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4,291 results on '"Chesi A"'

1. Universal Entanglement Revival of Topological Origin

Author

Chen, Dongni, Chesi, Stefano, and Choi, Mahn-Soo

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

We have analyzed the dynamics of entanglement in dissipative fermionic and bosonic Su-Schrieffer-Heeger (SSH) models and found that, when the decoherence channel preserves the chiral symmetry, they exhibit a revival of entanglement in a wide range of parameters. This behavior only emerges in the topological phase, with the visibility of the revival dropping to zero at the phase boundary. Furthermore, the revival acquires a universal character once the system size exceeds the localization length of the edge modes. Our findings indicate that the universal entanglement revival has its origin in the topological properties of the SSH model. These dynamical properties may be experimentally accessible, for example, using photonic quantum computers., Comment: 19 pages with 8 figures

Published
2024

2. LLM-Barber: Block-Aware Rebuilder for Sparsity Mask in One-Shot for Large Language Models

Author

Su, Yupeng, Guan, Ziyi, Liu, Xiaoqun, Jin, Tianlai, Wu, Dongkuan, Chesi, Graziano, Wong, Ngai, and Yu, Hao

Subjects
Computer Science - Machine Learning, Computer Science - Artificial Intelligence, Computer Science - Computation and Language
Abstract

Large language models (LLMs) have grown significantly in scale, leading to a critical need for efficient model pruning techniques. Existing post-training pruning techniques primarily focus on measuring weight importance on converged dense models to determine salient weights to retain. However, they often overlook the changes in weight importance during the pruning process, which can lead to performance degradation in the pruned models. To address this issue, we present LLM-Barber (Block-Aware Rebuilder for Sparsity Mask in One-Shot), a novel one-shot pruning framework that rebuilds the sparsity mask of pruned models without any retraining or weight reconstruction. LLM-Barber incorporates block-aware error optimization across Self-Attention and MLP blocks, ensuring global performance optimization. Inspired by the recent discovery of prominent outliers in LLMs, LLM-Barber introduces an innovative pruning metric that identifies weight importance using weights multiplied by gradients. Our experiments show that LLM-Barber can efficiently prune models like LLaMA and OPT families with 7B to 13B parameters on a single A100 GPU in just 30 minutes, achieving state-of-the-art results in both perplexity and zero-shot performance across various language benchmarks. Code is available at https://github.com/YupengSu/LLM-Barber.

Published
2024

3. Complementarity-based complementarity

Author

Serino, Laura, Chesi, Giovanni, Brecht, Benjamin, Maccone, Lorenzo, Macchiavello, Chiara, and Silberhorn, Christine

Subjects
Quantum Physics
Abstract

We show that the amount of complementarity that a quantum system can exhibit depends on which complementary properties one is considering. Consider a set of mutually unbiased bases (MUBs) which corresponds to the spectral decomposition of some maximally complementary properties: The perfect knowledge of one, i.e. the state of the system is one of the basis states, implies that all the others are completely unknown, namely the measurement of another property will find any of its possible outcomes with uniform probability. We show that, depending on which three of the MUBs we choose, a 5-dimensional system can have different degrees of complementarity, measured using the minimum over all the system states of the sum of the entropies and of the variances of the measurement outcomes related to the three chosen observables. This property was first found experimentally, and demonstrates that an experimental discovery can disclose quantum information effects., Comment: 6 pages, 5 figures

Published
2024

4. Optimized generation of entanglement based on the f-STIRAP technique

Author

Chen, Dongni, Li, Jiahui, Chesi, Stefano, and Wang, Ying-Dan

Subjects
Quantum Physics
Abstract

We consider generating maximally entangled states (Bell states) between two qubits coupled to a common bosonic mode, based on f-STIRAP. Utilizing the systematic approach developed in New J. Phys. 19 093016 (2017), we quantify the effects of non-adiabatic leakage and system dissipation on the entanglement generation, and optimize the entanglement by balancing non-adiabatic leakage and system dissipation. We find the analytical expressions of the optimal coupling profile, the operation time, and the maximal entanglement. Our findings have broad applications in quantum state engineering, especially in solid-state devices where dissipative effects cannot be neglected.

Published
2024

6. Principle of least action for quasi-adiabatic state transfers with dissipation

Author

Luo, Si, Fang, Yinan, Wang, Yingdan, and Chesi, Stefano

Subjects
Quantum Physics
Abstract

We discuss a general formalism to optimize quasi-adiabatic state-transfer protocols, where high fidelity is achieved by maintaining the system in a dark subspace protected from the dominant dissipative channels. We cast the residual fidelity loss, induced by a combination of dissipation and non-adiabatic transitions, in the form of a classical action where the time-dependent control parameters act as coordinates. This allows us to apply the least action principle, yielding the fidelity upper-bound and the corresponding optimal transfer time. As an application, we analyze a system of two qubits subject to weak relaxation and dephasing, interacting through a strongly dissipative quantum bus. In this case, our formalism, we obtain a full characterization of the optimal state-transfer fidelity., Comment: 13 pages,6 figures

Published
2024

7. Quantum second harmonic generation in terms of elementary processes

Author

Chesi, Giovanni

Subjects
Quantum Physics
Abstract

We address the quantum dynamics of second harmonic generation with a perturbative approach. By inspecting the Taylor expansion of the unitary evolution, we identify the subsequent application of annihilation and creation operators as elementary processes and find out how the expansion of the second-harmonic photon-number probability distribution can be expressed in terms of the interplay of these processes. We show that overlaps between the output states of different elementary processes contribute to the expansion of the probability distribution and provide a diagrammatic technique to analytically retrieve terms of the distribution expansion at any order.

Published
2024
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8. Spin fluctuations in the dissipative phase transitions of the quantum Rabi model

Author

Li, Jiahui, Fazio, Rosario, Wang, Yingdan, and Chesi, Stefano

Subjects
Quantum Physics
Abstract

We investigate the dissipative phase transitions of the anisotropic quantum Rabi model with cavity decay and demonstrate that large spin fluctuations persist in the stationary state, having important consequences on the phase diagram and the critical properties. In the second-order phase transition to the superradiant phase, there is a significant suppression of the order parameter and the appearance of non-universal factors, which directly reflect the spin populations. Furthermore, upon entering a parameter regime where mean-field theory predicts a tricritical phase, we find a first-order phase transition due to the unexpected collapse of superradiance. An accurate and physically transparent description going beyond mean-field theory is established by combining exact numerical simulations, the cumulant expansion, and analytical approximations based on reduced master equations and an effective equilibrium theory. Our findings, compared to the conventional thermodynamic limit of the Dicke model, indicate a general tendency of forming extreme non-equilibrium states in the single-spin system, thus have broad implications for dissipative phase transitions of few-body systems., Comment: 17 pages, 11 figures

Published
2023

10. Nonlinear dynamics in the balanced two-photon Dicke model with qubit dissipation

Author

Li, Jiahui and Chesi, Stefano

Subjects
Quantum Physics
Abstract

We study the complex nonlinear dynamics of the two-photon Dicke model in the semiclassical limit by considering cavity and qubit dissipation. In addition to the normal and super-radiant phases, another phase that contains abundant chaos-related phenomena is found under balanced rotating and counter-rotating couplings. In particular, chaos may manifest itself through period-doubling bifurcation, intermittent chaos, or quasi-periodic oscillation, depending on the value of qubit frequency. Transition mechanisms that exist in these three distinct routes are investigated through the system's long-time evolution and bifurcation diagram. Additionally, we provide a comprehensive phase diagram detailing both the existence of stable fixed points and the aforementioned chaos-related dynamics., Comment: 9 pages, 6 figures

