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2,629 results on '"Dive A"'

1. Rapid Assessment of Stable Crystal Structures in Single Phase High Entropy Alloys Via Graph Neural Network Based Surrogate Modelling

Author

Beaver, Nicholas, Dive, Aniruddha, Wong, Marina, Shimanuki, Keita, Patil, Ananya, Ferrell, Anthony, and Kivy, Mohsen B.

Subjects
Condensed Matter - Materials Science, Condensed Matter - Disordered Systems and Neural Networks
Abstract

In an effort to develop a rapid, reliable, and cost-effective method for predicting the structure of single-phase high entropy alloys, a Graph Neural Network (ALIGNN-FF) based approach was introduced. This method was successfully tested on 132 different high entropy alloys, and the results were analyzed and compared with density functional theory and valence electron concentration calculations. Additionally, the effects of various factors, including lattice parameters and the number of supercells with unique atomic configurations, on the prediction accuracy were investigated. The ALIGNN-FF based approach was subsequently used to predict the structure of a novel cobalt-free 3d high entropy alloy, and the result was experimentally verified., Comment: 16 pages, 8 Figures. To be published in Results Materials

Published
2024

2. The VALTIVE1 study protocol: a study for the validation of Tie2 as the first tumour vascular response biomarker for VEGF inhibitors

Author

Carucci, Margherita, Clamp, Andrew, Zhou, Cong, Hurt, Chris, Glasspool, Rosalind, Monaghan, Phillip J., Thirkettle, Sally, Wheatley, Michael, Mahmood, Madia, Narasimham, Monica, Cox, Tracy, Morrison, Hilary, Campbell, Susan, Nelson, Annmarie, Holland-Hart, Daniella, Hopewell-Kelly, Noreen, Thomas, Abin, Porter, Catharine, Slusarczyk, Magdalena, Irving, Alys, Dive, Caroline, Adams, Richard, and Jayson, Gordon C.

Published
2024
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3. Representation of genomic intratumor heterogeneity in multi-region non-small cell lung cancer patient-derived xenograft models

Author

Hynds, Robert E., Huebner, Ariana, Pearce, David R., Hill, Mark S., Akarca, Ayse U., Moore, David A., Ward, Sophia, Gowers, Kate H. C., Karasaki, Takahiro, Al Bakir, Maise, Wilson, Gareth A., Pich, Oriol, Martínez-Ruiz, Carlos, Hossain, A. S. Md Mukarram, Pearce, Simon P., Sivakumar, Monica, Ben Aissa, Assma, Grönroos, Eva, Chandrasekharan, Deepak, Kolluri, Krishna K., Towns, Rebecca, Wang, Kaiwen, Cook, Daniel E., Bosshard-Carter, Leticia, Naceur-Lombardelli, Cristina, Rowan, Andrew J., Veeriah, Selvaraju, Litchfield, Kevin, Crosbie, Philip A. J., Dive, Caroline, Quezada, Sergio A., Janes, Sam M., Jamal-Hanjani, Mariam, Marafioti, Teresa, McGranahan, Nicholas, and Swanton, Charles

Published
2024
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6. Lower Bounding Ground-State Energies of Local Hamiltonians Through the Renormalization Group

Author

Kull, Ilya, Schuch, Norbert, Dive, Ben, and Navascués, Miguel

Subjects
Quantum Physics, Condensed Matter - Strongly Correlated Electrons
Abstract

Given a renormalization scheme, we show how to formulate a tractable convex relaxation of the set of feasible local density matrices of a many-body quantum system. The relaxation is obtained by introducing a hierarchy of constraints between the reduced states of ever-growing sets of lattice sites. The coarse-graining maps of the underlying renormalization procedure serve to eliminate a vast number of those constraints, such that the remaining ones can be enforced with reasonable computational means. This can be used to obtain rigorous lower bounds on the ground state energy of arbitrary local Hamiltonians, by performing a linear optimization over the resulting convex relaxation of reduced quantum states. The quality of the bounds crucially depends on the particular renormalization scheme, which must be tailored to the target Hamiltonian. We apply our method to 1D translation-invariant spin models, obtaining energy bounds comparable to those attained by optimizing over locally translation-invariant states of $n\gtrsim 100$ spins. Beyond this demonstration, the general method can be applied to a wide range of other problems, such as spin systems in higher spatial dimensions, electronic structure problems, and various other many-body optimization problems, such as entanglement and nonlocality detection., Comment: Section III, that presents the general framework, was revised

Published
2022
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7. Metastatic lung malignancy to mandibular gingiva

Author

Moharil Rohit, Khandekar Shubhangi, and Dive Alka

Subjects
Lung cancer, metastasis, oral cavity, Dentistry, RK1-715
Abstract

Metastatic tumors of oral cavity are uncommon and may occur in oral soft tissues or jaw bones. Because of their rarity, metastasis to oral cavity are challenging to diagnose and difficult to treat. They often have vague symptoms that mimic dental infections. These lesions generally show poorly differentiated histopathologic picture and have poor prognosis. We reported a case of a 40-year-old male patient of metastatic lesion to the oral cavity and brain with primary tumor, diagnosed as an undifferentiated epithelial malignancy of lung.

Published
2010

8. Mining nucleic acid 'omics' to boost liquid biopsy in cancer

Author

Ann Tivey, Rebecca J. Lee, Alexandra Clipson, Steven M. Hill, Paul Lorigan, Dominic G. Rothwell, Caroline Dive, and Florent Mouliere

Subjects
Medicine (General), R5-920
Abstract

Summary: Treatments for cancer patients are becoming increasingly complex, and there is a growing desire from clinicians and patients for biomarkers that can account for this complexity to support informed decisions about clinical care. To achieve precision medicine, the new generation of biomarkers must reflect the spatial and temporal heterogeneity of cancer biology both between patients and within an individual patient. Mining the different layers of 'omics in a multi-modal way from a minimally invasive, easily repeatable, liquid biopsy has increasing potential in a range of clinical applications, and for improving our understanding of treatment response and resistance. Here, we detail the recent developments and methods allowing exploration of genomic, epigenomic, transcriptomic, and fragmentomic layers of 'omics from liquid biopsy, and their integration in a range of applications. We also consider the specific challenges that are posed by the clinical implementation of multi-omic liquid biopsies.

Published
2024
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9. Acute intermittent porphyria: A case report with an unlisted HMBS gene variant (c.345–2A>C)

Author

Julien Lerusse, Dominique Dive, and François Charles Wang

Subjects
Acute intermittent porphyria, Hmbs gene Heme, Acute polyradiculoneuritis, Neurology. Diseases of the nervous system, RC346-429
Abstract

We report a case of acute intermittent porphyria in a 19-year-old patient, linked to an unlisted variant of the gene encoding hydroxymethylbilane synthase c.345–2A>C. Given the very low prevalence of porphyria in the general population, diagnosis is rarely made initially and may mainly mimic Guillain-Barré syndrome. Considering this, we provide an overview addressing various ways the disease manifests, paraclinical investigations, pathophysiology, and available therapeutic options. Specifically, human heme therapy in the case of acute crises is nearly unanimous in the literature. However, there is no consensus on the management between crises if the current first line choice treatment, namely givosiran, is not accessible. We report the clinical follow-up proposed for this patient.

Published
2024
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10. A universal quantum rewinding protocol with an arbitrarily high probability of success

Author

Trillo, David, Dive, Benjamin, and Navascués, Miguel

Subjects
Quantum Physics
Abstract

We present a universal mechanism that, acting on any target qubit, propagates it to the state it had T time units before the experiment started. This protocol works by setting the target on a superposition of flight paths, where it is acted on by uncharacterized, but repeatable, quantum operations. Independently of the effect of each of these individual operations on the target, the successful interference of the paths causes it to leap to its past state. We prove that, for generic interaction effects, the system will reach the desired state with probability 1 after some finite number of steps., Comment: 4+4 pages, 3 figures

Published
2022
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11. Demonstration of universal time-reversal for quantum processes

Author

Schiansky, Peter, Strömberg, Teodor, Trillo, David, Saggio, Valeria, Dive, Ben, Navascués, Miguel, and Walther, Philip

Subjects
Quantum Physics
Abstract

Although the laws of classical physics are deterministic, thermodynamics gives rise to an arrow of time through irreversible processes. In quantum mechanics the unitary nature of the time evolution makes it intrinsically reversible, however the question of how to revert an unknown time evolution nevertheless remains. Remarkably, there have been several recent demonstrations of protocols for reverting unknown unitaries in scenarios where even the interactions with the target system are unknown. The practical use of these universal rewinding protocols is limited by their probabilistic nature, raising the fundamental question of whether time-reversal could be performed deterministically. Here we show that quantum physics indeed allows for deterministic universal time-reversal by exploiting the non-commuting nature of quantum operators, and demonstrate a recursive protocol for two-level quantum systems with an arbitrarily high probability of success. Using a photonic platform we demonstrate our protocol, reverting the discrete time evolution of a polarization state with an average state fidelity of over 95%. Our protocol, requiring no knowledge of the quantum process to be rewound, is optimal in its running time, and brings quantum rewinding into a regime of practical relevance.

Published
2022
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12. Immune biomarker evaluation of sequential tyrosine kinase inhibitor and nivolumab monotherapies in renal cell carcinoma: the phase I TRIBE trial

Author

K.S. Shohdy, M. Pillai, K.S. Abbas, J. Allison, T. Waddell, E. Darlington, S. Mohammad, S. Hood, S. Atkinson, K. Simpson, D. Morgan, P. Nathan, E. Kilgour, C. Dive, and F. Thistlethwaite

Subjects
predictive biomarkers, immune checkpoint blockade, metastatic renal cell carcinoma, nivolumab, progression-free survival, clinical benefit rate, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Background: Predictive biomarkers for immune checkpoint blockade in the second-line treatment of metastatic renal cell carcinoma (mRCC) are lacking. Materials and methods: Patients with histologically confirmed RCC who started nivolumab after at least 4 months of tyrosine kinase inhibitors (TKIs) were recruited for this study. Serial tissue and blood samples were collected for immune biomarker evaluation. The primary endpoint was to determine the association of specific T-cell subsets with clinical outcomes tested using Wilcoxon rank sum for clinical benefit rate (CBR) and log-rank test for progression-free survival (PFS). Results: Twenty patients were included in this trial with a median age of 64 years and followed-up for a median of 12 months. The median PFS for patients who received TKI was 13.8 months, while for those subsequently treated with nivolumab following TKI therapy, the median PFS was 2.6 months. CBR of nivolumab was 20% with two partial responses. Functionally active programmed cell death protein 1+ CD4+ T cells were enriched in non-responders (q = 0.003) and associated with worse PFS on nivolumab (P = 0.04). Responders showed a significant reduction in the effector CD4+T-cell (TEF) fraction compared to non-responders at 3 months on nivolumab (0.40 versus 0.80, P = 0.0005). CD127+CD4+ T cells were enriched in patients who developed immune-related adverse effects (q = 0.003). Using in-house validated multiplex immunohistochemistry for six markers, we measured tumour-associated immune cell densities in tissue samples. Responders to nivolumab showed a significantly higher mean of immune cell densities in tissue samples compared to non-responders (346 versus 87 cells/mm2, P = 0.04). Conclusions: In this small study, analysis of tissue-based and peripheral blood immune cell subsets predicted clinical outcomes of nivolumab. Further studies are warranted with larger populations to validate these observations.

