerslev, Eske, Malaspinas, Anna-Sapfo, and Delaneau, Olivier

Published
2023
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25. Imputation of ancient human genomes

Author

Bárbara Sousa da Mota, Simone Rubinacci, Diana Ivette Cruz Dávalos, Carlos Eduardo G. Amorim, Martin Sikora, Niels N. Johannsen, Marzena H. Szmyt, Piotr Włodarczak, Anita Szczepanek, Marcin M. Przybyła, Hannes Schroeder, Morten E. Allentoft, Eske Willerslev, Anna-Sapfo Malaspinas, and Olivier Delaneau

Subjects
Science
Abstract

Abstract Due to postmortem DNA degradation and microbial colonization, most ancient genomes have low depth of coverage, hindering genotype calling. Genotype imputation can improve genotyping accuracy for low-coverage genomes. However, it is unknown how accurate ancient DNA imputation is and whether imputation introduces bias to downstream analyses. Here we re-sequence an ancient trio (mother, father, son) and downsample and impute a total of 43 ancient genomes, including 42 high-coverage (above 10x) genomes. We assess imputation accuracy across ancestries, time, depth of coverage, and sequencing technology. We find that ancient and modern DNA imputation accuracies are comparable. When downsampled at 1x, 36 of the 42 genomes are imputed with low error rates (below 5%) while African genomes have higher error rates. We validate imputation and phasing results using the ancient trio data and an orthogonal approach based on Mendel’s rules of inheritance. We further compare the downstream analysis results between imputed and high-coverage genomes, notably principal component analysis, genetic clustering, and runs of homozygosity, observing similar results starting from 0.5x coverage, except for the African genomes. These results suggest that, for most populations and depths of coverage as low as 0.5x, imputation is a reliable method that can improve ancient DNA studies.

Published
2023
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26. Genotype imputation methods for next generation datasets

Author

Rubinacci, Simone, Marchini, Jonathan, and Palamara, Pier Francesco

Subjects
576.5072, Missing observations (Statistics), Mathematical statistics
Abstract

The advent of genome-wide association studies (GWAS) revolutionized the field of complex disease genetics. The primary goal of these studies is to achieve a better understanding of the biology of a complex disease and use this knowledge for prevention or better treatment of diseases. Genotype imputation is one of the key steps in such studies. The contribution of genotype imputation is to increase the power of study by boosting the coverage of genetic variation and to provide a natural framework for combining results across association studies that rely on different genotyping platforms. Genotype imputation is the process of statistical inference of unobserved genotypes in a sample of individuals. In the typical scenario, a reference panel of haplotypes is used to infer ungenotyped variants in a set of study samples. Increasing the sample size in the reference panel improves imputation accuracy, especially for variants with low minor allele frequencies, but big reference panels are also a computational challenge for imputation methods. The goal of this dissertation is to develop methods and protocols that scale genotype imputation to very large next generation reference panels. The main contribution of this dissertation is a genotype imputation method named IMPUTE5. It achieves fast, accurate, and memory-efficient imputation by selecting a small number of reference panel haplotypes using the Positional Burrows-Wheeler Transform. Imputation is performed only using the selected haplotypes, leading to a dramatic speed-up with no loss in accuracy compared to other methods. In order to facilitate other researchers to perform GWAS, a protocol to impute from a reference panel of phased haplotypes into a genome-wide association dataset is also described. We also present an efficient C++ implementation of the Positional Burrows-Wheeler Transform which allows fast string matching in a set of haplotypes. An evaluation of previous state selection algorithms is provided together with a qualitative measure of the accuracy of chromosome painting performed by IMPUTE5. A major application is the imputation of the UK Biobank dataset using the 100,000 Genomes Project reference panel. We show how the reference panel has been created and how imputation will be performed. Imputation of the UK Biobank represents an extremely valuable resource for researches, potentially providing new highlights for genome-wide association studies.

Published
2020

27. Efficient Motion Primitives-Based Trajectory Planning for UAVs in the Presence of Obstacles

Author

Marta Manzoni, Roberto Rubinacci, and Davide Invernizzi

Subjects
motion planning, kinodynamic planning, autonomous vehicles navigation, quadrotor UAV, obstacle avoidance, motion primitives, Motor vehicles. Aeronautics. Astronautics, TL1-4050
Abstract

The achievement of full autonomy in Unmanned Aerial Vehicles (UAVs) is significantly dependent on effective motion planning. Specifically, it is crucial to plan collision-free trajectories for smooth transitions from initial to final configurations. However, finding a solution executable by the actual system adds complexity: the planned motion must be dynamically feasible. This involves meeting rigorous criteria, including vehicle dynamics, input constraints, and state constraints. This work addresses optimal kinodynamic motion planning for UAVs in the presence of obstacles by employing a hybrid technique instead of conventional search-based or direct trajectory optimization approaches. This technique involves precomputing a library of motion primitives by solving several Two-Point-Boundary-Value Problems (TPBVP) offline. This library is then repeatedly used online within a graph-search framework. Moreover, to make the method computationally tractable, continuity between consecutive motion primitives is enforced only on a subset of the state variables. This approach is compared with a state-of-the-art quadrotor-tailored search-based approach, which generates motion primitives online through control input discretization and forward propagation of the dynamic equations of a simplified model. The effectiveness of both methods is assessed through simulations and real-world experiments, demonstrating their ability to generate resolution-complete, resolution-optimal, collision-free, and dynamically feasible trajectories. Finally, a comparative analysis highlights the advantages, disadvantages, and optimal usage scenarios for each approach.

Published
2024
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28. Magnetoquasistatic Resonances of Small Dielectric Objects

Author

Forestiere, Carlo, Miano, Giovanni, Pascale, Mariano, Rubinacci, Guglielmo, Tamburrino, Antonello, Tricarico, Roberto, and Ventre, Salvatore

Subjects
Physics - Optics, Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

A small dielectric object with positive permittivity may resonate when the free-space wavelength is large in comparison with the object dimensions if the permittivity is sufficiently high. We show that these resonances are described by the magnetoquasistatic approximation of the Maxwell's equations in which the normal component of the displacement current density field vanishes on the surface of the particle. They are associated to values of permittivities and frequencies for which source-free quasistatic magnetic fields exist, which are connected to the eigenvalues of a magnetostatic integral operator. We present the general physical properties of magnetoquasistatic resonances in dielectrics with arbitrary shape. They arise from the interplay between the polarization energy stored in the dielectric and the energy stored in the magnetic field. Our findings improve the understanding of resonances in high-permittivity dielectric objects and provide a powerful tool that greatly simplifies the analysis and design of high index resonators.