Published
2023

11. Work Fluctuations in Ergotropic Heat Engines

Author

Chesi, Giovanni, Macchiavello, Chiara, and Sacchi, Massimiliano Federico

Subjects
Quantum Physics, Condensed Matter - Statistical Mechanics
Abstract

We study the work fluctuations in ergotropic heat engines, namely two-strokes quantum Otto engines where the work stroke is designed to extract the ergotropy (the maximum amount of work by a cyclic unitary evolution) from a couple of quantum systems at canonical equilibrium at two different temperatures, whereas the heat stroke thermalizes back the systems to their respective reservoirs. We provide an exhaustive study for the case of two qutrits whose energy levels are equally spaced at two different frequencies by deriving the complete work statistics. By varying the values of temperatures and frequencies, only three kinds of optimal unitary strokes are found: the swap operator $U_1$, an idle swap $U_2$ (where one of the qutrits is regarded as an effective qubit), and a non trivial permutation of energy eigenstates $U_3$, which indeed corresponds to the composition of the two previous unitaries, namely $U_3=U_2 U_1$. While $U_1$ and $U_2$ are Hermitian (and hence involutions), $U_3$ is not. This point has an impact on the thermodynamic uncertainty relations (TURs) which bound the signal-to-noise ratio of the extracted work in terms of the entropy production. In fact, we show that all TURs derived from a strong detailed fluctuation theorem are violated by the transformation $U_3$., Comment: 30 pages, 21 figures. Improved version; new references

Published
2023
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12. Self-Purification and Entanglement Revival in Lambda Matter

Author

Chen, Dongni, Chesi, Stefano, and Choi, Mahn-Soo

Subjects
Quantum Physics
Abstract

In this study, we explore the dynamics of entanglement in an ensemble of three-level systems with a lambda-type level structure interacting with single-mode bosons. Our investigation focuses on zero-energy states within the subspace of totally symmetric wave functions. Remarkably, we observe a universal two-stage dynamics of entanglement with intriguing revival behavior. The revival of entanglement is a consequence of the self-purification process, where the quantum state relaxes and converges universally to a special dark state within the system., Comment: 15 pages, 10 figures; some clarifications for better readability in the revised version

Published
2023

13. Weekly carboplatin plus paclitaxel chemotherapy in advanced melanoma patients resistant to anti-PD-1 inhibitors: a retrospective, monocentric experience

Author

Francesca Romana Di Pietro, Daniele Marinelli, Sofia Verkhovskaia, Giulia Poti, Rosa Falcone, Maria Luigia Carbone, Maria Francesca Morelli, Albina Rita Zappalà, Zorika Christiana Di Rocco, Roberto Morese, Gabriele Piesco, Paolo Chesi, Paolo Marchetti, Cristina Maria Failla, and Federica De Galitiis

Subjects
Melanoma, Immunoresistance, Platinum-based chemotherapy, Palliative treatment, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Immunotherapy with anti-PD-1 antibodies significantly improved the prognosis in advanced melanoma patients, but most of them develop primary or secondary resistance to the treatment. In this study, we evaluated efficacy and safety of a chemotherapy regimen with weekly carboplatin plus paclitaxel (wCP) in patients previously treated with anti-PD-1 antibodies. We retrospectively identified 30 patients with advanced melanoma treated at our Institute over the last eight years with wCP. The co-primary endpoints of the study were overall survival (OS) and progression-free survival (PFS). In addition, we evaluated treatment tolerability. For this patient cohort, median PFS and OS were 3.25 and 7.69 months, respectively. All included patients had previously received anti-PD-1 immunotherapy, most of them had ECOG PS 0–1, and only 5 patients had a BRAF V600 mutation. In univariable analysis, we observed shorter OS in patients with > 2 involved metastatic sites, superficial spreading histology, and serum lactate dehydrogenase (LDH) values above the median. Liver metastases were associated with worse outcomes, while radiotherapy treatment of brain metastases was associated with improved OS. However, in a multivariable Cox regression model, only LDH above the median, superficial spreading histology, and female sex were significantly associated with worse OS. We reported grade 3 and 4 treatment-related toxicities in 4 and 0 patients, respectively. In conclusion, chemotherapy with wCP is a valid palliative treatment in advanced melanoma who progressed with anti-PD-1 antibodies.

Published
2024
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14. Discrete time crystal in an open optomechanical system

Author

Chen, Dongni, Peng, Zhengyang, Li, Jiahui, Chesi, Stefano, and Wang, Yingdan

Subjects
Quantum Physics
Abstract

The spontaneous breaking of time translation symmetry in periodically driven Floquet systems can lead to a discrete time crystal. Here we study the occurrence of such dynamical phase in a driven-dissipative optomechanical system with two membranes in the middle. We find that, under certian conditions, the system can be mapped to an open Dicke model and realizes a superradianttype phase transition. Furthermore, applying a suitable periodically modulated drive, the system dynamics exhibits a robust subharmonic oscillation persistent in the thermodynamic limit.

Published
2023
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15. Weekly carboplatin plus paclitaxel chemotherapy in advanced melanoma patients resistant to anti-PD-1 inhibitors: a retrospective, monocentric experience

Author

Di Pietro, Francesca Romana, Marinelli, Daniele, Verkhovskaia, Sofia, Poti, Giulia, Falcone, Rosa, Carbone, Maria Luigia, Morelli, Maria Francesca, Zappalà, Albina Rita, Di Rocco, Zorika Christiana, Morese, Roberto, Piesco, Gabriele, Chesi, Paolo, Marchetti, Paolo, Failla, Cristina Maria, and De Galitiis, Federica

Published
2024
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16. Author Correction: Trans-ancestral genome-wide association study of longitudinal pubertal height growth and shared heritability with adult health outcomes

Author

Bradfeld, Jonathan P., Kember, Rachel L., Ulrich, Anna, Balkhiyarova, Zhanna, Alyass, Akram, Aris, Izzuddin M., Bell, Joshua A., Broadaway, K. Alaine, Chen, Zhanghua, Chai, Jin-Fang, Davies, Neil M., Fernandez-Orth, Dietmar, Bustamante, Mariona, Fore, Ruby, Ganguli, Amitavo, Heiskala, Anni, Hottenga, Jouke-Jan, Íñiguez, Carmen, Kobes, Sayuko, Leinonen, Jaakko, Lowry, Estelle, Lyytikainen, Leo-Pekka, Mahajan, Anubha, Pitkänen, Niina, Schnurr, Theresia M., Have, Christian Theil, Strachan, David P., Thiering, Elisabeth, Vogelezang, Suzanne, Wade, Kaitlin H., Wang, Carol A., Wong, Andrew, Holm, Louise Aas, Chesi, Alessandra, Choong, Catherine, Cruz, Miguel, Elliott, Paul, Franks, Steve, Frithiof-Bøjsøe, Christine, Gauderman, W. James, Glessner, Joseph T., Gilsanz, Vicente, Griesman, Kendra, Hanson, Robert L., Kaakinen, Marika, Kalkwarf, Heidi, Kelly, Andrea, Kindler, Joseph, Kähönen, Mika, Lanca, Carla, Lappe, Joan, Lee, Nanette R., McCormack, Shana, Mentch, Frank D., Mitchell, Jonathan A., Mononen, Nina, Niinikoski, Harri, Oken, Emily, Pahkala, Katja, Sim, Xueling, Teo, Yik-Ying, Baier, Leslie J., van Beijsterveldt, Toos, Adair, Linda S., Boomsma, Dorret I., de Geus, Eco, Guxens, Mònica, Eriksson, Johan G., Felix, Janine F., Gilliland, Frank D., Hansen, Torben, Hardy, Rebecca, Hivert, Marie-France, Holm, Jens-Christian, Jaddoe, Vincent W. V., Järvelin, Marjo-Riitta, Lehtimäki, Terho, Mackey, David A., Meyre, David, Mohlke, Karen L., Mykkänen, Juha, Oberfeld, Sharon, Pennell, Craig E., Perry, John R. B., Raitakari, Olli, Rivadeneira, Fernando, Saw, Seang-Mei, Sebert, Sylvain, Shepherd, John A., Standl, Marie, Sørensen, Thorkild I. A., Timpson, Nicholas J., Torrent, Maties, Willemsen, Gonneke, Hypponen, Elina, Power, Chris, McCarthy, Mark I., Freathy, Rachel M., Widén, Elisabeth, Hakonarson, Hakon, Prokopenko, Inga, Voight, Benjamin F., Zemel, Babette S., Grant, Struan F. A., and Cousminer, Diana L.