Published
2024
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13. Medica-Plus: a Micromegas-based proof-of-concept detector for sub-becquerel tritium activity assessment at the service of oncological research

Author

Jambon, F., Aune, S., Baron, P., Benoit, T., Bey, T., Desforge, D., Ferrer-Ribas, E., Grabas, A., Kebbiri, M., Mandjavidze, I., Papaevangelou, T., Riallot, M., Vandenbroucke, M., Beau, F., Dive, V., Malgorn, C., Malloggi, F., Rousselot, A., Carrel, F., and Trocmé, M.

Subjects
Physics - Instrumentation and Detectors
Abstract

To fulfill needs in oncological research a new Micromegas detector has been developed to follow radiolabelled drugs in living organisms at the single cell level. This article describes the proof-of-concept of such a detector and compares its ability to detect and assess sub-becquerel \tritium~activities with a commercial $\beta$-imager, Comment: 14 pages, to be submitted to NIMA

Published
2021
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14. Author Correction: The evolution of lung cancer and impact of subclonal selection in TRACERx

Author

Frankell, Alexander M., Dietzen, Michelle, Al Bakir, Maise, Lim, Emilia L., Karasaki, Takahiro, Ward, Sophia, Veeriah, Selvaraju, Colliver, Emma, Huebner, Ariana, Bunkum, Abigail, Hill, Mark S., Grigoriadis, Kristiana, Moore, David A., Black, James R. M., Liu, Wing Kin, Thol, Kerstin, Pich, Oriol, Watkins, Thomas B. K., Naceur-Lombardelli, Cristina, Cook, Daniel E., Salgado, Roberto, Wilson, Gareth A., Bailey, Chris, Angelova, Mihaela, Bentham, Robert, Martínez-Ruiz, Carlos, Abbosh, Christopher, Nicholson, Andrew G., Le Quesne, John, Biswas, Dhruva, Rosenthal, Rachel, Puttick, Clare, Hessey, Sonya, Lee, Claudia, Prymas, Paulina, Toncheva, Antonia, Smith, Jon, Xing, Wei, Nicod, Jerome, Price, Gillian, Kerr, Keith M., Naidu, Babu, Middleton, Gary, Blyth, Kevin G., Fennell, Dean A., Forster, Martin D., Lee, Siow Ming, Falzon, Mary, Hewish, Madeleine, Shackcloth, Michael J., Lim, Eric, Benafif, Sarah, Russell, Peter, Boleti, Ekaterini, Krebs, Matthew G., Lester, Jason F., Papadatos-Pastos, Dionysis, Ahmad, Tanya, Thakrar, Ricky M., Lawrence, David, Navani, Neal, Janes, Sam M., Dive, Caroline, Blackhall, Fiona H., Summers, Yvonne, Cave, Judith, Marafioti, Teresa, Herrero, Javier, Quezada, Sergio A., Peggs, Karl S., Schwarz, Roland F., Van Loo, Peter, Miedema, Daniël M., Birkbak, Nicolai J., Hiley, Crispin T., Hackshaw, Allan, Zaccaria, Simone, Jamal-Hanjani, Mariam, McGranahan, Nicholas, and Swanton, Charles

Published
2024
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15. A conserved YAP/Notch/REST network controls the neuroendocrine cell fate in the lungs

Author

Shue, Yan Ting, Drainas, Alexandros P, Li, Nancy Yanzhe, Pearsall, Sarah M, Morgan, Derrick, Sinnott-Armstrong, Nasa, Hipkins, Susan Q, Coles, Garry L, Lim, Jing Shan, Oro, Anthony E, Simpson, Kathryn L, Dive, Caroline, and Sage, Julien

Subjects
Biochemistry and Cell Biology, Biological Sciences, Cancer, Lung, Genetics, Lung Cancer, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, Cell Differentiation, Humans, Lung Neoplasms, Neuroendocrine Cells, Receptors, Notch
Abstract

The Notch pathway is a conserved cell-cell communication pathway that controls cell fate decisions. Here we sought to determine how Notch pathway activation inhibits the neuroendocrine cell fate in the lungs, an archetypal process for cell fate decisions orchestrated by Notch signaling that has remained poorly understood at the molecular level. Using intratumoral heterogeneity in small-cell lung cancer as a tractable model system, we uncovered a role for the transcriptional regulators REST and YAP as promoters of the neuroendocrine to non-neuroendocrine transition. We further identified the specific neuroendocrine gene programs repressed by REST downstream of Notch in this process. Importantly, we validated the importance of REST and YAP in neuroendocrine to non-neuroendocrine cell fate switches in both developmental and tissue repair processes in the lungs. Altogether, these experiments identify conserved roles for REST and YAP in Notch-driven inhibition of the neuroendocrine cell fate in embryonic lungs, adult lungs, and lung cancer.

Published
2022

17. The evolution of non-small cell lung cancer metastases in TRACERx

Author

Al Bakir, Maise, Huebner, Ariana, Martínez-Ruiz, Carlos, Grigoriadis, Kristiana, Watkins, Thomas B. K., Pich, Oriol, Moore, David A., Veeriah, Selvaraju, Ward, Sophia, Laycock, Joanne, Johnson, Diana, Rowan, Andrew, Razaq, Maryam, Akther, Mita, Naceur-Lombardelli, Cristina, Prymas, Paulina, Toncheva, Antonia, Hessey, Sonya, Dietzen, Michelle, Colliver, Emma, Frankell, Alexander M., Bunkum, Abigail, Lim, Emilia L., Karasaki, Takahiro, Abbosh, Christopher, Hiley, Crispin T., Hill, Mark S., Cook, Daniel E., Wilson, Gareth A., Salgado, Roberto, Nye, Emma, Stone, Richard Kevin, Fennell, Dean A., Price, Gillian, Kerr, Keith M., Naidu, Babu, Middleton, Gary, Summers, Yvonne, Lindsay, Colin R., Blackhall, Fiona H., Cave, Judith, Blyth, Kevin G., Nair, Arjun, Ahmed, Asia, Taylor, Magali N., Procter, Alexander James, Falzon, Mary, Lawrence, David, Navani, Neal, Thakrar, Ricky M., Janes, Sam M., Papadatos-Pastos, Dionysis, Forster, Martin D., Lee, Siow Ming, Ahmad, Tanya, Quezada, Sergio A., Peggs, Karl S., Van Loo, Peter, Dive, Caroline, Hackshaw, Allan, Birkbak, Nicolai J., Zaccaria, Simone, Jamal-Hanjani, Mariam, McGranahan, Nicholas, and Swanton, Charles

Published
2023
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18. The evolution of lung cancer and impact of subclonal selection in TRACERx

Author

Frankell, Alexander M., Dietzen, Michelle, Al Bakir, Maise, Lim, Emilia L., Karasaki, Takahiro, Ward, Sophia, Veeriah, Selvaraju, Colliver, Emma, Huebner, Ariana, Bunkum, Abigail, Hill, Mark S., Grigoriadis, Kristiana, Moore, David A., Black, James R. M., Liu, Wing Kin, Thol, Kerstin, Pich, Oriol, Watkins, Thomas B. K., Naceur-Lombardelli, Cristina, Cook, Daniel E., Salgado, Roberto, Wilson, Gareth A., Bailey, Chris, Angelova, Mihaela, Bentham, Robert, Martínez-Ruiz, Carlos, Abbosh, Christopher, Nicholson, Andrew G., Le Quesne, John, Biswas, Dhruva, Rosenthal, Rachel, Puttick, Clare, Hessey, Sonya, Lee, Claudia, Prymas, Paulina, Toncheva, Antonia, Smith, Jon, Xing, Wei, Nicod, Jerome, Price, Gillian, Kerr, Keith M., Naidu, Babu, Middleton, Gary, Blyth, Kevin G., Fennell, Dean A., Forster, Martin D., Lee, Siow Ming, Falzon, Mary, Hewish, Madeleine, Shackcloth, Michael J., Lim, Eric, Benafif, Sarah, Russell, Peter, Boleti, Ekaterini, Krebs, Matthew G., Lester, Jason F., Papadatos-Pastos, Dionysis, Ahmad, Tanya, Thakrar, Ricky M., Lawrence, David, Navani, Neal, Janes, Sam M., Dive, Caroline, Blackhall, Fiona H., Summers, Yvonne, Cave, Judith, Marafioti, Teresa, Herrero, Javier, Quezada, Sergio A., Peggs, Karl S., Schwarz, Roland F., Van Loo, Peter, Miedema, Daniël M., Birkbak, Nicolai J., Hiley, Crispin T., Hackshaw, Allan, Zaccaria, Simone, Jamal-Hanjani, Mariam, McGranahan, Nicholas, and Swanton, Charles

Published
2023
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19. Clinical and economic burden of surgical complications during hospitalization for digestive cancer surgery in France

Author

Guillaume Piessen, Catherine Dive‐Pouletty, Aurélie Danel, Magali Laborey, and Benoît Thomé

Subjects
burden, digestive cancer surgery, infection, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background Surgical complications and particularly infections after digestive cancer surgery remain a major health and economic problem and its burden in France is not well documented. Aims The aim of this study was to analyse recent data regarding surgical complications in patients undergoing major digestive cancer surgery, and to estimate its burden for the French society. Methods and Results Using the 2018 French hospital discharge database and 2017 National CostStudy we studied hospital stays for surgical resection in patients withdigestive cancer. The population was divided into three groups based onpostoperative outcomes: no complications (NC), related infectious complications (RIC) and other complications. The main analysis compared the length and cost per stay between RIC and NC. Forty‐Four thousand one hundred and twenty‐three stays following a digestive cancer resection were identified. Lower gastro‐intestinal cancers were the most prevalent representing 74.8% of stays, the rate of malnutrition was 32.8% and 15.8% of patients presented RIC. Mean (SD) length of stay varied from 11,7 (9.0) days for NC to 25,5 days (19.5) for RIC (p 15%) and was associated with significantly longer length of stay and higher cost per stay. Although important prevention plans have been implemented in recent years, care strategies are still needed to alleviate the burden on patients and the healthcare system.

Published
2023
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20. Lineage Plasticity in SCLC Generates Non-Neuroendocrine Cells Primed for Vasculogenic Mimicry

Author

Pearsall, Sarah M., Williamson, Stuart C., Humphrey, Sam, Hughes, Ellyn, Morgan, Derrick, García Marqués, Fernando J., Awanis, Griselda, Carroll, Rebecca, Burks, Laura, Shue, Yan Ting, Bermudez, Abel, Frese, Kristopher K., Galvin, Melanie, Carter, Mathew, Priest, Lynsey, Kerr, Alastair, Zhou, Cong, Oliver, Trudy G., Humphries, Jonathan D., Humphries, Martin J., Blackhall, Fiona, Cannell, Ian G., Pitteri, Sharon J., Hannon, Gregory J., Sage, Julien, Dive, Caroline, and Simpson, Kathryn L.