Published
2019
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31. Parent-of-Origin inference for biobanks

Author

Robin J. Hofmeister, Simone Rubinacci, Diogo M. Ribeiro, Alfonso Buil, Zoltán Kutalik, and Olivier Delaneau

Subjects
Science
Abstract

Studies on parent-of-origin effects have been limited in terms of sample size due to lack of parental genomes or known genealogies. Here, the authors develop a method to infer the parent-of-origin of an individual alleles in biobank-scale datasets, without requiring parental genomes or prior knowledge of genealogy, allowing discovery of parent-of-origin effects with an unprecedented sample size.

Published
2022
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32. Overview of T and D–T results in JET with ITER-like wall

Author

C.F. Maggi, D. Abate, N. Abid, P. Abreu, O. Adabonyan, M. Afzal, I. Ahmad, M. Akhtar, R. Albanese, S. Aleiferis, E. Alessi, P. Aleynikov, J. Alguacil, J. Alhage, M. Ali, H. Allen, M. Allinson, M. Alonzo, E. Alves, R. Ambrosino, E. Andersson Sundén, P. Andrew, M. Angelone, C. Angioni, I. Antoniou, L. Appel, C. Appelbee, C. Aramunde, M. Ariola, G. Arnoux, G. Artaserse, J.-F. Artaud, W. Arter, V. Artigues, F.J. Artola, A. Ash, O. Asztalos, D. Auld, F. Auriemma, Y. Austin, L. Avotina, J. Ayllón, E. Aymerich, A. Baciero, L. Bähner, F. Bairaktaris, I. Balboa, M. Balden, N. Balshaw, V.K. Bandaru, J. Banks, A. Banon Navarro, C. Barcellona, O. Bardsley, M. Barnes, R. Barnsley, M. Baruzzo, M. Bassan, A. Batista, P. Batistoni, L. Baumane, B. Bauvir, L. Baylor, C. Bearcroft, P. Beaumont, D. Beckett, A. Begolli, M. Beidler, N. Bekris, M. Beldishevski, E. Belli, F. Belli, S. Benkadda, J. Bentley, E. Bernard, J. Bernardo, M. Bernert, M. Berry, L. Bertalot, H. Betar, M. Beurskens, P.G. Bhat, S. Bickerton, J. Bielecki, T. Biewer, R. Bilato, P. Bílková, G. Birkenmeier, R. Bisson, J.P.S. Bizarro, P. Blatchford, A. Bleasdale, V. Bobkov, A. Boboc, A. Bock, G. Bodnar, P. Bohm, L. Bonalumi, N. Bonanomi, D. Bonfiglio, X. Bonnin, P. Bonofiglo, J. Booth, D. Borba, D. Borodin, I. Borodkina, T.O.S.J. Bosman, C. Bourdelle, M. Bowden, I. Božičević Mihalić, S.C. Bradnam, B. Breizman, S. Brezinsek, D. Brida, M. Brix, P. Brown, D. Brunetti, M. Buckley, J. Buermans, H. Bufferand, P. Buratti, A. Burckhart, A. Burgess, A. Buscarino, A. Busse, D. Butcher, G. Calabrò, L. Calacci, R. Calado, R. Canavan, B. Cannas, M. Cannon, M. Cappelli, S. Carcangiu, P. Card, A. Cardinali, S. Carli, P. Carman, D. Carnevale, B. Carvalho, I.S. Carvalho, P. Carvalho, I. Casiraghi, F.J. Casson, C. Castaldo, J.P. Catalan, N. Catarino, F. Causa, M. Cavedon, M. Cecconello, L. Ceelen, C.D. Challis, B. Chamberlain, R. Chandra, C.S. Chang, A. Chankin, B. Chapman, P. Chauhan, M. Chernyshova, A. Chiariello, G.-C. Chira, P. Chmielewski, A. Chomiczewska, L. Chone, J. Cieslik, G. Ciraolo, D. Ciric, J. Citrin, Ł. Ciupinski, R. Clarkson, M. Cleverly, P. Coates, V. Coccorese, R. Coelho, J.W. Coenen, I.H. Coffey, A. Colangeli, L. Colas, J. Collins, S. Conroy, C. Contré, N.J. Conway, D. Coombs, P. Cooper, S. Cooper, L. Cordaro, C. Corradino, Y. Corre, G. Corrigan, D. Coster, T. Craciunescu, S. Cramp, D. Craven, R. Craven, G. Croci, D. Croft, K. Crombé, T. Cronin, N. Cruz, A. Cufar, A. Cullen, A. Dal Molin, S. Dalley, P. David, A. Davies, J. Davies, S. Davies, G. Davis, K. Dawson, S. Dawson, I. Day, G. De Tommasi, J. Deane, M. Dearing, M. De Bock, J. Decker, R. Dejarnac, E. Delabie, E. de la Cal, E. de la Luna, D. Del Sarto, A. Dempsey, W. Deng, A. Dennett, G.L. Derks, G. De Temmerman, F. Devasagayam, P. de Vries, P. Devynck, A. di Siena, D. Dickinson, T. Dickson, M. Diez, P. Dinca, T. Dittmar, L. Dittrich, J. Dobrashian, T. Dochnal, A.J.H. Donné, W. Dorland, S. Dorling, S. Dormido-Canto, R. Dotse, D. Douai, S. Dowson, R. Doyle, M. Dreval, P. Drews, G. Drummond, Ph. Duckworth, H.G. Dudding, R. Dumont, P. Dumortier, D. Dunai, T. Dunatov, M. Dunne, I. Ďuran, F. Durodié, R. Dux, T. Eade, E. Eardley, J. Edwards, T. Eich, A. Eksaeva, H. El-Haroun, R.D. Ellis, G. Ellwood, C. Elsmore, S. Emery, G. Ericsson, B. Eriksson, F. Eriksson, J. Eriksson, L.G. Eriksson, S. Ertmer, G. Evans, S. Evans, E. Fable, D. Fagan, M. Faitsch, D. Fajardo Jimenez, M. Falessi, A. Fanni, T. Farmer, I. Farquhar, B. Faugeras, S. Fazinić, N. Fedorczak, K. Felker, R. Felton, H. Fernandes, D.R. Ferreira, J. Ferreira, G. Ferrò, J. Fessey, O. Février, O. Ficker, A.R. Field, A. Figueiredo, J. Figueiredo, A. Fil, N. Fil, P. Finburg, U. Fischer, G. Fishpool, L. Fittill, M. Fitzgerald, D. Flammini, J. Flanagan, S. Foley, N. Fonnesu, M. Fontana, J.M. Fontdecaba, L. Fortuna, E. Fortuna-Zalesna, M. Fortune, C. Fowler, P. Fox, O. Franklin, E. Fransson, L. Frassinetti, R. Fresa, D. Frigione, T. Fülöp, M. Furseman, S. Gabriellini, D. Gadariya, S. Gadgil, K. Gál, S. Galeani, A. Galkowski, D. Gallart, M. Gambrioli, T. Gans, J. Garcia, M. García-Muñoz, L. Garzotti, J. Gaspar, R. Gatto, P. Gaudio, D. Gear, T. Gebhart, S. Gee, M. Gelfusa, R. George, S.N. Gerasimov, R. Gerru, G. Gervasini, M. Gethins, Z. Ghani, M. Gherendi, P.