Published
2024
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18. Targeting DNA2 overcomes metabolic reprogramming in multiple myeloma

Author

Thongon, Natthakan, Ma, Feiyang, Baran, Natalia, Lockyer, Pamela, Liu, Jintan, Jackson, Christopher, Rose, Ashley, Furudate, Ken, Wildeman, Bethany, Marchesini, Matteo, Marchica, Valentina, Storti, Paola, Todaro, Giannalisa, Ganan-Gomez, Irene, Adema, Vera, Rodriguez-Sevilla, Juan Jose, Qing, Yun, Ha, Min Jin, Fonseca, Rodrigo, Stein, Caleb, Class, Caleb, Tan, Lin, Attanasio, Sergio, Garcia-Manero, Guillermo, Giuliani, Nicola, Berrios Nolasco, David, Santoni, Andrea, Cerchione, Claudio, Bueso-Ramos, Carlos, Konopleva, Marina, Lorenzi, Philip, Takahashi, Koichi, Manasanch, Elisabet, Sammarelli, Gabriella, Kanagal-Shamanna, Rashmi, Viale, Andrea, Chesi, Marta, and Colla, Simona

Published
2024
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19. Trans-ancestral genome-wide association study of longitudinal pubertal height growth and shared heritability with adult health outcomes

Author

Bradfield, Jonathan P., Kember, Rachel L., Ulrich, Anna, Balkhiyarova, Zhanna, Alyass, Akram, Aris, Izzuddin M., Bell, Joshua A., Broadaway, K. Alaine, Chen, Zhanghua, Chai, Jin-Fang, Davies, Neil M., Fernandez-Orth, Dietmar, Bustamante, Mariona, Fore, Ruby, Ganguli, Amitavo, Heiskala, Anni, Hottenga, Jouke-Jan, Íñiguez, Carmen, Kobes, Sayuko, Leinonen, Jaakko, Lowry, Estelle, Lyytikainen, Leo-Pekka, Mahajan, Anubha, Pitkänen, Niina, Schnurr, Theresia M., Have, Christian Theil, Strachan, David P., Thiering, Elisabeth, Vogelezang, Suzanne, Wade, Kaitlin H., Wang, Carol A., Wong, Andrew, Holm, Louise Aas, Chesi, Alessandra, Choong, Catherine, Cruz, Miguel, Elliott, Paul, Franks, Steve, Frithioff-Bøjsøe, Christine, Gauderman, W. James, Glessner, Joseph T., Gilsanz, Vicente, Griesman, Kendra, Hanson, Robert L., Kaakinen, Marika, Kalkwarf, Heidi, Kelly, Andrea, Kindler, Joseph, Kähönen, Mika, Lanca, Carla, Lappe, Joan, Lee, Nanette R., McCormack, Shana, Mentch, Frank D., Mitchell, Jonathan A., Mononen, Nina, Niinikoski, Harri, Oken, Emily, Pahkala, Katja, Sim, Xueling, Teo, Yik-Ying, Baier, Leslie J., van Beijsterveldt, Toos, Adair, Linda S., Boomsma, Dorret I., de Geus, Eco, Guxens, Mònica, Eriksson, Johan G., Felix, Janine F., Gilliland, Frank D., Biobank, Penn Medicine, Hansen, Torben, Hardy, Rebecca, Hivert, Marie-France, Holm, Jens-Christian, Jaddoe, Vincent W. V., Järvelin, Marjo-Riitta, Lehtimäki, Terho, Mackey, David A., Meyre, David, Mohlke, Karen L., Mykkänen, Juha, Oberfield, Sharon, Pennell, Craig E., Perry, John R. B., Raitakari, Olli, Rivadeneira, Fernando, Saw, Seang-Mei, Sebert, Sylvain, Shepherd, John A., Standl, Marie, Sørensen, Thorkild I. A., Timpson, Nicholas J., Torrent, Maties, Willemsen, Gonneke, Hypponen, Elina, Power, Chris, McCarthy, Mark I., Freathy, Rachel M., Widén, Elisabeth, Hakonarson, Hakon, Prokopenko, Inga, Voight, Benjamin F., Zemel, Babette S., Grant, Struan F. A., and Cousminer, Diana L.

Published
2024
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21. A protocol for global multiphase estimation

Author

Chesi, Giovanni, Rubboli, Roberto, Riccardi, Alberto, Maccone, Lorenzo, and Macchiavello, Chiara

Subjects
Quantum Physics
Abstract

Global estimation strategies allow to extract information on a phase or a set of phases without any prior knowledge, which is, instead, required for local estimation strategies. We devise a global multiphase protocol based on Holevo's estimation theory and apply it to the case of digital estimation, i.e. we estimate the phases in terms of the mutual information between them and the corresponding estimators. In the single-phase scenario, the protocol encompasses two specific known optimal strategies. We extend them to the simultaneous estimation of two phases and evaluate their performance. Then, we retrieve the ultimate digital bound on precision when a generic number of phases is simultaneously estimated. We show that in the multiphase strategy there is only a constant quantum advantage with respect to a sequence of independent single-phase estimations. This extends a recent similar result, which settled a controversy on the search for the multiphase enhancement.

Published
2023
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23. Italian Seismic Damage Prevention Policies for the Built Heritage: Efficacy and New Perspectives

Author

Acito, Maurizio, Buzzetti, Martina, Chesi, Claudio, Milani, Gabriele, di Prisco, Marco, Series Editor, Chen, Sheng-Hong, Series Editor, Vayas, Ioannis, Series Editor, Kumar Shukla, Sanjay, Series Editor, Sharma, Anuj, Series Editor, Kumar, Nagesh, Series Editor, Wang, Chien Ming, Series Editor, Cui, Zhen-Dong, Series Editor, Cuong, Le Thanh, editor, Gandomi, Amir H., editor, Abualigah, Laith, editor, and Khatir, Samir, editor

Published
2024
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24. A Mobile Habitat for Human Lunar Exploration

Author

Sumini, Valentina, Chesi, Claudio, Florenzano, Daniele, Botti, Michela, Calogero, Lorenzo, Caracas, Ana Carolina Corrêa, Caruso, Alessandro, Comparini, Massimo C., Ferrone, Enrico, Hoffman, Jeffrey, Maggiore, Paolo, Mattioli, Marta, Paradiso, Joseph, Perino, Maria Antonietta, Portolani, Marco, Rizzo, Angela, Signorotto, Giulia, di Prisco, Marco, Series Editor, Chen, Sheng-Hong, Series Editor, Vayas, Ioannis, Series Editor, Kumar Shukla, Sanjay, Series Editor, Sharma, Anuj, Series Editor, Kumar, Nagesh, Series Editor, Wang, Chien Ming, Series Editor, Cui, Zhen-Dong, Series Editor, Gabriele, Stefano, editor, Manuello Bertetto, Amedeo, editor, Marmo, Francesco, editor, and Micheletti, Andrea, editor

Published
2024
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25. Recent advances in hole-spin qubits

Author

Fang, Yinan, Philippopoulos, Pericles, Culcer, Dimitrie, Coish, W. A., and Chesi, Stefano