Published
2023
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21. Entanglement Detection Beyond Measuring Fidelities

Author

Weilenmann, Mirjam, Dive, Benjamin, Trillo, David, Aguilar, Edgar A., and Navascués, Miguel

Subjects
Quantum Physics
Abstract

One of the most widespread methods to determine if a quantum state is entangled, or to quantify its entanglement dimensionality, is by measuring its fidelity with respect to a pure state. In this Letter we find a large class of states whose entanglement cannot be detected in this manner; we call them unfaithful. We find that unfaithful states are ubiquitous in information theory. For small dimensions, we check numerically that most bipartite states are both entangled and unfaithful. Similarly, numerical searches in low dimensions show that most pure entangled states remain entangled but become unfaithful when a certain amount of white noise is added. We also find that faithfulness can be self-activated, i.e., there exist instances of unfaithful states whose tensor powers are faithful. To explore how the fidelity approach limits the quantification of entanglement dimensionality, we generalize the notion of an unfaithful state to that of a D-unfaithful state, one that cannot be certified as D-dimensionally entangled by measuring its fidelity with respect to a pure state. For describing such states, we additionally introduce a hierarchy of semidefinite programming relaxations that fully characterizes the set of states of Schmidt rank at most D., Comment: 5+3 pages, 2 figures, 1 table. Supplemented with GitHub repository. v2: improved presentation (including new appendices that give additional technical details). v3: corrected errors in Table I

Published
2019
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22. Translating Uncontrolled Systems in Time

Author

Trillo, David, Dive, Benjamin, and Navascues, Miguel

Subjects
Quantum Physics
Abstract

We show that there exist non-relativistic scattering experiments which, if successful, freeze out, speed up or even reverse the free dynamics of any ensemble of quantum systems present in the scattering region. This time translation effect is universal, i.e., it is independent of the particular interaction between the scattering particles and the target systems, or the (possibly non-Hermitian) Hamiltonian governing the evolution of the latter. The protocols require careful preparation of the probes which are scattered, and success is heralded by projective measurements of these probes at the conclusion of the experiment. We fully characterize the possible time translations which we can effect on multiple target systems through a scattering protocol of fixed duration. The core results are: a) when the target is a single system, we can translate it backwards in time for an amount proportional to the experimental runtime; b) when n targets are present in the scattering region, we can make a single system evolve n times faster (backwards or forwards), at the cost of keeping the remaining systems stationary in time. For high n our protocols therefore allow one to map, in short experimental time, a system to the state it would have reached with a very long unperturbed evolution in either positive or negative time., Comment: 9+4 pages, 1 figure. v2: Improved readability without content changes. v3: Accepted for publication

Published
2019
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24. Hairy cell leukemia with an aggressive outcome: A case report with a review of the literature

Author

Adwaita Mashelkarm, Shirish Khatu, Prakash Dive, and S Sudhamani

Subjects
b cell leukemia, braf mutation, hairy cell, hairy cell leukemia, Medicine
Abstract

Hairy cell leukemia (HCL), an uncommon cancer affecting B-lymphocytes primarily in the bone marrow and spleen, is identified by abnormal projections on malignant B cells, which give the illness its name. This condition is less frequently observed in Asian populations compared with individuals from American and European backgrounds and tends to be diagnosed around the age of 55 years. The leading genetic association of this ailment is linked to the BRAFV600 mutation. Diagnosing HCL poses challenges due to its similarity to other conditions involving excessive lymphocyte growth. Here, we present a distinctive case of an aggressive disease course in a 46-year-old male.

Published
2023
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25. Characterisation of multi-level quantum coherence without ideal measurements

Author

Dive, Benjamin, Koukoulekidis, Nikolaos, Mousafeiris, Stefanos, and Mintert, Florian

Subjects
Quantum Physics
Abstract

Coherent superpositions are one of the hallmarks of quantum mechanics and are vital for any quantum mechanical device to outperform the classically achievable. Generically, superpositions are verified in interference experiments, but despite their longstanding central role we know very little about how to extract the number of coherently superposed amplitudes from a general interference pattern. A fundamental issue is that performing a phase-sensitive measurement is as challenging as creating a coherent superposition, so that assuming a perfectly implemented measurement for verification of quantum coherence is hard to justify. In order to overcome this issue, we construct a coherence certifier derived from simple statistical properties of an interference pattern, such that any imperfection in the measurement can never over-estimate the number of coherently superposed amplitudes. We numerically test how robust this measure is to under-estimating the coherence in the case of imperfect state preparation or measurement, and find it to be very resilient in both cases., Comment: Updated to published version

Published
2019
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26. Accelerating adiabatic protocols for entangling two qubits in circuit QED

Author

Petiziol, Francesco, Dive, Benjamin, Carretta, Stefano, Mannella, Riccardo, Mintert, Florian, and Wimberger, Sandro

Subjects
Quantum Physics
Abstract

We introduce a method to speed up adiabatic protocols for creating entanglement between two qubits dispersively coupled to a transmission line, while keeping fidelities high and maintaining robustness to control errors. The method takes genuinely adiabatic sweeps, ranging from a simple Landau-Zener drive to boundary cancellation methods and local adiabatic drivings, and adds fast oscillations to speed up the protocol while canceling unwanted transitions. We compare our protocol with existing adiabatic methods in a state-of-the-art parameter range and show substantial gains. Numerical simulations emphasize that this strategy is efficient also beyond the rotating-wave approximation and that the method is robust against random static biases in the control parameters and with respect to damping and decoherence effects., Comment: 15 pages, 9 figures

Published
2019
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27. Molecular interactions of PCSK9 with an inhibitory nanobody, CAP1 and HLA-C: Functional regulation of LDLR levels

Author

Fruchart Gaillard, Carole, Ouadda, Ali Ben Djoudi, Ciccone, Lidia, Girard, Emmanuelle, Mikaeeli, Sepideh, Evagelidis, Alexandra, Le Dévéhat, Maïlys, Susan-Resiga, Delia, Lajeunesse, Evelyne Cassar, Nozach, Hervé, Ramos, Oscar Henrique Pereira, Thureau, Aurélien, Legrand, Pierre, Prat, Annik, Dive, Vincent, and Seidah, Nabil G.

Published
2023
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29. Fast adiabatic evolution by oscillating initial Hamiltonians

Author

Petiziol, Francesco, Dive, Benjamin, Mintert, Florian, and Wimberger, Sandro

Subjects
Quantum Physics
Abstract

We propose a method to produce fast transitionless dynamics for finite-dimensional quantum systems without requiring additional Hamiltonian components not included in the initial control setup, remaining close to the true adiabatic path at all times. The strategy is based on the introduction of an effective counterdiabatic scheme: a correcting Hamiltonian is constructed which approximatively cancels nonadiabatic effects, inducing an evolution tracking the adiabatic states closely. This can be absorbed into the initial Hamiltonian by adding a fast oscillation in the control parameters. We show that a consistent speedup can be achieved without requiring strong control Hamiltonians, using it both as a stand-alone shortcut-to-adiabaticity and as a weak correcting field. A number of examples are treated, dealing with quantum state transfer in avoided-crossing problems and entanglement creation., Comment: 15 pages, 9 figures

Published
2018
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30. Prevalence of MRI lesions in men responding to a GP-led invitation for a prostate health check: a prospective cohort study

Author

Mieke Van Hemelrijck, Chris Brew-Graves, Neil McCartan, Louise Brown, Manuel Rodriguez-Justo, Aiman Haider, Alex Freeman, Mark Emberton, Kingshuk Pal, William Maynard, Aida Santaolalla, Nora Pashayan, Malcolm Mason, Tom Syer, Chris Parker, Caroline M Moore, Charlotte Bevan, Jayshireen Singh, Stuart Mackay-Thomas, Kate Walters, Mehul Mathukia, Charlotte Moss, David Sharpe, Kinnari Naik, Thomas Callender, Andrew Feber, Lee Berney, Anwar Padhani, Shonit Punwani, Hashim U Ahmed, Richard Kaplan, Teresa Marsden, Joanna Hadley, Steve Tuck, Saran Green, Ton Coolen, Elizabeth Isaac, Giorgio Brembilla, Douglas Kopcke, Francesco Giganti, Gerhardt Attard, Hina Pervez, Eric Aboagye, Elena Frangou, Fiona Gong, Louise C Brown, Aida Santa Olalla, Rosie Clow, Ged Corbett, Anna Wingate, Fatima Akbar, Suparna Thakali, Ashling Henderson, Dizem Tekin, Joey Clement, Harbit Sidhu, Teresita Beeston, Katerina Soteriou, Francesca Rawlins, Pirruntha Sivaharan, Savahnna Wolfe, Henry Tam, Heather Bholastewart, Sarp Keskin, Mariana Bertoncelli, Paul Boutros, Hayley Whitaker, Caroline Dive, Eytan Domany, Peter Parker, Andrew Prugia, Claire Chalmers-Watson, Alexander Gilkes, and Dr Hira

Subjects
Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Objective In men with a raised prostate-specific antigen (PSA), MRI increases the detection of clinically significant cancer and reduces overdiagnosis, with fewer biopsies. MRI as a screening tool has not been assessed independently of PSA in a formal screening study. We report a systematic community-based assessment of the prevalence of prostate MRI lesions in an age-selected population.Methods and analysis Men aged 50–75 were identified from participating general practice (GP) practices and randomly selected for invitation to a screening MRI and PSA. Men with a positive MRI or a raised PSA density (≥0.12 ng/mL2) were recommended for standard National Health Service (NHS) prostate cancer assessment.Results Eight GP practices sent invitations to 2096 men. 457 men (22%) responded and 303 completed both screening tests. Older white men were most likely to respond to the invitation, with black men having 20% of the acceptance rate of white men.One in six men (48/303 men, 16%) had a positive screening MRI, and an additional 1 in 20 men (16/303, 5%) had a raised PSA density alone. After NHS assessment, 29 men (9.6%) were diagnosed with clinically significant cancer and 3 men (1%) with clinically insignificant cancer.Two in three men with a positive MRI, and more than half of men with clinically significant disease had a PSA

Published
2023
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32. Mixed responses to targeted therapy driven by chromosomal instability through p53 dysfunction and genome doubling