-I. Gherghina, F. Ghezzi, L. Giacomelli, C. Gibson, L. Gil, M.R. Gilbert, A. Gillgren, E. Giovannozzi, C. Giroud, G. Giruzzi, J. Goff, V. Goloborodko, R. Gomes, J.-F. Gomez, B. Gonçalves, M. Goniche, J. Gonzalez-Martin, A. Goodyear, S. Gore, G. Gorini, T. Görler, N. Gotts, E. Gow, J.P. Graves, J. Green, H. Greuner, E. Grigore, F. Griph, W. Gromelski, M. Groth, C. Grove, R. Grove, N. Gupta, S. Hacquin, L. Hägg, A. Hakola, M. Halitovs, J. Hall, C.J. Ham, M. Hamed, M.R. Hardman, Y. Haresawa, G. Harrer, J.R. Harrison, D. Harting, D.R. Hatch, T. Haupt, J. Hawes, N.C. Hawkes, J. Hawkins, S. Hazael, J. Hearmon, P. Heesterman, P. Heinrich, M. Held, W. Helou, O. Hemming, S.S. Henderson, R. Henriques, R.B. Henriques, D. Hepple, J. Herfindal, G. Hermon, J.C. Hillesheim, K. Hizanidis, A. Hjalmarsson, A. Ho, J. Hobirk, O. Hoenen, C. Hogben, A. Hollingsworth, S. Hollis, E. Hollmann, M. Hölzl, M. Hook, M. Hoppe, J. Horáček, N. Horsten, A. Horton, L.D. Horton, L. Horvath, S. Hotchin, Z. Hu, Z. Huang, E. Hubenov, A. Huber, V. Huber, T. Huddleston, G.T.A. Huijsmans, Y. Husain, P. Huynh, A. Hynes, D. Iglesias, M.V. Iliasova, M. Imríšek, J. Ingleby, P. Innocente, V. Ioannou-Sougleridis, N. Isernia, I. Ivanova-Stanik, E. Ivings, S. Jachmich, T. Jackson, A.S. Jacobsen, P. Jacquet, H. Järleblad, A. Järvinen, F. Jaulmes, N. Jayasekera, F. Jenko, I. Jepu, E. Joffrin, T. Johnson, J. Johnston, C. Jones, E. Jones, G. Jones, L. Jones, T.T.C. Jones, A. Joyce, M. Juvonen, A. Kallenbach, P. Kalnina, D. Kalupin, P. Kanth, A. Kantor, A. Kappatou, O. Kardaun, J. Karhunen, E. Karsakos, Ye.O. Kazakov, V. Kazantzidis, D.L. Keeling, W. Kelly, M. Kempenaars, D. Kennedy, K. Khan, E. Khilkevich, C. Kiefer, H.-T. Kim, J. Kim, S.H. Kim, D.B. King, D.J. Kinna, V.G. Kiptily, A. Kirjasuo, K.K. Kirov, A. Kirschner, T. Kiviniemi, G. Kizane, C. Klepper, A. Klix, G. Kneale, M. Knight, P. Knight, R. Knights, S. Knipe, U. Knoche, M. Knolker, M. Kocan, F. Köchl, G. Kocsis, J.T.W. Koenders, Y. Kolesnichenko, Y. Kominis, M. Kong, B. Kool, V. Korovin, S.B. Korsholm, B. Kos, D. Kos, M. Koubiti, Y. Kovtun, E. Kowalska-Strzęciwilk, K. Koziol, Y. Krasikov, A. Krasilnikov, V. Krasilnikov, M. Kresina, A. Kreter, K. Krieger, A. Krivska, U. Kruezi, I. Książek, H. Kumpulainen, B. Kurzan, S. Kwak, O.J. Kwon, B. Labit, M. Lacquaniti, A. Lagoyannis, L. Laguardia, A. Laing, V. Laksharam, N. Lam, H.T. Lambertz, B. Lane, M. Langley, E. Lascas Neto, E. Łaszyńska, K.D. Lawson, A. Lazaros, E. Lazzaro, G. Learoyd, C. Lee, K. Lee, S. Leerink, T. Leeson, X. Lefebvre, H.J. Leggate, J. Lehmann, M. Lehnen, D. Leichtle, F. Leipold, I. Lengar, M. Lennholm, E. Leon Gutierrez, L.A. Leppin, E. Lerche, A. Lescinskis, S. Lesnoj, L. Lewin, J. Lewis, J. Likonen, Ch. Linsmeier, X. Litaudon, E. Litherland-Smith, F. Liu, T. Loarer, A. Loarte, R. Lobel, B. Lomanowski, P.J. Lomas, J. Lombardo, R. Lorenzini, S. Loreti, V.P. Loschiavo, M. Loughlin, T. Lowe, C. Lowry, T. Luce, R. Lucock, T. Luda Di Cortemiglia, M. Lungaroni, C.P. Lungu, T. Lunt, V. Lutsenko, B. Lyons, J. Macdonald, E. Macusova, R. Mäenpää, H. Maier, J. Mailloux, S. Makarov, P. Manas, A. Manning, P. Mantica, M.J. Mantsinen, J. Manyer, A. Manzanares, Ph. Maquet, M. Maraschek, G. Marceca, G. Marcer, C. Marchetto, O. Marchuk, A. Mariani, G. Mariano, M. Marin, A. Marin Roldan, M. Marinelli, T. Markovič, L. Marot, C. Marren, S. Marsden, S. Marsen, J. Marsh, R. Marshall, L. Martellucci, A.J. Martin, C. Martin, R. Martone, S. Maruyama, M. Maslov, M. Mattei, G.F. Matthews, D. Matveev, E. Matveeva, A. Mauriya, F. Maviglia, M. Mayer, M.