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

In recent years, hole-spin qubits based on semiconductor quantum dots have advanced at a rapid pace. We first review the main potential advantages of these hole-spin qubits with respect to their electron-spin counterparts, and give a general theoretical framework describing them. The basic features of spin-orbit coupling and hyperfine interaction in the valence band are discussed, together with consequences on coherence and spin manipulation. In the second part of the article we provide a survey of experimental realizations, which spans a relatively broad spectrum of devices based on GaAs, Si, or Si/Ge heterostructures. We conclude with a brief outlook., Comment: 46 pages, 5 figures

Published
2022
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26. Construction of efficient Schmidt number witnesses for high-dimensional quantum states

Author

Wyderka, Nikolai, Chesi, Giovanni, Kampermann, Hermann, Macchiavello, Chiara, and Bruß, Dagmar

Subjects
Quantum Physics, 81P42
Abstract

Recent progress in quantum optics has led to setups that are able to prepare high-dimensional quantum states for quantum information processing tasks. As such, it is of importance to benchmark the states generated by these setups in terms of their quantum mechanical properties, such as their Schmidt numbers, i.e., the number of entangled degrees of freedom. In this paper, we develop an iterative algorithm that finds Schmidt number witnesses tailored to the measurements available in specific experimental setups. We then apply the algorithm to find a witness that requires the measurement of a number of density matrix elements that scales linearly with the local dimension of the system. As a concrete example, we apply our construction method to an implementation with photonic temporal modes., Comment: 7 pages, 4 figures

Published
2022
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27. Subgap modes in two-dimensional magnetic Josephson junctions

Author

Fang, Yinan, Han, Seungju, Chesi, Stefano, and Choi, Mahn-Soo

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

We consider two-dimensional superconductor/ferromagnet/superconductor junctions and investigate the subgap modes along the junction interface. The subgap modes exhibit characteristics similar to the Yu-Shiba-Rusinov states that originate form the interplay between superconductivity and ferromagnetism in the magnetic junction. The dispersion relation of the subgap modes shows qualitatively different profiles depending on the transport state (metallic, half-metallic, or insulating) of the ferromagnet. As the spin splitting in the ferromagnet is increased, the subgap modes bring about a $0$-$\pi$ transition in the Josephson current across the junction, with the Josephson current density depending strongly on the momentum along the junction interface (i.e., the direction of the incident current). For clean superconductor-ferromagnet interfaces (i.e., strong coupling between superconductors and ferromagnet), the subgap modes develop flat quasi-particle bands that allow to engineer the wave functions of the subgap modes along an inhomogeneous magnetic junction., Comment: 11 pages, 9 figures

Published
2022
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28. The genomic landscape of Vk*MYC myeloma highlights shared pathways of transformation between mice and humans

Author

Francesco Maura, David G. Coffey, Caleb K. Stein, Esteban Braggio, Bachisio Ziccheddu, Meaghen E. Sharik, Megan T. Du, Yuliza Tafoya Alvarado, Chang-Xin Shi, Yuan Xiao Zhu, Erin W. Meermeier, Gareth J. Morgan, Ola Landgren, P. Leif Bergsagel, and Marta Chesi

Subjects
Science
Abstract

Abstract Multiple myeloma (MM) is a heterogeneous disease characterized by frequent MYC translocations. Sporadic MYC activation in the germinal center of genetically engineered Vk*MYC mice is sufficient to induce plasma cell tumors in which a variety of secondary mutations are spontaneously acquired and selected over time. Analysis of 119 Vk*MYC myeloma reveals recurrent copy number alterations, structural variations, chromothripsis, driver mutations, apolipoprotein B mRNA-editing enzyme, catalytic polypeptide (APOBEC) mutational activity, and a progressive decrease in immunoglobulin transcription that inversely correlates with proliferation. Moreover, we identify frequent insertional mutagenesis by endogenous retro-elements as a murine specific mechanism to activate NF-kB and IL6 signaling pathways shared with human MM. Despite the increased genomic complexity associated with progression, advanced tumors remain dependent on MYC. In summary, here we credential the Vk*MYC mouse as a unique resource to explore MM genomic evolution and describe a fully annotated collection of diverse and immortalized murine MM tumors.

Published
2024
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29. Tight bounds from multiple-observable entropic uncertainty relations

Author

Riccardi, Alberto, Chesi, Giovanni, Macchiavello, Chiara, and Maccone, Lorenzo

Subjects
Quantum Physics
Abstract

We investigate the additivity properties for both bipartite and multipartite systems by using entropic uncertainty relations (EUR) defined in terms of the joint Shannon entropy of probabilities of local measurement outcomes. In particular, we introduce state-independent and state-dependent entropic inequalities. Interestingly, the violation of these inequalities is strictly connected with the presence of quantum correlations. We show that the additivity of EUR holds only for EUR that involve two observables, while this is not the case for inequalities that consider more than two observables or the addition of the von Neumann entropy of a subsystem. We apply them to bipartite systems and to several classes of states of a three-qubit system., Comment: 10 pages, 5 figures

Published
2022

30. Nonlinear dynamics of the dissipative anisotropic two-photon Dicke model

Author

Li, Jiahui, Fazio, Rosario, and Chesi, Stefano

Subjects
Quantum Physics
Abstract

We study the semiclassical limit of the anisotropic two-photon Dicke model with a dissipative bosonic field and describe its rich nonlinear dynamics. Besides normal and 'superradiant'-like phases, the presence of localized fixed points reflects the spectral collapse of the closed-system Hamiltonian. Through Hopf bifurcations of superradiant and normal fixed points, limit cycles are formed in certain regions of parameters. We also identify a pole-flip transition induced by anisotropy and a region of chaotic dynamics, which appears from a cascade of period-doubling bifurcations. In the chaotic region, collision and fragmentation of symmetric attractors take place. Throughout the phase diagram we find several examples of phase coexistence, leading to the segmentation of phase space into distinct basins of attraction., Comment: 25 pages, 14 figures

Published
2022
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31. Case report: Fast disease progression during adjuvant therapy with anti-PD-1 in stage III melanoma patients

Author

Francesca Romana Di Pietro, Sofia Verkhovskaia, Rosa Falcone, Giulia Poti, Maria Luigia Carbone, Maria Francesca Morelli, Albina Rita Zappalà, Roberto Morese, Zorika Christiana Di Rocco, Gabriele Piesco, Paolo Chesi, Cristina Maria Failla, Paolo Marchetti, and Federica De Galitiis

Subjects
melanoma, adjuvant immunotherapy, anti-PD-1, hyperprogression disease, molecular profiling, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

BackgroundStage III surgically resected melanoma is a disease at high risk of recurrence. Immune checkpoint inhibitors (ICIs) and the target therapy with BRAF and MEK inhibitors significantly changed the outcome of patients with metastatic melanoma and several studies have also shown their benefit in the adjuvant setting for the delay of recurrence in stage III melanoma patients. Hyperprogression disease was observed as a possible adverse response to immunotherapy in the metastatic setting, suggesting that some patients could face additional risk of progression with ICIs, although no consensus was found for the correct definition of this event.Case presentationWe describe here two cases of rapid multiorgan metastatization during adjuvant immunotherapy in patients with stage III resected melanoma. Even though it would be not accurate to define this syndrome as hyperprogression because of apparent absence of the initial disease in the adjuvant setting, we observed in these two cases the same very rapid progression after first administration of adjuvant ICIs that resulted in death of patients within two months from the starting of treatment. Both patients had NRAS mutated melanoma.ConclusionThere is an urgent need for a better understanding of the causes of these fatal outcomes and for the identification of biomarkers that would allow to select the patients before offering them an adjuvant treatment, reducing the risk of hyperprogression. From these cases, we suggest that it could be useful a particular attention in proposing ICI adjuvant treatment based on the molecular profile.