Author

Hobor, S, Al Bakir, M, Hiley, C, Skrzypski, M, Frankell, A, Bakker, B, Watkins, T, Markovets, A, Dry, J, Brown, A, van der Aart, J, van den Bos, H, Spierings, D, Oukrif, D, Novelli, M, Chakrabarti, T, Rabinowitz, A, Ait Hassou, L, Litiere, S, Kerr, D, Tan, L, Kelly, G, Moore, D, Renshaw, M, Venkatesan, S, Hill, W, Huebner, A, Martinez-Ruiz, C, Black, J, Wu, W, Angelova, M, Mcgranahan, N, Downward, J, Chmielecki, J, Barrett, C, Litchfield, K, Chew, S, Blakely, C, de Bruin, E, Foijer, F, Vousden, K, Bivona, T, Lester, J, Bajaj, A, Nakas, A, Sodha-Ramdeen, A, Tufail, M, Scotland, M, Boyles, R, Rathinam, S, Wilson, C, Marrone, D, Dulloo, S, Fennell, D, Matharu, G, Shaw, J, Boleti, E, Cheyne, H, Khalil, M, Richardson, S, Cruickshank, T, Price, G, Kerr, K, Benafif, S, French, J, Gilbert, K, Naidu, B, Patel, A, Osman, A, Enstone, C, Langman, G, Shackleford, H, Djearaman, M, Kadiri, S, Middleton, G, Leek, A, Hodgkinson, J, Totton, N, Montero, A, Smith, E, Fontaine, E, Granato, F, Paiva-Correia, A, Novasio, J, Rammohan, K, Joseph, L, Bishop, P, Shah, R, Moss, S, Joshi, V, Crosbie, P, Brown, K, Carter, M, Chaturvedi, A, Oliveira, P, Lindsay, C, Blackhall, F, Krebs, M, Summers, Y, Clipson, A, Tugwood, J, Kerr, A, Rothwell, D, Dive, C, Aerts, H, Schwarz, R, Kaufmann, T, Wilson, G, Rosenthal, R, Van Loo, P, Birkbak, N, Szallasi, Z, Kisistok, J, Sokac, M, Salgado, R, Diossy, M, Demeulemeester, J, Bunkum, A, Dwornik, A, Magness, A, Rowan, A, Karamani, A, Toncheva, A, Chain, B, Castignani, C, Bailey, C, Abbosh, C, Puttick, C, Weeden, C, Lee, C, Richard, C, Naceur-Lombardelli, C, Pearce, D, Karagianni, D, Biswas, D, Levi, D, Larose Cadieux, E, Lim, E, Colliver, E, Nye, E, Galvez-Cancino, F, Gimeno-Valiente, F, Kassiotis, G, Stavrou, G, Mastrokalos, G, Lowe, H, Matos, I, Noorani, I, Goldman, J, Reading, J, Rane, J, Nicod, J, Hartley, J, Peggs, K, Enfield, K, Selvaraju, K, Thol, K, Ng, K, Chen, K, Dijkstra, K, Grigoriadis, K, Thakkar, K, Ensell, L, Shah, M, Litovchenko, M, Jamal-Hanjani, M, Werner Sunderland, M, Huska, M, Hill, M, Dietzen, M, Leung, M, Escudero, M, Tanic, M, Sivakumar, M, Chervova, O, Lucas, O, Pich, O, Al-Sawaf, O, Prymas, P, Hobson, P, Pawlik, P, Stone, R, Bentham, R, Vendramin, R, Saghafinia, S, Gamble, S, Veeriah, S, Ung, S, Quezada, S, Vanloo, S, Hessey, S, Ward, S, Harries, S, Boeing, S, Beck, S, Bola, S, Karasaki, T, Denner, T, Marafioti, T, Jones, T, Spanswick, V, Barbe, V, Lu, W, Liu, W, Wu, Y, Naito, Y, Ramsden, Z, Veiga, C, Royle, G, Collins-Fekete, C, Fraioli, F, Ashford, P, Forster, M, Lee, S, Borg, E, Falzon, M, Papadatos-Pastos, D, Wilson, J, Ahmad, T, Procter, A, Ahmed, A, Taylor, M, Nair, A, Lawrence, D, Patrini, D, Navani, N, Thakrar, R, Janes, S, Martinoni Hoogenboom, E, Monk, F, Holding, J, Choudhary, J, Bhakhri, K, Scarci, M, Gorman, P, Khiroya, R, Stephens, R, Wong, Y, Kaplar, Z, Bandula, S, Hackshaw, A, Hacker, A, Sharp, A, Smith, S, Kaur Dhanda, H, Pilotti, C, Leslie, R, Grapa, A, Zhang, H, Abduljabbar, K, Pan, X, Yuan, Y, Chuter, D, Mackenzie, M, Chee, S, Alzetani, A, Cave, J, Richards, J, De Sousa, P, Jordan, S, Rice, A, Raubenheimer, H, Bhayani, H, Ambrose, L, Devaraj, A, Chavan, H, Begum, S, Buderi, S, Kaniu, D, Malima, M, Booth, S, Nicholson, A, Fernandes, N, Shah, P, Proli, C, Hewish, M, Danson, S, Shackcloth, M, Robinson, L, Russell, P, Blyth, K, Kidd, A, Dick, C, Le Quesne, J, Kirk, A, Asif, M, Bilancia, R, Kostoulas, N, Thomas, M, Hynds, R, Kanu, N, Zaccaria, S, Gronroos, E, Swanton, C, Hobor S., Al Bakir M., Hiley C. T., Skrzypski M., Frankell A. M., Bakker B., Watkins T. B. K., Markovets A., Dry J. R., Brown A. P., van der Aart J., van den Bos H., Spierings D., Oukrif D., Novelli M., Chakrabarti T., Rabinowitz A. H., Ait Hassou L., Litiere S., Kerr D. L., Tan L., Kelly G., Moore D. A., Renshaw M. J., Venkatesan S., Hill W., Huebner A., Martinez-Ruiz C., Black J. R. M., Wu W., Angelova M., McGranahan N., Downward J., Chmielecki J., Barrett C., Litchfield K., Chew S. K., Blakely C. M., de Bruin E. C., Foijer F., Vousden K. H., Bivona T. G., Lester J. F., Bajaj A., Nakas A., Sodha-Ramdeen A., Tufail M., Scotland M., Boyles R., Rathinam S., Wilson C., Marrone D., Dulloo S., Fennell D. A., Matharu G., Shaw J. A., Boleti E., Cheyne H., Khalil M., Richardson S., Cruickshank T., Price G., Kerr K. M., Benafif S., French J., Gilbert K., Naidu B., Patel A. J., Osman A., Enstone C., Langman G., Shackleford H., Djearaman M., Kadiri S., Middleton G., Leek A., Hodgkinson J. D., Totton N., Montero A., Smith E., Fontaine E., Granato F., Paiva-Correia A., Novasio J., Rammohan K., Joseph L., Bishop P., Shah R., Moss S., Joshi V., Crosbie P. A. J., Brown K. D., Carter M., Chaturvedi A., Oliveira P., Lindsay C. R., Blackhall F. H., Krebs M. G., Summers Y., Clipson A., Tugwood J., Kerr A., Rothwell D. G., Dive C., Aerts H. J. W. L., Schwarz R. F., Kaufmann T. L., Wilson G. A., Rosenthal R., Van Loo P., Birkbak N. J., Szallasi Z., Kisistok J., Sokac M., Salgado R., Diossy M., Demeulemeester J., Bunkum A., Dwornik A., Magness A., Rowan A. J., Karamani A., Toncheva A., Chain B., Castignani C., Bailey C., Abbosh C., Puttick C., Weeden C. E., Lee C., Richard C., Naceur-Lombardelli C., Pearce D. R., Karagianni D., Biswas D., Levi D., Larose Cadieux E., Lim E. L., Colliver E., Nye E., Galvez-Cancino F., Gimeno-Valiente F., Kassiotis G., Stavrou G., Mastrokalos G. -T., Lowe H. L., Matos I. G., Noorani I., Goldman J., Reading J. L., Rane J. K., Nicod J., Hartley J. A., Peggs K. S., Enfield K. S. S., Selvaraju K., Thol K., Ng K. W., Chen K., Dijkstra K., Grigoriadis K., Thakkar K., Ensell L., Shah M., Litovchenko M., Jamal-Hanjani M., Werner Sunderland M., Huska M. R., Hill M. S., Dietzen M., Leung M. M., Escudero M., Tanic M., Sivakumar M., Chervova O., Lucas O., Pich O., Al-Sawaf O., Prymas P., Hobson P., Pawlik P., Stone R. K., Bentham R., Vendramin R., Saghafinia S., Gamble S., Veeriah S., Ung S. K. A., Quezada S. A., Vanloo S., Hessey S., Ward S., Harries S., Boeing S., Beck S., Bola S. K., Karasaki T., Denner T., Marafioti T., Jones T. P., Spanswick V., Barbe V., Lu W. -T., Liu W. K., Wu Y., Naito Y., Ramsden Z., Veiga C., Royle G., Collins-Fekete C. -A., Fraioli F., Ashford P., Forster M. D., Lee S. M., Borg E., Falzon M., Papadatos-Pastos D., Wilson J., Ahmad T., Procter A. J., Ahmed A., Taylor M. N., Nair A., Lawrence D., Patrini D., Navani N., Thakrar R. M., Janes S. M., Martinoni Hoogenboom E., Monk F., Holding J. W., Choudhary J., Bhakhri K., Scarci M., Gorman P., Khiroya R., Stephens R. C. M., Wong Y. N. S., Kaplar Z., Bandula S., Hackshaw A., Hacker A. -M., Sharp A., Smith S., Kaur Dhanda H., Pilotti C., Leslie R., Grapa A., Zhang H., AbdulJabbar K., Pan X., Yuan Y., Chuter D., MacKenzie M., Chee S., Alzetani A., Cave J., Richards J., Lim E., De Sousa P., Jordan S., Rice A., Raubenheimer H., Bhayani H., Ambrose L., Devaraj A., Chavan H., Begum S., Buderi S. I., Kaniu D., Malima M., Booth S., Nicholson A. G., Fernandes N., Shah P., Proli C., Hewish M., Danson S., Shackcloth M. J., Robinson L., Russell P., Blyth K. G., Kidd A., Dick C., Le Quesne J., Kirk A., Asif M., Bilancia R., Kostoulas N., Thomas M., Hynds R. E., Kanu N., Zaccaria S., Gronroos E., Swanton