-L. Mayoral, S. Mazzi, C. Mazzotta, R. McAdams, P.J. McCarthy, P. McCullen, R. McDermott, D.C. McDonald, D. McGuckin, V. McKay, L. McNamee, A. McShee, D. Mederick, M. Medland, S. Medley, K. Meghani, A.G. Meigs, S. Meitner, S. Menmuir, K. Mergia, S. Mianowski, P. Middleton, J. Mietelski, K. Mikszuta-Michalik, D. Milanesio, E. Milani, E. Militello-Asp, F. Militello, J. Milnes, A. Milocco, S. Minucci, I. Miron, J. Mitchell, J. Mlynář, V. Moiseenko, P. Monaghan, I. Monakhov, A. Montisci, S. Moon, R. Mooney, S. Moradi, R.B. Morales, L. Morgan, F. Moro, J. Morris, T. Mrowetz, L. Msero, S. Munot, A. Muñoz-Perez, M. Muraglia, A. Murari, A. Muraro, B. N’Konga, Y.S. Na, F. Nabais, R. Naish, F. Napoli, E. Nardon, V. Naulin, M.F.F. Nave, R. Neu, S. Ng, M. Nicassio, D. Nicolai, A.H. Nielsen, S.K. Nielsen, D. Nina, C. Noble, C.R. Nobs, M. Nocente, H. Nordman, S. Nowak, H. Nyström, J. O’Callaghan, M. O’Mullane, C. O’Neill, C. Olde, H.J.C. Oliver, R. Olney, J. Ongena, G.P. Orsitto, A. Osipov, R. Otin, N. Pace, L.W. Packer, E. Pajuste, D. Palade, J. Palgrave, O. Pan, N. Panadero, T. Pandya, E. Panontin, A. Papadopoulos, G. Papadopoulos, G. Papp, V.V. Parail, A. Parsloe, K. Paschalidis, M. Passeri, A. Patel, A. Pau, G. Pautasso, R. Pavlichenko, A. Pavone, E. Pawelec, C. Paz-Soldan, A. Peacock, M. Pearce, I.J. Pearson, E. Peluso, C. Penot, K. Pepperell, A. Perdas, T. Pereira, E. Perelli Cippo, C. Perez von Thun, D. Perry, P. Petersson, G. Petravich, N. Petrella, M. Peyman, L. Pigatto, M. Pillon, S. Pinches, G. Pintsuk, C. Piron, A. Pironti, F. Pisano, R. Pitts, U. Planck, N. Platt, V. Plyusnin, M. Podesta, G. Pokol, F.M. Poli, O.G. Pompilian, M. Poradzinski, M. Porkolab, C. Porosnicu, G. Poulipoulis, A.S. Poulsen, I. Predebon, A. Previti, D. Primetzhofer, G. Provatas, G. Pucella, P. Puglia, K. Purahoo, O. Putignano, T. Pütterich, A. Quercia, G. Radulescu, V. Radulovic, R. Ragona, M. Rainford, P. Raj, M. Rasinski, D. Rasmussen, J. Rasmussen, J.J. Rasmussen, A. Raso, G. Rattá, S. Ratynskaia, R. Rayaprolu, M. Rebai, A. Redl, D. Rees, D. Réfy, R. Reichle, H. Reimerdes, B.C.G. Reman, C. Reux, S. Reynolds, D. Rigamonti, E. Righi, F.G. Rimini, J. Risner, J.F. Rivero-Rodriguez, C.M. Roach, J. Roberts, R. Robins, S. Robinson, D. Robson, S. Rode, P. Rodrigues, P. Rodriguez-Fernandez, S. Romanelli, J. Romazanov, E. Rose, C. Rose-Innes, R. Rossi, S. Rowe, D. Rowlands, C. Rowley, M. Rubel, G. Rubinacci, G. Rubino, M. Rud, J. Ruiz Ruiz, F. Ryter, S. Saarelma, A. Sahlberg, M. Salewski, A. Salmi, R. Salmon, F. Salzedas, F. Sanchez, I. Sanders, D. Sandiford, F. Sanni, O. Sauter, P. Sauvan, G. Schettini, A. Shevelev, A.A. Schekochihin, K. Schmid, B.S. Schmidt, S. Schmuck, M. Schneider, P.A. Schneider, N. Schoonheere, R. Schramm, D. Scoon, S. Scully, M. Segato, J. Seidl, L. Senni, J. Seo, G. Sergienko, M. Sertoli, S.E. Sharapov, R. Sharma, A. Shaw, R. Shaw, H. Sheikh, U. Sheikh, N. Shi, P. Shigin, D. Shiraki, G. Sias, M. Siccinio, B. Sieglin, S.A. Silburn, A. Silva, C. Silva, J. Silva, D. Silvagni, D. Simfukwe, J. Simpson, P. Sirén, A. Sirinelli, H. Sjöstrand, N. Skinner, J. Slater, T. Smart, R.D. Smirnov, N. Smith, P. Smith, T. Smith, J. Snell, L. Snoj, E.R. Solano, V. Solokha, C. Sommariva, K. Soni, M. Sos, J. Sousa, C. Sozzi, T. Spelzini, F. Spineanu, L. Spolladore, D. Spong, C. Srinivasan, G. Staebler, A. Stagni, I. Stamatelatos, M.F. Stamp, Ž. Štancar, P.A. Staniec, G. Stankūnas, M. Stead, B. Stein-Lubrano, A. Stephen, J. Stephens, P. Stevenson, C. Steventon, M. Stojanov, D.A. St-Onge, P. Strand, S. Strikwerda, C.I. Stuart, S. Sturgeon, H.J. Sun, S. Surendran, W. Suttrop, J. Svensson, J. Svoboda, R. Sweeney, G. Szepesi, M. Szoke, T. Tadić, B. Tal, T. Tala, P. Tamain, K. Tanaka, W. Tang, G. Tardini, M. Tardocchi, D. Taylor, A.S. Teimane, G. Telesca, A. Teplukhina, A. Terra, D. Terranova, N. Terranova, D. Testa, B. Thomas, V.K. Thompson, A. Thorman, A.S. Thrysoe, W. Tierens, R.A. Tinguely, A. Tipton, H. Todd, M. Tomeš, A. Tookey, P. Tsavalas, D. Tskhakaya, L.-P. Turică, A. Turner, I. Turner, M. Turner, M.M. Turner, G. Tvalashvili, A. Tykhyy, S. Tyrrell, A. Uccello, V. Udintsev, A. Vadgama, D.F. Valcarcel, A. Valentini, M. Valisa, M. Vallar, M. Valovic, M. Van Berkel, K.L. van de Plassche, M. van Rossem, D. Van Eester, J. Varela, J. Varje, T. Vasilopoulou, G. Vayakis, M. Vecsei, J. Vega, M. Veis, P. Veis, S. Ventre, M. Veranda, G. Verdoolaege, C. Verona, G. Verona Rinati, E. Veshchev, N. Vianello, E. Viezzer, L. Vignitchouk, R. Vila, R. Villari, F. Villone, P. Vincenzi, A. Vitins, Z. Vizvary, M. Vlad, I. Voldiner, U. Von Toussaint, P. Vondráček, B. Wakeling, M. Walker, R. Walker, M. Walsh, R. Walton, E. Wang, F. Warren, R. Warren, J. Waterhouse, C. Watts, T. Webster, M. Weiland, H. Weisen, M. Weiszflog, N. Wendler, A. West, M. Wheatley, S. Whetham, A. Whitehead, D. Whittaker, A. Widdowson, S. Wiesen, M. Willensdorfer, J. Williams, I. Wilson, T. Wilson, M. Wischmeier, A. Withycombe, D. Witts, A. Wojcik-Gargula, E. Wolfrum, R. Wood, R. Woodley, R. Worrall, I. Wyss, T. Xu, D. Yadykin, Y. Yakovenko, Y. Yang, V. Yanovskiy, R. Yi, I. Young, R. Young, B. Zaar, R.J. Zabolockis, L. Zakharov, P. Zanca, A. Zarins, D. Zarzoso Fernandez, K.-D. Zastrow, Y. Zayachuk, M. Zerbini, W. Zhang, B. Zimmermann, M. Zlobinski, A. Zocco, V.K. Zotta, M. Zuin, W. Zwingmann, and I. Zychor