Published
2024
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36. Fate of the Quasi-condensed State for Bias-driven Hard-Core Bosons in one Dimension

Author

Puel, T. O., Chesi, S., Kirchner, S., and Ribeiro, P.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics, Condensed Matter - Strongly Correlated Electrons, Quantum Physics
Abstract

Bosons in one dimension display a phenomenon called quasi-condensation, where correlations decay in a powerlaw fashion. We study the fate of quasi-condensation in the non-equilibrium steady-state of a chain of hard-core bosons coupled to macroscopic leads which are held at different chemical potentials. It is found that a finite bias destroys the quasi-condensed state and the critical scaling function of the quasi-condensed fraction, near the zero bias transition, is determined. Associated critical exponents are determined and numerically verified. Away from equilibrium, the system exhibits exponentially decaying correlations that are characterized by a bias-dependent correlation length that diverges in equilibrium. In addition, power-law corrections are found, which are characterized by an exponent that depends on the chain-leads coupling and is non-analytic at zero bias. This exactly-solvable nonequilibrium strongly-interacting system has the remarkable property that, the near-equilibrium state at infinitesimal bias, cannot be obtained within linear response. These results aid in unraveling the intricate properties spawned by strong interactions once liberated from equilibrium constraints., Comment: 7 pages, 4 figures

Published
2022
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37. Commensurate-Incommensurate Transitions of the 1D Disordered Chiral Clock Model

Author

Liang, Pengfei, Fazio, Rosario, and Chesi, Stefano

Subjects
Condensed Matter - Disordered Systems and Neural Networks
Abstract

We study the effects of quenched disorder on the commensurate-incommensurate transitions in the 1D $\mathbb{Z}_N$ chiral clock model. The interplay of domain walls and rare regions rounds the sharp transitions of the pure model. The density of domain walls displays an essential singularity, while the order parameter develops a discontinuity at the transition. We perform extensive density-matrix renormalization group calculations to support theoretical predictions. Our results provide a distinct rounding mechanism of continuous phase transitions in disordered systems., Comment: 13 pages, 11 figures

Published
2022

38. Deformable Butterfly: A Highly Structured and Sparse Linear Transform

Author

Lin, Rui, Ran, Jie, Chiu, King Hung, Chesi, Graziano, and Wong, Ngai

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning
Abstract

We introduce a new kind of linear transform named Deformable Butterfly (DeBut) that generalizes the conventional butterfly matrices and can be adapted to various input-output dimensions. It inherits the fine-to-coarse-grained learnable hierarchy of traditional butterflies and when deployed to neural networks, the prominent structures and sparsity in a DeBut layer constitutes a new way for network compression. We apply DeBut as a drop-in replacement of standard fully connected and convolutional layers, and demonstrate its superiority in homogenizing a neural network and rendering it favorable properties such as light weight and low inference complexity, without compromising accuracy. The natural complexity-accuracy tradeoff arising from the myriad deformations of a DeBut layer also opens up new rooms for analytical and practical research. The codes and Appendix are publicly available at: https://github.com/ruilin0212/DeBut.

Published
2022

39. A saturated map of common genetic variants associated with human height

Author

Yengo, Loïc, Vedantam, Sailaja, Marouli, Eirini, Sidorenko, Julia, Bartell, Eric, Sakaue, Saori, Graff, Marielisa, Eliasen, Anders U, Jiang, Yunxuan, Raghavan, Sridharan, Miao, Jenkai, Arias, Joshua D, Graham, Sarah E, Mukamel, Ronen E, Spracklen, Cassandra N, Yin, Xianyong, Chen, Shyh-Huei, Ferreira, Teresa, Highland, Heather H, Ji, Yingjie, Karaderi, Tugce, Lin, Kuang, Lüll, Kreete, Malden, Deborah E, Medina-Gomez, Carolina, Machado, Moara, Moore, Amy, Rüeger, Sina, Sim, Xueling, Vrieze, Scott, Ahluwalia, Tarunveer S, Akiyama, Masato, Allison, Matthew A, Alvarez, Marcus, Andersen, Mette K, Ani, Alireza, Appadurai, Vivek, Arbeeva, Liubov, Bhaskar, Seema, Bielak, Lawrence F, Bollepalli, Sailalitha, Bonnycastle, Lori L, Bork-Jensen, Jette, Bradfield, Jonathan P, Bradford, Yuki, Braund, Peter S, Brody, Jennifer A, Burgdorf, Kristoffer S, Cade, Brian E, Cai, Hui, Cai, Qiuyin, Campbell, Archie, Cañadas-Garre, Marisa, Catamo, Eulalia, Chai, Jin-Fang, Chai, Xiaoran, Chang, Li-Ching, Chang, Yi-Cheng, Chen, Chien-Hsiun, Chesi, Alessandra, Choi, Seung Hoan, Chung, Ren-Hua, Cocca, Massimiliano, Concas, Maria Pina, Couture, Christian, Cuellar-Partida, Gabriel, Danning, Rebecca, Daw, E Warwick, Degenhard, Frauke, Delgado, Graciela E, Delitala, Alessandro, Demirkan, Ayse, Deng, Xuan, Devineni, Poornima, Dietl, Alexander, Dimitriou, Maria, Dimitrov, Latchezar, Dorajoo, Rajkumar, Ekici, Arif B, Engmann, Jorgen E, Fairhurst-Hunter, Zammy, Farmaki, Aliki-Eleni, Faul, Jessica D, Fernandez-Lopez, Juan-Carlos, Forer, Lukas, Francescatto, Margherita, Freitag-Wolf, Sandra, Fuchsberger, Christian, Galesloot, Tessel E, Gao, Yan, Gao, Zishan, Geller, Frank, Giannakopoulou, Olga, Giulianini, Franco, Gjesing, Anette P, Goel, Anuj, Gordon, Scott D, Gorski, Mathias, Grove, Jakob, and Guo, Xiuqing

Subjects
Epidemiology, Biological Sciences, Health Sciences, Genetics, Human Genome, Humans, Body Height, Gene Frequency, Genome, Human, Genome-Wide Association Study, Haplotypes, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Europe, Sample Size, Phenotype, Chromosome Mapping, 23andMe Research Team, VA Million Veteran Program, DiscovEHR, eMERGE, Lifelines Cohort Study, PRACTICAL Consortium, Understanding Society Scientific Group, General Science & Technology
Abstract

Common single-nucleotide polymorphisms (SNPs) are predicted to collectively explain 40-50% of phenotypic variation in human height, but identifying the specific variants and associated regions requires huge sample sizes1. Here, using data from a genome-wide association study of 5.4 million individuals of diverse ancestries, we show that 12,111 independent SNPs that are significantly associated with height account for nearly all of the common SNP-based heritability. These SNPs are clustered within 7,209 non-overlapping genomic segments with a mean size of around 90 kb, covering about 21% of the genome. The density of independent associations varies across the genome and the regions of increased density are enriched for biologically relevant genes. In out-of-sample estimation and prediction, the 12,111 SNPs (or all SNPs in the HapMap 3 panel2) account for 40% (45%) of phenotypic variance in populations of European ancestry but only around 10-20% (14-24%) in populations of other ancestries. Effect sizes, associated regions and gene prioritization are similar across ancestries, indicating that reduced prediction accuracy is likely to be explained by linkage disequilibrium and differences in allele frequency within associated regions. Finally, we show that the relevant biological pathways are detectable with smaller sample sizes than are needed to implicate causal genes and variants. Overall, this study provides a comprehensive map of specific genomic regions that contain the vast majority of common height-associated variants. Although this map is saturated for populations of European ancestry, further research is needed to achieve equivalent saturation in other ancestries.