C., Hobor, S, Al Bakir, M, Hiley, C, Skrzypski, M, Frankell, A, Bakker, B, Watkins, T, Markovets, A, Dry, J, Brown, A, van der Aart, J, van den Bos, H, Spierings, D, Oukrif, D, Novelli, M, Chakrabarti, T, Rabinowitz, A, Ait Hassou, L, Litiere, S, Kerr, D, Tan, L, Kelly, G, Moore, D, Renshaw, M, Venkatesan, S, Hill, W, Huebner, A, Martinez-Ruiz, C, Black, J, Wu, W, Angelova, M, Mcgranahan, N, Downward, J, Chmielecki, J, Barrett, C, Litchfield, K, Chew, S, Blakely, C, de Bruin, E, Foijer, F, Vousden, K, Bivona, T, Lester, J, Bajaj, A, Nakas, A, Sodha-Ramdeen, A, Tufail, M, Scotland, M, Boyles, R, Rathinam, S, Wilson, C, Marrone, D, Dulloo, S, Fennell, D, Matharu, G, Shaw, J, Boleti, E, Cheyne, H, Khalil, M, Richardson, S, Cruickshank, T, Price, G, Kerr, K, Benafif, S, French, J, Gilbert, K, Naidu, B, Patel, A, Osman, A, Enstone, C, Langman, G, Shackleford, H, Djearaman, M, Kadiri, S, Middleton, G, Leek, A, Hodgkinson, J, Totton, N, Montero, A, Smith, E, Fontaine, E, Granato, F, Paiva-Correia, A, Novasio, J, Rammohan, K, Joseph, L, Bishop, P, Shah, R, Moss, S, Joshi, V, Crosbie, P, Brown, K, Carter, M, Chaturvedi, A, Oliveira, P, Lindsay, C, Blackhall, F, Krebs, M, Summers, Y, Clipson, A, Tugwood, J, Kerr, A, Rothwell, D, Dive, C, Aerts, H, Schwarz, R, Kaufmann, T, Wilson, G, Rosenthal, R, Van Loo, P, Birkbak, N, Szallasi, Z, Kisistok, J, Sokac, M, Salgado, R, Diossy, M, Demeulemeester, J, Bunkum, A, Dwornik, A, Magness, A, Rowan, A, Karamani, A, Toncheva, A, Chain, B, Castignani, C, Bailey, C, Abbosh, C, Puttick, C, Weeden, C, Lee, C, Richard, C, Naceur-Lombardelli, C, Pearce, D, Karagianni, D, Biswas, D, Levi, D, Larose Cadieux, E, Lim, E, Colliver, E, Nye, E, Galvez-Cancino, F, Gimeno-Valiente, F, Kassiotis, G, Stavrou, G, Mastrokalos, G, Lowe, H, Matos, I, Noorani, I, Goldman, J, Reading, J, Rane, J, Nicod, J, Hartley, J, Peggs, K, Enfield, K, Selvaraju, K, Thol, K, Ng, K, Chen, K, Dijkstra, K, Grigoriadis, K, Thakkar, K, Ensell, L, Shah, M, Litovchenko, M, Jamal-Hanjani, M, Werner Sunderland, M, Huska, M, Hill, M, Dietzen, M, Leung, M, Escudero, M, Tanic, M, Sivakumar, M, Chervova, O, Lucas, O, Pich, O, Al-Sawaf, O, Prymas, P, Hobson, P, Pawlik, P, Stone, R, Bentham, R, Vendramin, R, Saghafinia, S, Gamble, S, Veeriah, S, Ung, S, Quezada, S, Vanloo, S, Hessey, S, Ward, S, Harries, S, Boeing, S, Beck, S, Bola, S, Karasaki, T, Denner, T, Marafioti, T, Jones, T, Spanswick, V, Barbe, V, Lu, W, Liu, W, Wu, Y, Naito, Y, Ramsden, Z, Veiga, C, Royle, G, Collins-Fekete, C, Fraioli, F, Ashford, P, Forster, M, Lee, S, Borg, E, Falzon, M, Papadatos-Pastos, D, Wilson, J, Ahmad, T, Procter, A, Ahmed, A, Taylor, M, Nair, A, Lawrence, D, Patrini, D, Navani, N, Thakrar, R, Janes, S, Martinoni Hoogenboom, E, Monk, F, Holding, J, Choudhary, J, Bhakhri, K, Scarci, M, Gorman, P, Khiroya, R, Stephens, R, Wong, Y, Kaplar, Z, Bandula, S, Hackshaw, A, Hacker, A, Sharp, A, Smith, S, Kaur Dhanda, H, Pilotti, C, Leslie, R, Grapa, A, Zhang, H, Abduljabbar, K, Pan, X, Yuan, Y, Chuter, D, Mackenzie, M, Chee, S, Alzetani, A, Cave, J, Richards, J, De Sousa, P, Jordan, S, Rice, A, Raubenheimer, H, Bhayani, H, Ambrose, L, Devaraj, A, Chavan, H, Begum, S, Buderi, S, Kaniu, D, Malima, M, Booth, S, Nicholson, A, Fernandes, N, Shah, P, Proli, C, Hewish, M, Danson, S, Shackcloth, M, Robinson, L, Russell, P, Blyth, K, Kidd, A, Dick, C, Le Quesne, J, Kirk, A, Asif, M, Bilancia, R, Kostoulas, N, Thomas, M, Hynds, R, Kanu, N, Zaccaria, S, Gronroos, E, Swanton, C, Hobor S., Al Bakir M., Hiley C. T., Skrzypski M., Frankell A. M., Bakker B., Watkins T. B. K., Markovets A., Dry J. R., Brown A. P., van der Aart J., van den Bos H., Spierings D., Oukrif D., Novelli M., Chakrabarti T., Rabinowitz A. H., Ait Hassou L., Litiere S., Kerr D. L., Tan L., Kelly G., Moore D. A., Renshaw M. J., Venkatesan S., Hill W., Huebner A., Martinez-Ruiz C., Black J. R. M., Wu W., Angelova M., McGranahan N., Downward J., Chmielecki J., Barrett C., Litchfield K., Chew S. K., Blakely C. M., de Bruin E. C., Foijer F., Vousden K. H., Bivona T. G., Lester J. F., Bajaj A., Nakas A., Sodha-Ramdeen A., Tufail M., Scotland M., Boyles R., Rathinam S., Wilson C., Marrone D., Dulloo S., Fennell D. A., Matharu G., Shaw J. A., Boleti E., Cheyne H., Khalil M., Richardson S., Cruickshank T., Price G., Kerr K. M., Benafif S., French J., Gilbert K., Naidu B., Patel A. J., Osman A., Enstone C., Langman G., Shackleford H., Djearaman M., Kadiri S., Middleton G., Leek A., Hodgkinson J. D., Totton N., Montero A., Smith E., Fontaine E., Granato F., Paiva-Correia A., Novasio J., Rammohan K., Joseph L., Bishop P., Shah R., Moss S., Joshi V., Crosbie P. A. J., Brown K. D., Carter M., Chaturvedi A., Oliveira P., Lindsay C. R., Blackhall F. H., Krebs M. G., Summers Y., Clipson A., Tugwood J., Kerr A., Rothwell D. G., Dive C., Aerts H. J. W. L., Schwarz R. F., Kaufmann T. L., Wilson G. A., Rosenthal R., Van Loo P., Birkbak N. J., Szallasi Z., Kisistok J., Sokac M., Salgado R., Diossy M., Demeulemeester J., Bunkum A., Dwornik A., Magness A., Rowan A. J., Karamani A., Toncheva A., Chain B., Castignani C., Bailey C., Abbosh C., Puttick C., Weeden C. E., Lee C., Richard C., Naceur-Lombardelli C., Pearce D. R., Karagianni D., Biswas D., Levi D., Larose Cadieux E., Lim E. L., Colliver E., Nye E., Galvez-Cancino F., Gimeno-Valiente F., Kassiotis G., Stavrou G., Mastrokalos G. -T., Lowe H. L., Matos I. G., Noorani I., Goldman J., Reading J. L., Rane J. K., Nicod J., Hartley J. A., Peggs K. S., Enfield K. S. S., Selvaraju K., Thol K., Ng K. W., Chen K., Dijkstra K., Grigoriadis K., Thakkar K., Ensell L., Shah M., Litovchenko M., Jamal-Hanjani M., Werner Sunderland M., Huska M. R., Hill M. S., Dietzen M., Leung M. M., Escudero M., Tanic M., Sivakumar M., Chervova O., Lucas O., Pich O., Al-Sawaf O., Prymas P., Hobson P., Pawlik P., Stone R. K., Bentham R., Vendramin R., Saghafinia S., Gamble S., Veeriah S., Ung S. K. A., Quezada S. A., Vanloo S., Hessey S., Ward S., Harries S., Boeing S., Beck S., Bola S. K., Karasaki T., Denner T., Marafioti T., Jones T. P., Spanswick V., Barbe V., Lu W. -T., Liu W. K., Wu Y., Naito Y., Ramsden Z., Veiga C., Royle G., Collins-Fekete C. -A., Fraioli F., Ashford P., Forster M. D., Lee S. M., Borg E., Falzon M., Papadatos-Pastos D., Wilson J., Ahmad T., Procter A. J., Ahmed A., Taylor M. N., Nair A., Lawrence D., Patrini D., Navani N., Thakrar R. M., Janes S. M., Martinoni Hoogenboom E., Monk F., Holding J. W., Choudhary J., Bhakhri K., Scarci M., Gorman P., Khiroya R., Stephens R. C. M., Wong Y. N. S., Kaplar Z., Bandula S., Hackshaw A., Hacker A. -M., Sharp A., Smith S., Kaur Dhanda H., Pilotti C., Leslie R., Grapa A., Zhang H., AbdulJabbar K., Pan X., Yuan Y., Chuter D., MacKenzie M., Chee S., Alzetani A., Cave J., Richards J., Lim E., De Sousa P., Jordan S., Rice A., Raubenheimer H., Bhayani H., Ambrose L., Devaraj A., Chavan H., Begum S., Buderi S. I., Kaniu D., Malima M., Booth S., Nicholson A. G., Fernandes N., Shah P., Proli C., Hewish M., Danson S., Shackcloth M. J., Robinson L., Russell P., Blyth K. G., Kidd A., Dick C., Le Quesne J., Kirk A., Asif M., Bilancia R., Kostoulas N., Thomas M., Hynds R. E., Kanu N., Zaccaria S., Gronroos E., and Swanton C.