Subjects
magnetic fusion, JET-ILW, D–T, tritium, alpha particles, fusion prediction, Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract

In 2021 JET exploited its unique capabilities to operate with T and D–T fuel with an ITER-like Be/W wall (JET-ILW). This second major JET D–T campaign (DTE2), after DTE1 in 1997, represented the culmination of a series of JET enhancements—new fusion diagnostics, new T injection capabilities, refurbishment of the T plant, increased auxiliary heating, in-vessel calibration of 14 MeV neutron yield monitors—as well as significant advances in plasma theory and modelling in the fusion community. DTE2 was complemented by a sequence of isotope physics campaigns encompassing operation in pure tritium at high T-NBI power. Carefully conducted for safe operation with tritium, the new T and D–T experiments used 1 kg of T (vs 100 g in DTE1), yielding the most fusion reactor relevant D–T plasmas to date and expanding our understanding of isotopes and D–T mixture physics. Furthermore, since the JET T and DTE2 campaigns occurred almost 25 years after the last major D–T tokamak experiment, it was also a strategic goal of the European fusion programme to refresh operational experience of a nuclear tokamak to prepare staff for ITER operation. The key physics results of the JET T and DTE2 experiments, carried out within the EUROfusion JET1 work package, are reported in this paper. Progress in the technological exploitation of JET D–T operations, development and validation of nuclear codes, neutronic tools and techniques for ITER operations carried out by EUROfusion (started within the Horizon 2020 Framework Programme and continuing under the Horizon Europe FP) are reported in (Litaudon et al Nucl. Fusion accepted), while JET experience on T and D–T operations is presented in (King et al Nucl. Fusion submitted).

Published
2024
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33. Non-linear MHD modelling of transients in tokamaks: a review of recent advances with the JOREK code

Author

M. Hoelzl, G.T.A. Huijsmans, F.J. Artola, E. Nardon, M. Becoulet, N. Schwarz, A. Cathey, S.J.P. Pamela, K. Aleynikova, F. Antlitz, V. Bandaru, H. Bergström, A. Bhole, T. Bogaarts, D. Bonfiglio, F. Cipolletta, T. Driessen, L. Edes, S. Futatani, G. Hao, F. Hindenlang, I. Holod, D. Hu, S. Hu, N. Isernia, H. Isliker, S.K. Kim, M. Kong, S. Korving, L. Kos, I. Krebs, S.J. Lee, Y.C. Liang, Z. Liang, S.J. Liu, Z.X. Lu, L. Meier, L. Messfeldt, V. Mitterauer, N. Nikulsin, B. Nkonga, R. Ramasamy, J. Reinking, C. Rogge, G. Rubinacci, K. Särkimäki, T. Smits, C. Sommariva, R. Sparago, K. Strien, M. Szucs, W. Tang, J. van Tongeren, F. Vannini, S. Ventre, F. Villone, C. Wang, L. Wang, F. Wieschollek, F. Wouters, J. Zielinski, and H. Zhang

Subjects
non-linear MHD, transient plasma instabilities, magnetic confinement fusion, disruptions, pedestal instabilities, Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract

Transient magneto-hydrodynamic (MHD) events like edge localized modes (ELMs) or disruptions are a concern for magnetic confinement fusion power plants. Research with the MHD code JOREK towards understanding control of such instabilities is reviewed here in a concise way to provide a complete overview, while we refer to the original publications for details. Experimental validation for unmitigated vertical displacement events progressed. The mechanism of vertical force mitigation by impurity injection was identified. Two-way eddy current coupling to CARIDDI was completed. Shattered pellet injection was simulated in JET, KSTAR, ASDEX Upgrade (AUG) and ITER. Benign runaway electron beam termination in JET and ITER was studied. Coupling of kinetic REs to the MHD is ongoing and a virtual RE synchrotron radiation diagnostic was developed. Regarding pedestal physics, regimes devoid of large ELMs in AUG were simulated and predictive JT60-SA simulations are ongoing. For ELM suppression by resonant magnetic perturbations (RMPs), AUG, ITER and EAST simulations were performed. A free boundary RMP model was validated against experiments. Evidence for penetrated magnetic islands at the pedestal top based on AUG experiments and simulations was found. Simulations of the naturally ELM-free quiescent H-mode in AUG and HL-3 show external kink mode formation prevents pedestal build-up towards an ELM within windows of the edge safety factor. With kinetic neutral particles, high field side high density formation in ITER was simulated and with kinetic impurities, tungsten transport in AUG RMP plasmas was studied. To capture turbulent transport, electro-static full-f particle in cell models for ion temperature gradient and trapped electron modes were established and benchmarked. Application to RMP plasmas shows enhanced turbulence in comparison to unperturbed states. Energetic particle interactions with MHD were studied. Flux pumping that prevents the safety factor on axis from dropping below unity was simulated. First non-linear stellarator applications include current relaxation in l = 2 stellarators, while verification for advanced stellarators progresses.