Published
2022

40. Author Correction: Trans-ancestral genome-wide association study of longitudinal pubertal height growth and shared heritability with adult health outcomes

Author

Jonathan P. Bradfeld, Rachel L. Kember, Anna Ulrich, Zhanna Balkhiyarova, Akram Alyass, Izzuddin M. Aris, Joshua A. Bell, K. Alaine Broadaway, Zhanghua Chen, Jin-Fang Chai, Neil M. Davies, Dietmar Fernandez-Orth, Mariona Bustamante, Ruby Fore, Amitavo Ganguli, Anni Heiskala, Jouke-Jan Hottenga, Carmen Íñiguez, Sayuko Kobes, Jaakko Leinonen, Estelle Lowry, Leo-Pekka Lyytikainen, Anubha Mahajan, Niina Pitkänen, Theresia M. Schnurr, Christian Theil Have, David P. Strachan, Elisabeth Thiering, Suzanne Vogelezang, Kaitlin H. Wade, Carol A. Wang, Andrew Wong, Louise Aas Holm, Alessandra Chesi, Catherine Choong, Miguel Cruz, Paul Elliott, Steve Franks, Christine Frithiof-Bøjsøe, W. James Gauderman, Joseph T. Glessner, Vicente Gilsanz, Kendra Griesman, Robert L. Hanson, Marika Kaakinen, Heidi Kalkwarf, Andrea Kelly, Joseph Kindler, Mika Kähönen, Carla Lanca, Joan Lappe, Nanette R. Lee, Shana McCormack, Frank D. Mentch, Jonathan A. Mitchell, Nina Mononen, Harri Niinikoski, Emily Oken, Katja Pahkala, Xueling Sim, Yik-Ying Teo, Leslie J. Baier, Toos van Beijsterveldt, Linda S. Adair, Dorret I. Boomsma, Eco de Geus, Mònica Guxens, Johan G. Eriksson, Janine F. Felix, Frank D. Gilliland, Penn Medicine Biobank, Torben Hansen, Rebecca Hardy, Marie-France Hivert, Jens-Christian Holm, Vincent W. V. Jaddoe, Marjo-Riitta Järvelin, Terho Lehtimäki, David A. Mackey, David Meyre, Karen L. Mohlke, Juha Mykkänen, Sharon Oberfeld, Craig E. Pennell, John R. B. Perry, Olli Raitakari, Fernando Rivadeneira, Seang-Mei Saw, Sylvain Sebert, John A. Shepherd, Marie Standl, Thorkild I. A. Sørensen, Nicholas J. Timpson, Maties Torrent, Gonneke Willemsen, Elina Hypponen, Chris Power, The Early Growth Genetics Consortium, Mark I. McCarthy, Rachel M. Freathy, Elisabeth Widén, Hakon Hakonarson, Inga Prokopenko, Benjamin F. Voight, Babette S. Zemel, Struan F. A. Grant, and Diana L. Cousminer

Subjects
Biology (General), QH301-705.5, Genetics, QH426-470
Published
2024
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42. Identification of hemodynamically stable patients with acute pulmonary embolism at high risk for death: external validation of different models

Author

Becattini, Cecilia, Gulizia, Michele M., Agnelli, Giancarlo, Dentali, Francesco, Di Lenarda, Andrea, Enea, Iolanda, Fabbri, Andrea, Maggioni, Aldo P., Pomero, Fulvio, Ruggeri, Maria Pia, Lucci, Donata, Vedovati, Maria Cristina, Duranti, Michele, Guercini, Francesco, Groff, Paolo, Verso, Melina, Fabbri, Gianna, Savoia, Martina, Baldini, Ester, Mecatti, Barbara Bartolomei, Bianchini, Francesca, Ceseri, Martina, Gonzini, Lucio, Gorini, Marco, Lorimer, Andrea, Orsini, Giampietro, Tricoli, Martina, Cimini, L.A., Becattini, C., Agnelli, G., Cesarini, V., Sanna, M., Pepe, G., Marchetti, C., Roldan, M. Olivan, Lenzi, L., Cozzio, S., Tomio, P., Diamanti, M., Beltrame, A., Glinski, L., Treleani, M., Coppa, A., Vanni, S., Bartalucci, P., Taccone, A., Costacurta, C., Bortolotti, P., Bortolussi, M., De Vecchi, M., Zanardi, F., Greco, I., Cosentini, R., Gerloni, R., Artusi, N., Cominotto, F., Sisto, U.G., Picariello, C., Roncon, L., Maddalozzo, A., Nitti, C., Riccomi, F., Buzzo, M., Bassanelli, G., Savonitto, S., Bianchi, A., Bilato, C., Lobascio, I., Dalla Valle, C., Pomata, D.P., Giostra, F., Tinuper, A.L., Zalunardo, B., Visonà, A., Panzavolta, C., Novelli, A., Bertini, A., Granai, C., Colombo, S., Periti, E., Bonacchini, L., Abrignani, M.G., Casciolo, M.F., D'Amato, A., Scardovi, A.B., Ricci, R., Iosi, S., Fontana, M.C., Marrazzo, A., Borselli, M., Di Fusco, S.A., Colivicchi, F., Enea, I., Triggiani, M., Papa, I., Pasini, G.F., Fioravanti, C., Panarello, S., Raggi, F., Marzolo, M., Cuppini, S., Milan, M., Barchetti, M., De Laura, D., Caldarola, P., Fiorini, R., Rastelli, G., Ameri, P., La Malfa, G., Cinelli, F., Sganzerla, P.C., Ubaldi, S., Sanchez, F.A., Forgione, C., Cuccia, C., Predieri, S., Fusco, S., Mumoli, N., Porta, C., Romei, M., Lucidi, M., Romaniello, A., Volpe, M., Mogni, P., Pizzolato, E., Martino, G.P., Bitti, G., Righini, G., Bandiera, G., Pennacchio, E., Limauro, S., Dachille, A., Ignone, G., Fuscaldo, G.F., De Rosa, F.M., Vazzana, N., Chesi, G., Di Filippo, F., Pierpaoli, L., Corapi, A., Vatrano, M., Angotti, C., Baccetti, F., Harari, S.A., Luisi, F., Daghini, E., De Curtis, E., Lucà, F., Ciancia, F., Blandizzi, S., Lettica, G.V., D'Orazio, S., Cosmi, F., Zaccaroni, S., Silingardi, M., Valeriano, V., Pugliese, F.R., Murgia, A.P., Parpaglia, P. Pinna, Martinelli, L., Caponi, C., Clemente, M.A., Ciccarone, A., Bongarzoni, A., Garagiola, M., Leone, M.C., Veropalumbo, M.R., Sacco, M., Morella, P., Dorigoni, S., Peterlana, D., Di Paola, R., Felis, S., Correale, M., Brunetti, N.D., Petrelli, G., Feliziani, F.T., Mastroiacovo, D., Romualdi, R., Pasin, F., Bonardi, S., Delfino, P., Scifo, C., Savioli, G., Ceresa, I.F., Galeotalanza, M., Benazzi, B., Porzio, M., Rosini, F., Ancona, C., Verrelli, C., Pasini, A. Fratta, Dalle Carbonare, L., Bozza, N., Nacci, F., Scarabelli, M.A., Amico, F., Marchesi, C., Mazzone, A., Di Tommaso, R., Cocco, F., Pezzuto, G., Luciani, A., Zamboni, P., Muriago, M., Del Pesce, L., Lucarini, A.R., Guglielmelli, E., Vannucchi, V., Moroni, F., Fichera, D., Malatino, L., Sgroi, C., Morana, I.M., Cicero, S., La Rosa, D., Mete, F., Gino, M., De Palma, A., Alessandri, M., Maestripieri, V., Battocchio, M., De Santis, M.T., Saladini, F., Corsi, D.C., Macarone Palmieri, N., Pierfranceschi, M. Giorgi, Palmonari, V., Fontanella, L., Airoldi, L., Bonocore, M., Paliani, U., Prat, L. Iogna, Chiecchi, L., Cuonzo, M., Paludo, A., Padula, D., Antonelli, A., Bicchi, M., Tota, G., Ariello, M., Sai, R., Civita, M., Tucci, M., Barbati, G., Conti, M., Cettina, R., Magnani, O., Levato, M., Gessi, V., De Rui, M., Bellizzi, A., Farneti, L., Salomone, P., Mannarini, A., Grifoni, E., Del Ghianda, S., Campodonico, J., De Cesare, N., Mutone, D., Pasoli, P., Meloni, S., Frenda, A., Viola, G., Torromeo, C., Campana, C., Pistone, M.C., Caravita, S., La Creta, C.P., Miscio, F., Loreno, M., Fenu, P., Mazzetti, M., Rossini, D., Brunacci, M., Capuano, A., Tagliamonte, G., Pinelli, M., Ballocca, F., Parca, G., Pasini, S.M., Maragno, M.G., Vecchi, F., Mancinelli, L., Cavalli, A., Di Mare, F., Conficoni, E., Miceli, R., Pecoraro, R., Fonti, C., Pegoraro, S., Piccinni, G.C., Caruso, G., Boriani, G., Lanzillotta, P., Piccolo, P., Calò, L., Stolfo, D., Mangiacapra, S., Marziali, A., Volponi, M.C., Querci, G., Terribile, R., Menabue, M., Fiorentini, A., Musci, R.L., Uras, S., Cicini, M.P., Manetti, S., Francese, G.M., Melchio, R., Scorpiglione, N., Carrara, D., Pani, A., Morisco, C., Rodolico, M., Colombo, Silvia, Vanni, Simone, Abrignani, Maurizio Giuseppe, Scardovi, Angela Beatrice, Marrazzo, Alessandra, Borselli, Matteo, Barchetti, Marco, and Maggioni, Aldo Pietro