Abstract

The phenomenon of mixed/heterogenous treatment responses to cancer therapies within an individual patient presents a challenging clinical scenario. Furthermore, the molecular basis of mixed intra-patient tumor responses remains unclear. Here, we show that patients with metastatic lung adenocarcinoma harbouring co-mutations of EGFR and TP53, are more likely to have mixed intra-patient tumor responses to EGFR tyrosine kinase inhibition (TKI), compared to those with an EGFR mutation alone. The combined presence of whole genome doubling (WGD) and TP53 co-mutations leads to increased genome instability and genomic copy number aberrations in genes implicated in EGFR TKI resistance. Using mouse models and an in vitro isogenic p53-mutant model system, we provide evidence that WGD provides diverse routes to drug resistance by increasing the probability of acquiring copy-number gains or losses relative to non-WGD cells. These data provide a molecular basis for mixed tumor responses to targeted therapy, within an individual patient, with implications for therapeutic strategies.

Published
2024

33. The artificial intelligence-based model ANORAK improves histopathological grading of lung adenocarcinoma

Author

Pan, X, Abduljabbar, K, Coelho-Lima, J, Grapa, A, Zhang, H, Cheung, A, Baena, J, Karasaki, T, Wilson, C, Sereno, M, Veeriah, S, Aitken, S, Hackshaw, A, Nicholson, A, Jamal-Hanjani, M, Le Quesne, J, Janes, S, Hacker, A, Sharp, A, Smith, S, Dhanda, H, Chan, K, Pilotti, C, Leslie, R, Chuter, D, Mackenzie, M, Chee, S, Alzetani, A, Lim, E, De Sousa, P, Jordan, S, Rice, A, Raubenheimer, H, Bhayani, H, Ambrose, L, Devaraj, A, Chavan, H, Begum, S, Buderi, S, Kaniu, D, Malima, M, Booth, S, Fernandes, N, Shah, P, Proli, C, Hewish, M, Danson, S, Shackcloth, M, Robinson, L, Russell, P, Blyth, K, Kidd, A, Kirk, A, Asif, M, Bilancia, R, Kostoulas, N, Thomas, M, Dick, C, Lester, J, Bajaj, A, Nakas, A, Sodha-Ramdeen, A, Tufail, M, Scotland, M, Boyles, R, Rathinam, S, Fennell, D, Marrone, D, Dulloo, S, Matharu, G, Shaw, J, Riley, J, Primrose, L, Boleti, E, Cheyne, H, Khalil, M, Richardson, S, Cruickshank, T, Price, G, Kerr, K, Benafif, S, Papadatos-Pastos, D, Wilson, J, Ahmad, T, French, J, Gilbert, K, Naidu, B, Patel, A, Osman, A, Lacson, C, Langman, G, Shackleford, H, Djearaman, M, Kadiri, S, Middleton, G, Leek, A, Hodgkinson, J, Totten, N, Montero, A, Smith, E, Fontaine, E, Granato, F, Novasio, J, Rammohan, K, Joseph, L, Bishop, P, Shah, R, Moss, S, Joshi, V, Crosbie, P, Paiva-Correia, A, Chaturvedi, A, Priest, L, Oliveira, P, Gomes, F, Brown, K, Carter, M, Lindsay, C, Blackhall, F, Krebs, M, Summers, Y, Clipson, A, Tugwood, J, Kerr, A, Rothwell, D, Dive, C, Aerts, H, Schwarz, R, Kaufmann, T, Van Loo, P, Wilson, G, Rosenthal, R, Rowan, A, Bailey, C, Lee, C, Colliver, E, Enfield, K, Hill, M, Angelova, M, Pich, O, Leung, M, Frankell, A, Hiley, C, Zhai, H, Bakir, M, Birkbak, N, Lucas, O, Huebner, A, Puttick, C, Grigoriadis, K, Dietzen, M, Biswas, D, Athanasopoulou, F, Ward, S, Demeulemeester, J, Castignani, C, Cadieux, E, Kisistok, J, Sokac, M, Szallasi, Z, Diossy, M, Salgado, R, Stewart, A, Magness, A, Weeden, C, Levi, D, Gronroos, E, Noorani, I, Goldman, J, Escudero, M, Hobson, P, Vendramin, R, Boeing, S, Denner, T, Barbe, V, Lu, W, Hill, W, Naito, Y, Ramsden, Z, Kassiotis, G, Dwornik, A, Karamani, A, Chain, B, Pearce, D, Karagianni, D, Galvez-Cancino, F, Stavrou, G, Mastrokalos, G, Lowe, H, Matos, I, Reading, J, Hartley, J, Selvaraju, K, Chen, K, Ensell, L, Shah, M, Litovchenko, M, Chervova, O, Pawlik, P, Hynds, R, Gamble, S, Ung, S, Bola, S, Spanswick, V, Wu, Y, Al-Sawaf, O, Jones, T, Beck, S, Tanic, M, Marafioti, T, Borg, E, Falzon, M, Khiroya, R, Toncheva, A, Abbosh, C, Richard, C, Naceur-Lombardelli, C, Gimeno-Valiente, F, Thakkar, K, Sunderland, M, Sivakumar, M, Kanu, N, Prymas, P, Saghafinia, S, Vanloo, S, Lam, J, Liu, W, Bunkum, A, Hessey, S, Zaccaria, S, Martinez-Ruiz, C, Black, J, Thol, K, Bentham, R, Litchfield, K, Mcgranahan, N, Quezada, S, Forster, M, Lee, S, Herrero, J, Nye, E, Stone, R, Nicod, J, Rane, J, Peggs, K, Ng, K, Dijkstra, K, Huska, M, Hoogenboom, E, Monk, F, Holding, J, Choudhary, J, Bhakhri, K, Scarci, M, Gorman, P, Stephens, R, Wong, Y, Kaplar, Z, Bandula, S, Watkins, T, Veiga, C, Royle, G, Collins-Fekete, C, Fraioli, F, Ashford, P, Procter, A, Ahmed, A, Taylor, M, Nair, A, Lawrence, D, Patrini, D, Navani, N, Thakrar, R, Swanton, C, Yuan, Y, Moore, D, Pan X., AbdulJabbar K., Coelho-Lima J., Grapa A. -I., Zhang H., Cheung A. H. K., Baena J., Karasaki T., Wilson C. R., Sereno M., Veeriah S., Aitken S. J., Hackshaw A., Nicholson A. G., Jamal-Hanjani M., Le Quesne J., Janes S. M., Hacker A. -M., Sharp A., Smith S., Dhanda H. K., Chan K., Pilotti C., Leslie R., Chuter D., MacKenzie M., Chee S., Alzetani A., Lim E., De Sousa P., Jordan S., Rice A., Raubenheimer H., Bhayani H., Ambrose L., Devaraj A., Chavan H., Begum S., Buderi S. I., Kaniu D., Malima M., Booth S., Fernandes N., Shah P., Proli C., Hewish M., Danson S., Shackcloth M. J., Robinson L., Russell P., Blyth K. G., Kidd A., Kirk A., Asif M., Bilancia R., Kostoulas N., Thomas M., Dick C., Lester J. F., Bajaj A., Nakas A., Sodha-Ramdeen A., Tufail M., Scotland M., Boyles R., Rathinam S., Fennell D. A., Wilson C., Marrone D., Dulloo S., Matharu G., Shaw J. A., Riley J., Primrose L., Boleti E., Cheyne H., Khalil M., Richardson S., Cruickshank T., Price G., Kerr K. M., Benafif S., Papadatos-Pastos D., Wilson J., Ahmad T., French J., Gilbert K., Naidu B., Patel A. J., Osman A., Lacson C., Langman G., Shackleford H., Djearaman M., Kadiri S., Middleton G., Leek A., Hodgkinson J. D., Totten N., Montero A., Smith E., Fontaine E., Granato F., Novasio J., Rammohan K., Joseph L., Bishop P., Shah R., Moss S., Joshi V., Crosbie P., Paiva-Correia A., Chaturvedi A., Priest L., Oliveira P., Gomes F., Brown K., Carter M., Lindsay C. R., Blackhall F. H., Krebs M. G., Summers Y., Clipson A., Tugwood J., Kerr A., Rothwell D. G., Dive C., Aerts H. J. W. L., Schwarz R. F., Kaufmann T. L., Van Loo P., Wilson G. A., Rosenthal R., Rowan A., Bailey C., Lee C., Colliver E., Enfield K. S. S., Hill M. S., Angelova M., Pich O., Leung M., Frankell A. M., Hiley C. T., Lim E. L., Zhai H., Bakir M. A., Birkbak N. J., Lucas O., Huebner A., Puttick C., Grigoriadis K., Dietzen M., Biswas D., Athanasopoulou F., Ward S., Demeulemeester J., Castignani C., Cadieux E. L., Kisistok J., Sokac M., Szallasi Z., Diossy M., Salgado R., Stewart A., Magness A., Weeden C. E., Levi D., Gronroos E., Noorani I., Goldman J., Escudero M., Hobson P., Vendramin R., Boeing S., Denner T., Barbe V., Lu W. -T., Hill W., Naito Y., Ramsden Z., Kassiotis G., Dwornik A., Karamani A., Chain B., Pearce D. R., Karagianni D., Galvez-Cancino F., Stavrou G., Mastrokalos G., Lowe H. L., Matos I. G., Reading J. L., Hartley J. A., Selvaraju K., Chen K., Ensell L., Shah M., Litovchenko M., Chervova O., Pawlik P., Hynds R. E., Gamble S., Ung S. K. A., Bola S. K., Spanswick V., Wu Y., Al-Sawaf O., Jones T. P., Beck S., Tanic M., Marafioti T., Borg E., Falzon M., Khiroya R., Toncheva A., Abbosh C., Richard C., Naceur-Lombardelli C., Gimeno-Valiente F., Thakkar K., Sunderland M. W., Sivakumar M., Kanu N., Prymas P., Saghafinia S., Vanloo S., Lam J. M., Liu W. K., Bunkum A., Hessey S., Zaccaria S., Martinez-Ruiz C., Black J. R. M., Thol K., Bentham R., Litchfield K., McGranahan N., Quezada S. A., Forster M. D., Lee S. M., Herrero J., Nye E., Stone R. K., Nicod J., Rane J. K., Peggs K. S., Ng K. W., Dijkstra K., Huska M. R., Hoogenboom E. M., Monk F., Holding J. W., Choudhary J., Bhakhri K., Scarci M., Gorman P., Stephens R. C. M., Wong Y. N. S., Kaplar Z., Bandula S., Watkins T. B. K., Veiga C., Royle G., Collins-Fekete C. -A., Fraioli F., Ashford P., Procter A. J., Ahmed A., Taylor M. N., Nair A., Lawrence D., Patrini D., Navani N., Thakrar R. M., Swanton C., Yuan Y., Moore D. A., Pan, X, Abduljabbar, K, Coelho-Lima, J, Grapa, A, Zhang, H, Cheung, A, Baena, J, Karasaki, T, Wilson, C, Sereno, M, Veeriah, S, Aitken, S, Hackshaw, A, Nicholson, A, Jamal-Hanjani, M, Le Quesne, J, Janes, S, Hacker, A, Sharp, A, Smith, S, Dhanda, H, Chan, K, Pilotti, C, Leslie, R, Chuter, D, Mackenzie, M, Chee, S, Alzetani, A, Lim, E, De Sousa, P, Jordan, S, Rice, A, Raubenheimer, H, Bhayani, H, Ambrose, L, Devaraj, A, Chavan, H, Begum, S, Buderi, S, Kaniu, D, Malima, M, Booth, S, Fernandes, N, Shah, P, Proli, C, Hewish, M, Danson, S, Shackcloth, M, Robinson, L, Russell, P, Blyth, K, Kidd, A, Kirk, A, Asif, M, Bilancia, R, Kostoulas, N, Thomas, M, Dick, C, Lester, J, Bajaj, A, Nakas, A, Sodha-Ramdeen, A, Tufail, M, Scotland, M, Boyles, R, Rathinam, S, Fennell, D, Marrone, D, Dulloo, S, Matharu, G, Shaw, J, Riley, J, Primrose, L, Boleti, E, Cheyne, H, Khalil, M, Richardson, S, Cruickshank, T, Price, G, Kerr, K, Benafif, S, Papadatos-Pastos, D, Wilson, J, Ahmad, T, French, J, Gilbert, K, Naidu, B, Patel, A, Osman, A, Lacson, C, Langman, G, Shackleford, H, Djearaman, M, Kadiri, S, Middleton, G, Leek, A, Hodgkinson, J, Totten, N, Montero, A, Smith, E, Fontaine, E, Granato, F, Novasio, J, Rammohan, K, Joseph, L, Bishop, P, Shah, R, Moss, S, Joshi, V, Crosbie, P, Paiva-Correia, A, Chaturvedi, A, Priest, L, Oliveira, P, Gomes, F, Brown, K, Carter, M, Lindsay, C, Blackhall, F, Krebs, M, Summers, Y, Clipson, A, Tugwood, J, Kerr, A, Rothwell, D, Dive, C, Aerts, H, Schwarz, R, Kaufmann, T, Van Loo, P, Wilson, G, Rosenthal, R, Rowan, A, Bailey, C, Lee, C, Colliver, E, Enfield, K, Hill, M, Angelova, M, Pich, O, Leung, M, Frankell, A, Hiley, C, Zhai, H, Bakir, M, Birkbak, N, Lucas, O, Huebner, A, Puttick, C, Grigoriadis, K, Dietzen, M, Biswas, D, Athanasopoulou, F, Ward, S, Demeulemeester, J, Castignani, C, Cadieux, E, Kisistok, J, Sokac, M, Szallasi, Z, Diossy, M, Salgado, R, Stewart, A, Magness, A, Weeden, C, Levi, D, Gronroos, E, Noorani, I, Goldman, J, Escudero, M, Hobson, P, Vendramin, R, Boeing, S, Denner, T, Barbe, V, Lu, W, Hill, W, Naito, Y, Ramsden, Z, Kassiotis, G, Dwornik, A, Karamani, A, Chain, B, Pearce, D, Karagianni, D, Galvez-Cancino, F, Stavrou, G, Mastrokalos, G, Lowe, H, Matos, I, Reading, J, Hartley, J, Selvaraju, K, Chen, K, Ensell, L, Shah, M, Litovchenko, M, Chervova, O, Pawlik, P, Hynds, R, Gamble, S, Ung, S, Bola, S, Spanswick, V, Wu, Y, Al-Sawaf, O, Jones, T, Beck, S, Tanic, M, Marafioti, T, Borg, E, Falzon, M, Khiroya, R, Toncheva, A, Abbosh, C, Richard, C, Naceur-Lombardelli, C, Gimeno-Valiente, F, Thakkar, K, Sunderland, M, Sivakumar, M, Kanu, N, Prymas, P, Saghafinia, S, Vanloo, S, Lam, J, Liu, W, Bunkum, A, Hessey, S, Zaccaria, S, Martinez-Ruiz, C, Black, J, Thol, K, Bentham, R, Litchfield, K, Mcgranahan, N, Quezada, S, Forster, M, Lee, S, Herrero, J, Nye, E, Stone, R, Nicod, J, Rane, J, Peggs, K, Ng, K, Dijkstra, K, Huska, M, Hoogenboom, E, Monk, F, Holding, J, Choudhary, J, Bhakhri, K, Scarci, M, Gorman, P, Stephens, R, Wong, Y, Kaplar, Z, Bandula, S, Watkins, T, Veiga, C, Royle, G, Collins-Fekete, C, Fraioli, F, Ashford, P, Procter, A, Ahmed, A, Taylor, M, Nair, A, Lawrence, D, Patrini, D, Navani, N, Thakrar, R, Swanton, C, Yuan, Y, Moore, D, Pan X., AbdulJabbar K., Coelho-Lima J., Grapa A. -I., Zhang H., Cheung A. H. K., Baena J., Karasaki T., Wilson C. R., Sereno M., Veeriah S., Aitken S. J., Hackshaw A., Nicholson A. G., Jamal-Hanjani M., Le Quesne J., Janes S. M., Hacker A. -M., Sharp A., Smith S., Dhanda H. K., Chan K., Pilotti C., Leslie R., Chuter D., MacKenzie M., Chee S., Alzetani A., Lim E., De Sousa P., Jordan S., Rice A., Raubenheimer H., Bhayani H., Ambrose L., Devaraj A., Chavan H., Begum S., Buderi S. I., Kaniu D., Malima M., Booth S., Fernandes N., Shah P., Proli C., Hewish M., Danson S., Shackcloth M. J., Robinson L., Russell P., Blyth K. G., Kidd A., Kirk A., Asif M., Bilancia R., Kostoulas N., Thomas M., Dick C., Lester J. F., Bajaj A., Nakas A., Sodha-Ramdeen A., Tufail M., Scotland M., Boyles R., Rathinam S., Fennell D. A., Wilson C., Marrone D., Dulloo S., Matharu G., Shaw J. A., Riley J., Primrose L., Boleti E., Cheyne H., Khalil M., Richardson S., Cruickshank T., Price G., Kerr K. M., Benafif S., Papadatos-Pastos D., Wilson J., Ahmad T., French J., Gilbert K., Naidu B., Patel A. J., Osman A., Lacson C., Langman G., Shackleford H., Djearaman M., Kadiri S., Middleton G., Leek A., Hodgkinson J. D., Totten N., Montero A., Smith E., Fontaine E., Granato F., Novasio J., Rammohan K., Joseph L., Bishop P., Shah R., Moss S., Joshi V., Crosbie P., Paiva-Correia A., Chaturvedi A., Priest L., Oliveira P., Gomes F., Brown K., Carter M., Lindsay C. R., Blackhall F. H., Krebs M. G., Summers Y., Clipson A., Tugwood J., Kerr A., Rothwell D. G., Dive C., Aerts H. J. W. L., Schwarz R. F., Kaufmann T. L., Van Loo P., Wilson G. A., Rosenthal R., Rowan A., Bailey C., Lee C., Colliver E., Enfield K. S. S., Hill M. S., Angelova M., Pich O., Leung M., Frankell A. M., Hiley C. T., Lim E. L., Zhai H., Bakir M. A., Birkbak N. J., Lucas O., Huebner A., Puttick C., Grigoriadis K., Dietzen M., Biswas D., Athanasopoulou F., Ward S., Demeulemeester J., Castignani C., Cadieux E. L., Kisistok J., Sokac M., Szallasi Z., Diossy M., Salgado R., Stewart A., Magness A., Weeden C. E., Levi D., Gronroos E., Noorani I., Goldman J., Escudero M., Hobson P., Vendramin R., Boeing S., Denner T., Barbe V., Lu W. -T., Hill W., Naito Y., Ramsden Z., Kassiotis G., Dwornik A., Karamani A., Chain B., Pearce D. R., Karagianni D., Galvez-Cancino F., Stavrou G., Mastrokalos G., Lowe H. L., Matos I. G., Reading J. L., Hartley J. A., Selvaraju K., Chen K., Ensell L., Shah M., Litovchenko M., Chervova O., Pawlik P., Hynds R. E., Gamble S., Ung S. K. A., Bola S. K., Spanswick V., Wu Y., Al-Sawaf O., Jones T. P., Beck S., Tanic M., Marafioti T., Borg E., Falzon M., Khiroya R., Toncheva A., Abbosh C., Richard C., Naceur-Lombardelli C., Gimeno-Valiente F., Thakkar K., Sunderland M. W., Sivakumar M., Kanu N., Prymas P., Saghafinia S., Vanloo S., Lam J. M., Liu W. K., Bunkum A., Hessey S., Zaccaria S., Martinez-Ruiz C., Black J. R. M., Thol K., Bentham R., Litchfield K., McGranahan N., Quezada S. A., Forster M. D., Lee S. M., Herrero J., Nye E., Stone R. K., Nicod J., Rane J. K., Peggs K. S., Ng K. W., Dijkstra K., Huska M. R., Hoogenboom E. M., Monk F., Holding J. W., Choudhary J., Bhakhri K., Scarci M., Gorman P., Stephens R. C. M., Wong Y. N. S., Kaplar Z., Bandula S., Watkins T. B. K., Veiga C., Royle G., Collins-Fekete C. -A., Fraioli F., Ashford P., Procter A. J., Ahmed A., Taylor M. N., Nair A., Lawrence D., Patrini D., Navani N., Thakrar R. M., Swanton C., Yuan Y., and Moore D. A.