Published
2024
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34. Divertor Tokamak Test facility project: status of design and implementation

Author

Francesco Romanelli, on behalf of DTT Contributors, D. Abate, E. Acampora, D. Agguiaro, R. Agnello, P. Agostinetti, M. Agostini, A. Aimetta, R. Albanese, G. Alberti, M. Albino, E. Alessi, S. Almaviva, M. Alonzo, R. Ambrosino, P. Andreoli, M. Angelone, M. Angelucci, C. Angioni, A. Angrisani Armenio, P. Antonini, D. Aprile, G. Apruzzese, M. Aquilini, G. Aragone, P. Arena, M. Ariola, G. Artaserse, L. Aucone, A. Augieri, F. Auriemma, J. Ayllon Guerola, N. Badodi, B. Baiocchi, L. Balbinot, C. Baldacchini, A. Balestri, T. Barberis, G. Barone, L. Barucca, M. Baruzzo, S. Begozzi, V. Belardi, F. Belli, A. Belpane, F. Beone, S. Bertolami, S. Bianucci, S. Bifaretti, S. Bigioni, W. Bin, P. Boccali, B. Boeswirth, E. Bogazzi, R. Bojoi, S. Bollanti, T. Bolzonella, F. Bombarda, M. Bonan, N. Bonanomi, A. Bonaventura, L. Boncagni, M. Bonesso, D. Bonfiglio, R. Bonifetto, D. Bonomi, D. Borgogno, T. Borzone, S. Botti, E. Boz, F. Braghin, M. Brena, S. Brezinsek, M. Brombin, A. Bruschi, S. Buonocore, P. Buratti, D. Busi, G. Calabrò, M. Caldora, G. Calvo, G. Camera, G. Campana, S. Candela, V. Candela, F. Cani, L. Cantone, F. Capaldo, S. Cappello, M. Caponero, S. Carchella, A. Cardinali, D. Carnevale, L. Carraro, C. Carrelli, V. Casalegno, I. Casiraghi, C. Castaldo, A. Castaldo, G. Castro, A. Carpignano, F. Causa, R. Cavazzana, M. Cavedon, M. Cavenago, M. Cecchini, S. Ceccuzzi, G. Celentano, L. Celona, C. Centioli, G.V. Centomani, S. Cesaroni, A.G. Chiariello, R. Chomicz, C. Cianfarani, F. Cichocki, M. Cinque, A. Cioffi, M. Ciotti, M. Cipriani, S. Ciufo, V. Claps, G. Claps, V. Coccorese, D. Coccorese, A. Colangeli, T. Coltella, F. Consoli, F. Cordella, D. Corradini, O. Costa, F. Crea, A. Cremona, F. Crescenzi, F. Crisanti, G. Cristofari, G. Croci, A. Cucchiaro, D. D’Ambrosio, M. Dal Molin, M. Dalla Palma, F. Danè, C. Day, M. De Angeli, V. De Leo, R. De Luca, E. De Marchi, G. De Marzi, G. De Masi, E. De Nardi, C. De Piccoli, G. De Sano, M. De Santis, G. De Tommasi, A. Del Nevo, A. Delfino, A. Della Corte, P. Deodati, S. Desiderati, E. Di Ferdinando, M.G. Di Florio, G. Di Gironimo, L.E. Di Grazia, V. Di Marzo, F. Di Paolo, E. Di Pietro, M. Di Pietrantonio, M. Di Prinzio, A. Di Silvestre, A. Di Zenobio, R. Dima, A. Domenichelli, A. Doria, G. Dose, S. Dubbioso, S. Dulla, I. Duran, M. Eboli, M. Elitropi, E. Emanuelli, B. Esposito, P. Ettorre, C. Fabbri, F. Fabbri, M. Fadone, M.M. Faggiano, F. Falcioni, M.V. Falessi, F. Fanale, P. Fanelli, A. Fassina, M. Favaretto, G. Favero, M. Ferraris, F. Ferrazza, C. Ferretti, A. Ferro, N. Ferron, C. Fiamozzi Zignani, L. Figini, F. Filippi, M. Filippini, A. Fimiani, M. Fincato, F. Fiorenza, D. Fiorucci, D. Flammini, F. Flora, N. Fonnesu, P. Franz, L. Frassinetti, A. Frattolillo, R. Freda, R. Fresa, A. Frescura, P. Frosi, M. Fulici, M. Furno Palumbo, V. Fusco, P. Fusco, L. Gabellier, P. Gaetani, E. Gaio, E. Gajetti, A. Galatà, J. Galdon Quiroga, D.L. Galindo Huertas, S. Gammino, G. Gandolfo, S. Garavaglia, J. Garcia Lopez, M. Garcia Muñoz, P. Gaudio, M. Gelfusa, G. Gervasini, L. Giannini, M. Giarrusso, C. Gil, F. Giorgetti, E. Giovannozzi, G. Giruzzi, L. Giudicotti, M. Gobbin, G. Gorini, G. Granucci, D. Grasso, T. Grasso, S. Grazioso, H. Greuner, G. Griva, G. Grosso, S. Guerini, J.P. Gunn, V. Hauer, J. Hidalgo Salaverri, M. Hoppe, M. Houry, M. Hoelzl, A. Iaboni, M. Iafrati, A. Iaiunese, V. Imbriani, D. Indrigo, P. Innocente, F. Koechl, B. Končar, A. Kryzhanovskyy, L. Laguardia, D.A. Lampasi, C. Lanchi, F. Lanzotti, A. Lanzotti, M. Laquaniti, F. Leone, J. Li, M. Libè, F. Lisanti, D. Liuzza, F. Locati, R. Lombroni, R. Lorenzini, P. Lorusso, L. Lotto, J. Loureiro, F. Lucca, T. Luda Di Cortemiglia, P. Maccari, G. Maddaluno, S. Magagnino, G. Manca, A. Mancini, P. Mandalà, B. Mandolesi, F. Mandrile, G. Manduchi, S. Manfrin, M. Manganelli, P. Mantica, G. Marchiori, N. Marconato, G. Marelli, A. Mariani, A. Marin, R. Marinari, M. Marinelli, F. Marino, P. Marino, D. Marocco, R. Marsilio, E. Martelli, P. Martin, F. Martinelli, G. Martini, R. Martone, A. Marucci, D. Marzullo, V. Masala, D. Mascali, F. Mascari, A. Masi, N. Massanova, S. Mastrostefano, M. Mattei, G. Mauro, S. Mauro, C. Meineri, L. Melaragni, A. Mele, P. Meller, S. Meloni, I. Menicucci, G. Messina, L. Mezi, G. Miccichè, M. Micheletti, S. Migliori, D. Milanesio, F. Milazzo, R. Milazzo, P. Minelli, S. Minucci, F. Mirizzi, M. Missirlian, D. Monarca, C. Monti, M. Mori, A. Moriani, L. Morici, A. Moro, F. Moro, P. Mosetti, R. Mozzillo, A. Murari, A. Muraro, D. Murra, P. Muscente, S. Musumeci, L. Muzzi, G.F. Nallo, F. Napoli, E. Nardon, E. Naselli, R. Neu, M. Nocente, M. Notazio, S. Nowak, E. Ocello, A. Oliva, V. Orsetti, A. Orsini, F.P. Orsitto, M. Ortino, M. Ottavi, G. Paccagnella, D. Pacella, I. Pagani, N. Paganucci, A. Pagliaro, V. Palazzolo, M. Palermo, S. Palomba, F. Panza, D. Paoletti, M. Parisi, R. Pasqualotto, S. Passarello, M. Passoni, T. Patton, L. Pelliccia, A. Peloso, A. Pepato, E. Perelli, A. Perencin, S. Peruzzo, A. Pesenti, N. Pedroni, P. Petrolini, V. Piergotti, A. Pidatella, L. Pigatto, M. Pillon, T. Pinna, S. Pipolo, S. Piras, C. Piron, L. Piron, A. Pironti, M. Pistilli, D. Placido, A. Pizzuto, P. Platania, A. Polimadei, F. Pollastrone, G.M. Polli, N. Pomaro, F. Pompili, C. Ponti, F. Porcelli, V. Prandelli, A. Previti, A. Princiotta, G. Pucino, F. Quaglia, A. Quercia, F. Raffaelli, G. Ramogida, G. Ranieri, B. Raspante, D. Ravarotto, G.L. Ravera, A. Reale, P. Rebesan, M. Recchia, D. Regine, F. Renno, B. Riccardi, D. Ricci, D. Rigamonti, M. Ripani, N. Rispoli, S. Roccella, G. Rocchi, H. Roche, M. Romanato, F. Romanelli, G. Romanelli, R. Romaniello, A. Romano, M. Romano, R. Romano, R. Rossi, G. Rubinacci, G. Rubino, S. Rubino, J. Rueda Rueda, A. Rufoloni, C. Salvia, P. Salvini, M. Scarpari, A. Salvitti, L. Salvò, S. Sandri, F. Santoro, A. Satriano, L. Savoldi, C. Scardino, G. Schettini, S. Schmuck, J. Scionti, M. Scisciò, M. Scungio, K. Sedlak, L. Senni, G. Sias, A. Sibio, A. Simonetto, L. Singh, A. Sirignano, C. Sozzi, I. Spada, S. Spagnolo, L. Spinicci, G. Spizzo, M. Spolaore, C. Stefanini, H. Strobel, F. Subba, F. Taccogna, B. Taheri, C. Tantos, A. Tarallo, M. Tarantino, G. Tardini, M. Tardocchi, P. Tarfila, A. Tenaglia, C. Terlizzi, D. Terranova, D. Testa, E. Testa, R. Testoni, V. Toigo, G. Torrisi, A. Trotta, G. Trovato, E. Tsitrone, A. Tuccillo, O. Tudisco, M. Turcato, S. Turtù, A. Uccello, M. Ugoletti, O. Uras, M. Uras, M. Utili, V. Vaccaro, F. Valentini, L. Valletti, M. Valisa, D. Van Eester, D. Vanzan, E. Vassallo, G. Vecchi, M. Vellucci, I. Venneri, G. Ventura, M. Veranda, L. Verdini, C. Verona, G. Verona Rinati, F. Veronese, N. Vianello, F. Viganò, O. Villano, R. Villari, F. Villone, P. Vincenzi, V. Vitale, F. Vivio, G. Vlad, M. Wischmeier, H.S. Wu, I. Wyss, R. Zanino, B. Zaniol, F. Zanon, A. Zappatore, G. Zavarise, P. Zito, A. Zoppoli, M. Zucchetti, M. Zuin, and P. Zumbolo