Published
2024
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43. Targeting DNA2 overcomes metabolic reprogramming in multiple myeloma

Author

Natthakan Thongon, Feiyang Ma, Natalia Baran, Pamela Lockyer, Jintan Liu, Christopher Jackson, Ashley Rose, Ken Furudate, Bethany Wildeman, Matteo Marchesini, Valentina Marchica, Paola Storti, Giannalisa Todaro, Irene Ganan-Gomez, Vera Adema, Juan Jose Rodriguez-Sevilla, Yun Qing, Min Jin Ha, Rodrigo Fonseca, Caleb Stein, Caleb Class, Lin Tan, Sergio Attanasio, Guillermo Garcia-Manero, Nicola Giuliani, David Berrios Nolasco, Andrea Santoni, Claudio Cerchione, Carlos Bueso-Ramos, Marina Konopleva, Philip Lorenzi, Koichi Takahashi, Elisabet Manasanch, Gabriella Sammarelli, Rashmi Kanagal-Shamanna, Andrea Viale, Marta Chesi, and Simona Colla

Subjects
Science
Abstract

Abstract DNA damage resistance is a major barrier to effective DNA-damaging therapy in multiple myeloma (MM). To discover mechanisms through which MM cells overcome DNA damage, we investigate how MM cells become resistant to antisense oligonucleotide (ASO) therapy targeting Interleukin enhancer binding factor 2 (ILF2), a DNA damage regulator that is overexpressed in 70% of MM patients whose disease has progressed after standard therapies have failed. Here, we show that MM cells undergo adaptive metabolic rewiring to restore energy balance and promote survival in response to DNA damage activation. Using a CRISPR/Cas9 screening strategy, we identify the mitochondrial DNA repair protein DNA2, whose loss of function suppresses MM cells’ ability to overcome ILF2 ASO−induced DNA damage, as being essential to counteracting oxidative DNA damage. Our study reveals a mechanism of vulnerability of MM cells that have an increased demand for mitochondrial metabolism upon DNA damage activation.

Published
2024
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44. Trans-ancestral genome-wide association study of longitudinal pubertal height growth and shared heritability with adult health outcomes

Author

Jonathan P. Bradfield, Rachel L. Kember, Anna Ulrich, Zhanna Balkhiyarova, Akram Alyass, Izzuddin M. Aris, Joshua A. Bell, K. Alaine Broadaway, Zhanghua Chen, Jin-Fang Chai, Neil M. Davies, Dietmar Fernandez-Orth, Mariona Bustamante, Ruby Fore, Amitavo Ganguli, Anni Heiskala, Jouke-Jan Hottenga, Carmen Íñiguez, Sayuko Kobes, Jaakko Leinonen, Estelle Lowry, Leo-Pekka Lyytikainen, Anubha Mahajan, Niina Pitkänen, Theresia M. Schnurr, Christian Theil Have, David P. Strachan, Elisabeth Thiering, Suzanne Vogelezang, Kaitlin H. Wade, Carol A. Wang, Andrew Wong, Louise Aas Holm, Alessandra Chesi, Catherine Choong, Miguel Cruz, Paul Elliott, Steve Franks, Christine Frithioff-Bøjsøe, W. James Gauderman, Joseph T. Glessner, Vicente Gilsanz, Kendra Griesman, Robert L. Hanson, Marika Kaakinen, Heidi Kalkwarf, Andrea Kelly, Joseph Kindler, Mika Kähönen, Carla Lanca, Joan Lappe, Nanette R. Lee, Shana McCormack, Frank D. Mentch, Jonathan A. Mitchell, Nina Mononen, Harri Niinikoski, Emily Oken, Katja Pahkala, Xueling Sim, Yik-Ying Teo, Leslie J. Baier, Toos van Beijsterveldt, Linda S. Adair, Dorret I. Boomsma, Eco de Geus, Mònica Guxens, Johan G. Eriksson, Janine F. Felix, Frank D. Gilliland, Penn Medicine Biobank, Torben Hansen, Rebecca Hardy, Marie-France Hivert, Jens-Christian Holm, Vincent W. V. Jaddoe, Marjo-Riitta Järvelin, Terho Lehtimäki, David A. Mackey, David Meyre, Karen L. Mohlke, Juha Mykkänen, Sharon Oberfield, Craig E. Pennell, John R. B. Perry, Olli Raitakari, Fernando Rivadeneira, Seang-Mei Saw, Sylvain Sebert, John A. Shepherd, Marie Standl, Thorkild I. A. Sørensen, Nicholas J. Timpson, Maties Torrent, Gonneke Willemsen, Elina Hypponen, Chris Power, The Early Growth Genetics Consortium, Mark I. McCarthy, Rachel M. Freathy, Elisabeth Widén, Hakon Hakonarson, Inga Prokopenko, Benjamin F. Voight, Babette S. Zemel, Struan F. A. Grant, and Diana L. Cousminer

Subjects
Biology (General), QH301-705.5, Genetics, QH426-470
Abstract

Abstract Background Pubertal growth patterns correlate with future health outcomes. However, the genetic mechanisms mediating growth trajectories remain largely unknown. Here, we modeled longitudinal height growth with Super-Imposition by Translation And Rotation (SITAR) growth curve analysis on ~ 56,000 trans-ancestry samples with repeated height measurements from age 5 years to adulthood. We performed genetic analysis on six phenotypes representing the magnitude, timing, and intensity of the pubertal growth spurt. To investigate the lifelong impact of genetic variants associated with pubertal growth trajectories, we performed genetic correlation analyses and phenome-wide association studies in the Penn Medicine BioBank and the UK Biobank. Results Large-scale growth modeling enables an unprecedented view of adolescent growth across contemporary and 20th-century pediatric cohorts. We identify 26 genome-wide significant loci and leverage trans-ancestry data to perform fine-mapping. Our data reveals genetic relationships between pediatric height growth and health across the life course, with different growth trajectories correlated with different outcomes. For instance, a faster tempo of pubertal growth correlates with higher bone mineral density, HOMA-IR, fasting insulin, type 2 diabetes, and lung cancer, whereas being taller at early puberty, taller across puberty, and having quicker pubertal growth were associated with higher risk for atrial fibrillation. Conclusion We report novel genetic associations with the tempo of pubertal growth and find that genetic determinants of growth are correlated with reproductive, glycemic, respiratory, and cardiac traits in adulthood. These results aid in identifying specific growth trajectories impacting lifelong health and show that there may not be a single “optimal” pubertal growth pattern.