Abstract

The introduction of the International Association for the Study of Lung Cancer grading system has furthered interest in histopathological grading for risk stratification in lung adenocarcinoma. Complex morphology and high intratumoral heterogeneity present challenges to pathologists, prompting the development of artificial intelligence (AI) methods. Here we developed ANORAK (pyrAmid pooliNg crOss stReam Attention networK), encoding multiresolution inputs with an attention mechanism, to delineate growth patterns from hematoxylin and eosin-stained slides. In 1,372 lung adenocarcinomas across four independent cohorts, AI-based grading was prognostic of disease-free survival, and further assisted pathologists by consistently improving prognostication in stage I tumors. Tumors with discrepant patterns between AI and pathologists had notably higher intratumoral heterogeneity. Furthermore, ANORAK facilitates the morphological and spatial assessment of the acinar pattern, capturing acinus variations with pattern transition. Collectively, our AI method enabled the precision quantification and morphology investigation of growth patterns, reflecting intratumoral histological transitions in lung adenocarcinoma.

Published
2024

37. Serial monitoring of genomic alterations in circulating tumor cells of ER‐positive/HER2‐negative advanced breast cancer: feasibility of precision oncology biomarker detection

Author

Andi K. Cani, Emily M. Dolce, Elizabeth P. Darga, Kevin Hu, Chia‐Jen Liu, Jackie Pierce, Kieran Bradbury, Elaine Kilgour, Kimberly Aung, Gaia Schiavon, Danielle Carroll, T. Hedley Carr, Teresa Klinowska, Justin Lindemann, Gayle Marshall, Vicky Rowlands, Elizabeth A. Harrington, J. Carl Barrett, Nitharsan Sathiyayogan, Christopher Morrow, Valeria Sero, Anne C. Armstrong, Richard Baird, Erika Hamilton, Seock‐Ah Im, Komal Jhaveri, Manish R. Patel, Caroline Dive, Scott A. Tomlins, Aaron M. Udager, Daniel F. Hayes, and Costanza Paoletti

Subjects
circulating tumor cells, circulating tumor DNA, liquid biopsy, precision medicine, tumor evolution, tumor heterogeneity, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Nearly all estrogen receptor (ER)‐positive (POS) metastatic breast cancers become refractory to endocrine (ET) and other therapies, leading to lethal disease presumably due to evolving genomic alterations. Timely monitoring of the molecular events associated with response/progression by serial tissue biopsies is logistically difficult. Use of liquid biopsies, including circulating tumor cells (CTC) and circulating tumor DNA (ctDNA), might provide highly informative, yet easily obtainable, evidence for better precision oncology care. Although ctDNA profiling has been well investigated, the CTC precision oncology genomic landscape and the advantages it may offer over ctDNA in ER‐POS breast cancer remain largely unexplored. Whole‐blood (WB) specimens were collected at serial time points from patients with advanced ER‐POS/HER2‐negative (NEG) advanced breast cancer in a phase I trial of AZD9496, an oral selective ER degrader (SERD) ET. Individual CTC were isolated from WB using tandem CellSearch®/DEPArray™ technologies and genomically profiled by targeted single‐cell DNA next‐generation sequencing (scNGS). High‐quality CTC (n = 123) from 12 patients profiled by scNGS showed 100% concordance with ctDNA detection of driver estrogen receptor α (ESR1) mutations. We developed a novel CTC‐based framework for precision medicine actionability reporting (MI‐CTCseq) that incorporates novel features, such as clonal predominance and zygosity of targetable alterations, both unambiguously identifiable in CTC compared to ctDNA. Thus, we nominated opportunities for targeted therapies in 73% of patients, directed at alterations in phosphatidylinositol‐4,5‐bisphosphate 3‐kinase catalytic subunit alpha (PIK3CA), fibroblast growth factor receptor 2 (FGFR2), and KIT proto‐oncogene, receptor tyrosine kinase (KIT). Intrapatient, inter‐CTC genomic heterogeneity was observed, at times between time points, in subclonal alterations. Our analysis suggests that serial monitoring of the CTC genome is feasible and should enable real‐time tracking of tumor evolution during progression, permitting more combination precision medicine interventions.

Published
2022
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38. A conserved YAP/Notch/REST network controls the neuroendocrine cell fate in the lungs

Author

Yan Ting Shue, Alexandros P. Drainas, Nancy Yanzhe Li, Sarah M. Pearsall, Derrick Morgan, Nasa Sinnott-Armstrong, Susan Q. Hipkins, Garry L. Coles, Jing Shan Lim, Anthony E. Oro, Kathryn L. Simpson, Caroline Dive, and Julien Sage

Subjects
Science
Abstract

Notch signaling is known to control neuroendocrine fate in the lungs. Shue and colleagues further identify the REST and YAP transcriptional regulators as key components of the Notch signaling pathway in the control of the neuroendocrine cell fate in lung development, lung injury response, and small-cell lung cancer.

Published
2022
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39. Interrogating the precancerous evolution of pathway dysfunction in lung squamous cell carcinoma using XTABLE

Author

Matthew Roberts, Julia Ogden, AS Mukarram Hossain, Anshuman Chaturvedi, Alastair RW Kerr, Caroline Dive, Jennifer Ellen Beane, and Carlos Lopez-Garcia

Subjects
precancerous lesions, lung squamous cell carcinoma, transcriptomics, chromosomal instability, shiny app, Medicine, Science, Biology (General), QH301-705.5
Abstract

Lung squamous cell carcinoma (LUSC) is a type of lung cancer with a dismal prognosis that lacks adequate therapies and actionable targets. This disease is characterized by a sequence of low- and high-grade preinvasive stages with increasing probability of malignant progression. Increasing our knowledge about the biology of these premalignant lesions (PMLs) is necessary to design new methods of early detection and prevention, and to identify the molecular processes that are key for malignant progression. To facilitate this research, we have designed XTABLE (Exploring Transcriptomes of Bronchial Lesions), an open-source application that integrates the most extensive transcriptomic databases of PMLs published so far. With this tool, users can stratify samples using multiple parameters and interrogate PML biology in multiple manners, such as two- and multiple-group comparisons, interrogation of genes of interests, and transcriptional signatures. Using XTABLE, we have carried out a comparative study of the potential role of chromosomal instability scores as biomarkers of PML progression and mapped the onset of the most relevant LUSC pathways to the sequence of LUSC developmental stages. XTABLE will critically facilitate new research for the identification of early detection biomarkers and acquire a better understanding of the LUSC precancerous stages.