Subjects
divertor, exhaust, plasma scenarios, Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract

An overview is presented of the progress since 2021 in the construction and scientific programme preparation of the Divertor Tokamak Test (DTT) facility. Licensing for building construction has been granted at the end of 2021. Licensing for Cat. A radiologic source has been also granted in 2022. The construction of the toroidal field magnet system is progressing. The prototype of the 170 GHz gyrotron has been produced and it is now under test on the FALCON facility. The design of the vacuum vessel, the poloidal field coils and the civil infrastructures has been completed. The shape of the first DTT divertor has been agreed with EUROfusion to test different plasma and exhaust scenarios: single null, double null, X-divertor and negative triangularity plasmas. A detailed research plan is being elaborated with the involvement of the EUROfusion laboratories.

Published
2024
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36. Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy

Author

Victoria N. Parikh, Alexander G. Ioannidis, David Jimenez-Morales, John E. Gorzynski, Hannah N. De Jong, Xiran Liu, Jonasel Roque, Victoria P. Cepeda-Espinoza, Kazutoyo Osoegawa, Chris Hughes, Shirley C. Sutton, Nathan Youlton, Ruchi Joshi, David Amar, Yosuke Tanigawa, Douglas Russo, Justin Wong, Jessie T. Lauzon, Jacob Edelson, Daniel Mas Montserrat, Yongchan Kwon, Simone Rubinacci, Olivier Delaneau, Lorenzo Cappello, Jaehee Kim, Massa J. Shoura, Archana N. Raja, Nathaniel Watson, Nathan Hammond, Elizabeth Spiteri, Kalyan C. Mallempati, Gonzalo Montero-Martín, Jeffrey Christle, Jennifer Kim, Anna Kirillova, Kinya Seo, Yong Huang, Chunli Zhao, Sonia Moreno-Grau, Steven G. Hershman, Karen P. Dalton, Jimmy Zhen, Jack Kamm, Karan D. Bhatt, Alina Isakova, Maurizio Morri, Thanmayi Ranganath, Catherine A. Blish, Angela J. Rogers, Kari Nadeau, Samuel Yang, Andra Blomkalns, Ruth O’Hara, Norma F. Neff, Christopher DeBoever, Sándor Szalma, Matthew T. Wheeler, Christian M. Gates, Kyle Farh, Gary P. Schroth, Phil Febbo, Francis deSouza, Omar E. Cornejo, Marcelo Fernandez-Vina, Amy Kistler, Julia A. Palacios, Benjamin A. Pinsky, Carlos D. Bustamante, Manuel A. Rivas, and Euan A. Ashley

Subjects
Science
Abstract

There is a genetic component to the risk of severe COVID-19, but the genetic effects are difficult to separate from social constructs that covary with genetic ancestry. To address this, the authors identify determinants of COVID-19 severity using admixture mapping, viral phylodynamics, and host immune and metagenomic sequencing.