Published
2024
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45. Quantum dynamics of Gaudin magnets

Author

He, Wen-Bin, Chesi, Stefano, Lin, H. -Q., and Guan, Xi-Wen

Subjects
Condensed Matter - Strongly Correlated Electrons
Abstract

Quantum dynamics of many-body systems is a fascinating and significant subject for both theory and experiment. The question of how an isolated many-body system evolves to its steady state after a sudden perturbation or quench still remains challenging. In this paper, using the Bethe ansatz wave function, we study the quantum dynamics of an inhomogeneous Gaudin magnet. We derive explicit analytical expressions for various local dynamic quantities with an arbitrary number of flipped bath spins, such as: the spin distribution function, the spin-spin correlation function, and the Loschmidt echo. We also numerically study the relaxation behavior of these dynamic properties, gaining considerable insight into coherence and entanglement between the central spin and the bath. In particular, we find that the spin-spin correlations relax to their steady value via a nearly logarithmic scaling, whereas the Loschmidt echo shows an exponential relaxation to its steady value. Our results advance the understanding of relaxation dynamics and quantum correlations of long-range interacting models of Gaudin type.

Published
2022
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48. A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids

Author

Ramdas, Shweta, Judd, Jonathan, Graham, Sarah E, Kanoni, Stavroula, Wang, Yuxuan, Surakka, Ida, Wenz, Brandon, Clarke, Shoa L, Chesi, Alessandra, Wells, Andrew, Bhatti, Konain Fatima, Vedantam, Sailaja, Winkler, Thomas W, Locke, Adam E, Marouli, Eirini, Zajac, Greg JM, Wu, Kuan-Han H, Ntalla, Ioanna, Hui, Qin, Klarin, Derek, Hilliard, Austin T, Wang, Zeyuan, Xue, Chao, Thorleifsson, Gudmar, Helgadottir, Anna, Gudbjartsson, Daniel F, Holm, Hilma, Olafsson, Isleifur, Hwang, Mi Yeong, Han, Sohee, Akiyama, Masato, Sakaue, Saori, Terao, Chikashi, Kanai, Masahiro, Zhou, Wei, Brumpton, Ben M, Rasheed, Humaira, Havulinna, Aki S, Veturi, Yogasudha, Pacheco, Jennifer Allen, Rosenthal, Elisabeth A, Lingren, Todd, Feng, QiPing, Kullo, Iftikhar J, Narita, Akira, Takayama, Jun, Martin, Hilary C, Hunt, Karen A, Trivedi, Bhavi, Haessler, Jeffrey, Giulianini, Franco, Bradford, Yuki, Miller, Jason E, Campbell, Archie, Lin, Kuang, Millwood, Iona Y, Rasheed, Asif, Hindy, George, Faul, Jessica D, Zhao, Wei, Weir, David R, Turman, Constance, Huang, Hongyan, Graff, Mariaelisa, Choudhury, Ananyo, Sengupta, Dhriti, Mahajan, Anubha, Brown, Michael R, Zhang, Weihua, Yu, Ketian, Schmidt, Ellen M, Pandit, Anita, Gustafsson, Stefan, Yin, Xianyong, Luan, Jian’an, Zhao, Jing-Hua, Matsuda, Fumihiko, Jang, Hye-Mi, Yoon, Kyungheon, Medina-Gomez, Carolina, Pitsillides, Achilleas, Hottenga, Jouke Jan, Wood, Andrew R, Ji, Yingji, Gao, Zishan, Haworth, Simon, Mitchell, Ruth E, Chai, Jin Fang, Aadahl, Mette, Bjerregaard, Anne A, Yao, Jie, Manichaikul, Ani, Lee, Wen-Jane, Hsiung, Chao Agnes, Warren, Helen R, Ramirez, Julia, Bork-Jensen, Jette, Kårhus, Line L, Goel, Anuj, and Sabater-Lleal, Maria

Subjects
Human Genome, Biotechnology, Genetics, 2.1 Biological and endogenous factors, Aetiology, Chromatin, Genome-Wide Association Study, Genomics, Humans, Lipids, Polymorphism, Single Nucleotide, Million Veterans Program, Global Lipids Genetics Consortium, complex traits, fine-mapping, functional genomics, lipid biology, post-GWAS, regulatory mechanism, variant prioritization, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

A major challenge of genome-wide association studies (GWASs) is to translate phenotypic associations into biological insights. Here, we integrate a large GWAS on blood lipids involving 1.6 million individuals from five ancestries with a wide array of functional genomic datasets to discover regulatory mechanisms underlying lipid associations. We first prioritize lipid-associated genes with expression quantitative trait locus (eQTL) colocalizations and then add chromatin interaction data to narrow the search for functional genes. Polygenic enrichment analysis across 697 annotations from a host of tissues and cell types confirms the central role of the liver in lipid levels and highlights the selective enrichment of adipose-specific chromatin marks in high-density lipoprotein cholesterol and triglycerides. Overlapping transcription factor (TF) binding sites with lipid-associated loci identifies TFs relevant in lipid biology. In addition, we present an integrative framework to prioritize causal variants at GWAS loci, producing a comprehensive list of candidate causal genes and variants with multiple layers of functional evidence. We highlight two of the prioritized genes, CREBRF and RRBP1, which show convergent evidence across functional datasets supporting their roles in lipid biology.

Published
2022

49. Expectation-based Minimalist Grammars

Author

Chesi, Cristiano

Subjects
Computer Science - Computation and Language, Computer Science - Computational Complexity
Abstract

Expectation-based Minimalist Grammars (e-MGs) are simplified versions of the (Conflated) Minimalist Grammars, (C)MGs, formalized by Stabler (Stabler, 2011, 2013, 1997) and Phase-based Minimalist Grammars, PMGs (Chesi, 2005, 2007; Stabler, 2011). The crucial simplification consists of driving structure building only by relying on lexically encoded categorial top-down expectations. The commitment on a top-down derivation (as in e-MGs and PMGs, as opposed to (C)MGs, Chomsky, 1995; Stabler, 2011) allows us to define a core derivation that should be the same in both parsing and generation (Momma & Phillips, 2018)., Comment: This is an extended version of a paper published in CLiC-it 2021 - Italian Conference on Computational Linguistics 2021 - Proceedings of the Eighth Italian Conference on Computational Linguistics Milan, Italy, January 26-28, 2022. Edited by Elisabetta Fersini, Marco Passarotti, Viviana Patti. CEUR-WS.org, ISSN 1613-0073

Published
2021

50. Lung UltrasouNd Guided surfactant therapy in preterm infants: an international multicenter randomized control trial (LUNG study)

Author

Corsini, Iuri, Rodriguez-Fanjul, Javier, Raimondi, Francesco, Boni, Luca, Berardi, Alberto, Aldecoa-Bilbao, Victoria, Alonso-Ojembarrena, Almudena, Ancora, Gina, Aversa, Salvatore, Beghini, Renzo, Meseguer, Nerea Bilbao, Capasso, Letizia, Chesi, Francesca, Ciarcià, Martina, Concheiro, Ana, Corvaglia, Luigi, Ficial, Benjamim, Filippi, Luca, Carballal, Jesus Fuentes, Fusco, Monica, Gatto, Sara, Ginovart, Gemma, Gregorio-Hernández, Rebeca, Lista, Gianluca, Sánchez-Luna, Manuel, Martini, Silvia, Massenzi, Luca, Miselli, Francesca, Mercadante, Domenica, Mosca, Fabio, Palacio, Marta Teresa, Perri, Alessandro, Piano, Francesca, Prieto, Marcelino Pumarada, Fernandez, Lorena Rodeno, Risso, Francesco Maria, Savoia, Marilena, Staffler, Alex, Vento, Giovanni, and Dani, Carlo

Published
2023
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