Published
2023
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41. Atezolizumab Treatment for Progressive Multifocal Leukoencephalopathy

Author

Lambert, Nicolas, Dauby, Solene, Dive, Dominique, Sadzot, Bernard, and Maquet, Pierre

Subjects
Drug therapy, Usage, Case studies, Atezolizumab -- Usage -- Case studies, Progressive multifocal leukoencephalopathy -- Drug therapy -- Case studies, Leukoencephalopathy, Progressive multifocal -- Drug therapy -- Case studies
Abstract

Progressive multifocal leukoencephalopathy (PML) is a devastating infectious disease of the brain that is caused by JC virus (JCV) in the context of cellular immunodeficiency. To date, no effective antiviral [...]

Published
2022

42. Immune biomarker evaluation of sequential tyrosine kinase inhibitor and nivolumab monotherapies in renal cell carcinoma: the phase I TRIBE trial

Author

Shohdy, K.S., primary, Pillai, M., additional, Abbas, K.S., additional, Allison, J., additional, Waddell, T., additional, Darlington, E., additional, Mohammad, S., additional, Hood, S., additional, Atkinson, S., additional, Simpson, K., additional, Morgan, D., additional, Nathan, P., additional, Kilgour, E., additional, Dive, C., additional, and Thistlethwaite, F., additional

Published
2024
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43. Atezolizumab Treatment for Progressive Multifocal Leukoencephalopathy

Author

Nicolas Lambert, Solène Dauby, Dominique Dive, Bernard Sadzot, and Pierre Maquet

Subjects
progressive multifocal leukoencephalopathy, immunotherapy, JC virus, immune reconstitution inflammatory syndrome, Belgium, viruses, Medicine, Infectious and parasitic diseases, RC109-216
Abstract

Atezolizumab successfully reinvigorated JC virus immunity in a patient in Belgium with progressive multifocal leukoencephalopathy, as demonstrated by clinical, virologic, and radiologic response to treatment. However, the treatment also resulted in immune reconstitution inflammatory syndrome and life-threatening immune-related adverse events. These conditions were treated with corticosteroids, leading to treatment resistance.

Published
2022
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44. Controlling open quantum systems

Author

Dive, Benjamin, Burgarth, Daniel, and Mintert, Florian

Subjects
530
Abstract

All physical quantum systems are in contact with the external world which is inevitably a source of noise. It is therefore necessary to take into account this dissipation when designing controls that accomplish useful tasks in quantum information processing. This thesis is on that overlap of open quantum systems and control theory; it looks at what dynamics can happen with the use of external driving, and how this driving can be chosen to accomplish a desired goal. The first result looks at how a given quantum dissipator can be manipulated, using coherent controls, into replicating the action of a different type of noise. This results in no-go theorems for how noise can be transformed based on its isotropy, with applications in simulating open systems. Another way of doing simulations is to use only unitary dynamics over the system and a finite dimensional ancilla, and it is proved that there always exists a dilation Hamiltonian that replicates the noisy dynamics continuously in time. This also highlights the fact that adding controls on noise can result in a different evolution than if the controls were done on the under- lying system-environment level. A conjecture is introduced and studied which states that both approaches are equivalent in the special case of the controls commuting with the Lindbladian. A way around this difficulty is to use a quantum system to compute in situ which controls are best for achieving a desired task on itself. This problem is studied in the context of reaching entangling gates on a quantum simulator in order to upgrade it into a quantum computer. The experimental cost of doing so is found to be polynomial in the number of qubits in simulations. The same underlying principle is also used to find error correcting codes tailored to the dissipation in a system.

Published
2018
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45. In situ upgrade of quantum simulators to universal computers

Author

Dive, Benjamin, Pitchford, Alexander, Mintert, Florian, and Burgarth, Daniel

Subjects
Quantum Physics
Abstract

Quantum simulators, machines that can replicate the dynamics of quantum systems, are being built as useful devices and are seen as a stepping stone to universal quantum computers. A key difference between the two is that computers have the ability to perform the logic gates that make up algorithms. We propose a method for learning how to construct these gates efficiently by using the simulator to perform optimal control on itself. This bypasses two major problems of purely classical approaches to the control problem: the need to have an accurate model of the system, and a classical computer more powerful than the quantum one to carry out the required simulations. Strong evidence that the scheme scales polynomially in the number of qubits, for systems of up to 9 qubits with Ising interactions, is presented from numerical simulations carried out in different topologies. This suggests that this in situ approach is a practical way of upgrading quantum simulators to computers.

Published
2017
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47. Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma

Author

Abbosh, Chris, Shiu, Kai-Keen, Bridgewater, John, Hochhauser, Daniel, Forster, Martin, Lee, Siow-Ming, Ahmad, Tanya, Papadatos-Pastos, Dionysis, Janes, Sam, Van Loo, Peter, Enfield, Katey, McGranahan, Nicholas, Huebner, Ariana, Beck, Stephan, Parker, Peter, Walczak, Henning, Enver, Tariq, Hynds, Rob, Sinclair, Ron, Lok, Chi-wah, Rhodes, Zoe, Moore, David, Khiroya, Reena, Trevisan, Giorgia, Ellery, Peter, Linch, Mark, Brandner, Sebastian, Hiley, Crispin, Veeriah, Selvaraju, Razaq, Maryam, Shaw, Heather, Attard, Gert, Akther, Mita Afroza, Naceur-Lombardelli, Cristina, Manzano, Lizi, Al-Bakir, Maise, Summan, Simranpreet, Kanu, Nnenna, Ward, Sophie, Asghar, Uzma, Lim, Emilia, Gishen, Faye, Tookman, Adrian, Stone, Paddy, Stirling, Caroline, Hunter, Nikki, Vaughan, Sarah, Mangwende, Mary, Spain, Lavinia, Yan, Haixi, Shum, Ben, Carlyle, Eleanor, Yousaf, Nadia, Popat, Sanjay, Curtis, Olivia, Stamp, Gordon, Toncheva, Antonia, Nye, Emma, Murra, Aida, Korteweg, Justine, Josephs, Debra, Chandra, Ashish, Spicer, James, Stewart, Ruby, Iredale, Lara-Rose, Mackay, Tina, Deakin, Ben, Enting, Debra, Rudman, Sarah, Ghosh, Sharmistha, Karapagniotou, Lena, Pintus, Elias, Tutt, Andrew, Howlett, Sarah, Michalarea, Vasiliki, Brenton, James, Caldas, Carlos, Fitzgerald, Rebecca, Jimenez-Linan, Merche, Provenzano, Elena, Cluroe, Alison, Stewart, Grant, Watts, Colin, Gilbertson, Richard, McDermott, Ultan, Tavare, Simon, Beddowes, Emma, Roxburgh, Patricia, Biankin, Andrew, Chalmers, Anthony, Fraser, Sioban, Oien, Karin, Kidd, Andrew, Blyth, Kevin, Krebs, Matt, Blackhall, Fiona, Summers, Yvonne, Dive, Caroline, Marais, Richard, Gomes, Fabio, Carter, Mat, Dransfield, Jo, Le Quesne, John, Fennell, Dean, Shaw, Jacqui, Naidu, Babu, Baijal, Shobhit, Tanchel, Bruce, Langman, Gerald, Robinson, Andrew, Collard, Martin, Cockcroft, Peter, Ferris, Charlotte, Bancroft, Hollie, Kerr, Amy, Middleton, Gary, Webb, Joanne, Kadiri, Salma, Colloby, Peter, Olisemeke, Bernard, Wilson, Rodelaine, Tomlinson, Ian, Jogai, Sanjay, Ottensmeier, Christian, Harrison, David, Loda, Massimo, Flanagan, Adrienne, McKenzie, Mairead, Hackshaw, Allan, Ledermann, Jonathan, Chan, Kitty, Sharp, Abby, Farrelly, Laura, Bridger, Hayley, Challacombe, Ben, Chowdhury, Simon, Drake, William, Fernando, Archana, Harrison-Phipps, Karen, Hazell, Steve, Hill, Peter, Horsfield, Catherine, O'Brien, Tim, Olsburgh, Jonathon, Polson, Alexander, Varia, Mary, Verma, Hema, Au, Lewis, Hatipoglu, Emine, Robert de Massy, Marc, Litchfield, Kevin, Beattie, Gordon, Rowan, Andrew, Schnidrig, Desiree, Thompson, Rachael, Byrne, Fiona, Horswell, Stuart, Fotiadis, Nicos, Nicol, David, Shepherd, Scott T.C., Fendler, Annika, Mason, Robert, Del Rosario, Lyra, Edmonds, Kim, Lingard, Karla, Sarker, Sarah, Attig, Jan, Joshi, Kroopa, Uddin, Imran, Becker, Pablo D., Sunderland, Mariana Werner, Akarca, Ayse, Puccio, Ignazio, Yang, William W., Lund, Tom, Dhillon, Kim, Vasquez, Marcos Duran, Ghorani, Ehsan, Xu, Hang, Spencer, Charlotte, López, José I., Green, Anna, Mahadeva, Ula, Borg, Elaine, Mitchison, Miriam, Moore, David A., Proctor, Ian, Falzon, Mary, Pickering, Lisa, Furness, Andrew J.S., Reading, James L., Salgado, Roberto, Marafioti, Teresa, Jamal-Hanjani, Mariam, Kassiotis, George, Chain, Benny, Larkin, James, Swanton, Charles, Quezada, Sergio A., and Turajlic, Samra

Published
2021
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48. Liquid Biopsy for Advanced NSCLC: A Consensus Statement From the International Association for the Study of Lung Cancer

Author

Rolfo, Christian, Mack, Philip, Scagliotti, Giorgio V., Aggarwal, Charu, Arcila, Maria E., Barlesi, Fabrice, Bivona, Trever, Diehn, Maximilian, Dive, Caroline, Dziadziuszko, Rafal, Leighl, Natasha, Malapelle, Umberto, Mok, Tony, Peled, Nir, Raez, Luis E., Sequist, Lecia, Sholl, Lynette, Swanton, Charles, Abbosh, Chris, Tan, Daniel, Wakelee, Heather, Wistuba, Ignacio, Bunn, Rebecca, Freeman-Daily, Janet, Wynes, Murry, Belani, Chandra, Mitsudomi, Tetsuya, and Gandara, David

Published
2021
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50. Isotropy and control of dissipative quantum dynamics

Author

Dive, Benjamin, Burgarth, Daniel, and Mintert, Florian

Subjects
Quantum Physics
Abstract

We investigate the problem of what evolutions an open quantum system described by a time-local Master equation can undergo with universal coherent controls. A series of conditions are given which exclude channels from being reachable by any unitary controls, assuming that the coupling to the environment is not being modified. These conditions primarily arise by defining decay rates for the generator of the dynamics of the open system, and then showing that controlling the system can only make these rates more isotropic. This forms a series of constraints on the shape and non-unitality of allowed evolutions, as well as an expression for the time required to reach a given goal. We give numerical examples of the usefulness of these criteria, and explore some similarities they have with quantum thermodynamics.

Published
2015
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