Published
2022
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37. Bone remodeling: an operational process ensuring survival and bone mechanical competence

Author

Simona Bolamperti, Isabella Villa, and Alessandro Rubinacci

Subjects
Biology (General), QH301-705.5, Physiology, QP1-981
Abstract

Abstract Bone remodeling replaces old and damaged bone with new bone through a sequence of cellular events occurring on the same surface without any change in bone shape. It was initially thought that the basic multicellular unit (BMU) responsible for bone remodeling consists of osteoclasts and osteoblasts functioning through a hierarchical sequence of events organized into distinct stages. However, recent discoveries have indicated that all bone cells participate in BMU formation by interacting both simultaneously and at different differentiation stages with their progenitors, other cells, and bone matrix constituents. Therefore, bone remodeling is currently considered a physiological outcome of continuous cellular operational processes optimized to confer a survival advantage. Bone remodeling defines the primary activities that BMUs need to perform to renew successfully bone structural units. Hence, this review summarizes the current understanding of bone remodeling and future research directions with the aim of providing a clinically relevant biological background with which to identify targets for therapeutic strategies in osteoporosis.

Published
2022
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38. Simple Parametric Model for Calculation of Lateral Electromagnetic Loads in Tokamaks at Asymmetric Vertical Displacement Events (AVDE)

Author

Sergey Sadakov, Fabio Villone, Guglielmo Rubinacci, and Salvatore Ventre

Subjects
tokamak, plasma, asymmetric, vertical, event, parametric, Physics, QC1-999, Plasma physics. Ionized gases, QC717.6-718.8
Abstract

This paper describes a family of relatively simple numerical models for calculation of asymmetric electromagnetic (EM) loads at all tokamak structures and coils at asymmetric vertical plasma displacement events (AVDE). Unlike currently known AVDE studies concentrated on plasma physics, these models have a practical purpose to calculate detailed time-dependent patterns of AVDE-induced EM loads everywhere in the tokamak. They are built to intrinsically assure good-enough EM load balance (opposite net forces and torques for the Vacuum Vessel and the Magnets with zero total for the entire tokamak), as needed for consequent simulation of the tokamak’s dynamic response to AVDE, as well as for the development of tokamak monitoring algorithms and tokamak simulators. To achieve these practical goals, the models work in a manner of parametric study. They do not intervene in details of plasma physics, but run at widely varied input assumptions on AVDE evolution and severity. Their outputs will fill a library of ready-for-use lateral EM loads for multiple variants of AVDE evolution and severity. The tokamak physics community can select any variant from the library, and engineers can pick ready-for-use AVDE loads. Investigated here, EM models represent one already known approach and one newly suggested. The latter attempts to reflect the helical pattern of halo currents in plasma and delivers richer outcomes and, thus, can be preferred as the single practical model for parametric calculations.

Published
2022
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43. Volume Integral Formulation for the Calculation of Material Independent Modes of Dielectric Scatterers

Author

Forestiere, Carlo, Miano, Giovanni, Rubinacci, Guglielmo, Tamburrino, Antonello, Tricarico, Roberto, and Ventre, Salvatore

Subjects
Physics - Optics
Abstract

In the frame of volume integral equation methods, we introduce an alternative representation of the electromagnetic field scattered by a homogeneous object of arbitrary shape at a given frequency, in terms of a set of modes independent of its permittivity. This is accomplished by introducing an auxiliary eigenvalue problem, based on a volume integral operator. With this modal basis the expansion coefficients of the scattered field are simple rational functions of the permittivity of the scatterer. We show, by studying the electromagnetic scattering from a sphere and a cylinder of dimensions comparable to the incident wavelength, that only a moderate number of modes is needed to accurately describe the scattered far field. This method can be used to investigate resonant scattering phenomena, including plasmonic and photonic resonances, and to design the permittivity of the object to pursue a prescribed tailoring of the scattered field. Moreover, the presented modal expansion is computationally advantageous compared to direct solution of the volume integral equation when the scattered field has to be computed for many different values of the dielectric permittivity, given the size and shape of the dielectric body.

Published
2017
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48. Elsa Morante e il Mondo salvato dalla poesia

Author

Antonella Rubinacci

Subjects
Elsa Morante, Il mondo salvato dai ragazzini, Poesia contemporanea, Sessantotto, modelli letterari, Literature (General), PN1-6790
Abstract

Obiettivo di questo contributo è indagare il ruolo della produzione in versi nell’opera di Elsa Morante, soffermandosi, nello specifico, sul secondo esperimento poetico dell’autrice Il mondo salvato dai ragazzini, pubblicato nel 1968. Accanto all’analisi delle principali caratteristiche formali di un’opera estremamente eterogenea, si intende riflettere sui significati che la scelta della parola poetica veicola per un’autrice tradizionalmente più conosciuta per la scrittura in prosa. L’articolo intende, inoltre, tener conto anche dei rapporti che questo libro intesse con i suoi modelli letterari o filosofici e della sua collocazione nello scenario socioculturale contemporaneo.

Published
2022
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49. The molecular basis, genetic control and pleiotropic effects of local gene co-expression

Author

Diogo M. Ribeiro, Simone Rubinacci, Anna Ramisch, Robin J. Hofmeister, Emmanouil T. Dermitzakis, and Olivier Delaneau

Subjects
Science
Abstract

Local gene co-expression is found throughout the genome, but systematic analysis of these co-expressed genes is needed. Here, the authors identify local co-expressed genes in 49 tissues and characterize the genetic variants which may affect their expression and contribute to disease.

Published
2021
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50. 58MO Evaluation of three pexidartinib doses in a global phase IV clinical study of patients with tenosynovial giant cell tumor (TGCT) who chose to continue treatment

Author

Stacchiotti, S, Wagner, AJ, Garcia, ICC, Cesari, M, Gordon, M, Lin, C-C, Papai, Z, Ryan, CW, Tap, WD, Trent, JC, Gelderblom, H, Grimison, P, Pousa, AL, Van Tine, BA, Rubinacci, M, Tecson, K, Wooddell, M, Desai, J, Stacchiotti, S, Wagner, AJ, Garcia, ICC, Cesari, M, Gordon, M, Lin, C-C, Papai, Z, Ryan, CW, Tap, WD, Trent, JC, Gelderblom, H, Grimison, P, Pousa, AL, Van Tine, BA, Rubinacci, M, Tecson, K, Wooddell, M, and Desai, J

Published
2024

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