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1. Ionization potential of radium monofluoride

Author

Wilkins, S. G., Perrett, H. A., Udrescu, S. M., Kyuberis, A. A., Pašteka, L. F., Au, M., Belošević, I., Berger, R., Binnersley, C. L., Bissell, M. L., Borschevsky, A., Breier, A. A., Brinson, A. J., Chrysalidis, K., Cocolios, T. E., Cooper, B. S., de Groote, R. P., Dorne, A., Eliav, E., Field, R. W., Flanagan, K. T., Franchoo, S., Ruiz, R. F. Garcia, Gaul, K., Geldhof, S., Giesen, T. F., Gustafsson, F. P., Hanstorp, D., Heinke, R., Koszorús, Á., Kujanpää, S., Lalanne, L., Neyens, G., Nichols, M., Reilly, J. R., Ricketts, C. M., Rothe, S., Sunaga, A., Borne, B. van den, Vernon, A. R., Wang, Q., Wessolek, J., Wienholtz, F., Yang, X. F., Zhou, Y., and Zülch, C.

Subjects
Physics - Atomic Physics, Nuclear Experiment, Physics - Chemical Physics, Physics - Computational Physics
Abstract

The ionization potential (IP) of radium monofluoride (RaF) was measured to be 4.969(2)[10] eV, revealing a relativistic enhancement in the series of alkaline earth monofluorides. The results are in agreement with a relativistic coupled-cluster prediction of 4.969[7] eV, incorporating up to quantum electrodynamics corrections. Using the same computational methodology, an improved calculation for the dissociation energy ($D_{0}$) of 5.54[5] eV is presented. This confirms that radium monofluoride joins the small group of diatomic molecules for which $D_{0}>\mathrm{IP}$, paving the way for precision control and interrogation of its Rydberg states.

Published
2024

2. Electromagnetic properties of indium isotopes illuminate the doubly magic character of 100Sn

Author

Karthein, J., Ricketts, C. M., Garcia Ruiz, R. F., Billowes, J., Binnersley, C. L., Cocolios, T. E., Dobaczewski, J., Farooq-Smith, G. J., Flanagan, K. T., Georgiev, G., Gins, W., de Groote, R. P., Gustafsson, F. P., Holt, J. D., Kanellakopoulos, A., Koszorús, Á., Leimbach, D., Lynch, K. M., Miyagi, T., Nazarewicz, W., Neyens, G., Reinhard, P.-G., Sahoo, B. K., Vernon, A. R., Wilkins, S. G., Yang, X. F., and Yordanov, D. T.

Published
2024
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3. Electromagnetic Properties of Indium Isotopes Elucidate the Doubly Magic Character of $^{100}$Sn

Author

Karthein, J., Ricketts, C. M., Ruiz, R. F. Garcia, Billowes, J., Binnersley, C. L., Cocolios, T. E., Dobaczewski, J., Farooq-Smith, G. J., Flanagan, K. T., Georgiev, G., Gins, W., de Groote, R. P., Gustafsson, F. P., Holt, J. D., Kanellakopoulos, A., Koszorús, Á., Leimbach, D., Lynch, K. M., Miyagi, T., Nazarewicz, W., Neyens, G., Reinhard, P. -G., Sahoo, B. K., Vernon, A. R., Wilkins, S. G., Yang, X. F., and Yordanov, D. T.

Subjects
Nuclear Experiment, Nuclear Theory, Physics - Atomic Physics
Abstract

Our understanding of nuclear properties in the vicinity of $^{100}$Sn, suggested to be the heaviest doubly magic nucleus with equal numbers of protons (Z=50) and neutrons (N=50), has been a long-standing challenge for experimental and theoretical nuclear physics. Contradictory experimental evidence exists on the role of nuclear collectivity in this region of the nuclear chart. Using precision laser spectroscopy, we measured the ground-state electromagnetic moments of indium (Z=49) isotopes approaching the N=50 neutron number down to 101In, and nuclear charge radii of 101-131In spanning almost the complete range between the two major neutron closed-shells at N=50 and N=82. Our results for both nuclear charge radii and quadrupole moments reveal striking parabolic trends as a function of the neutron number, with a clear reduction toward these two neutron closed-shells, thus supporting a doubly magic character of $^{100}$Sn. Two complementary nuclear many-body frameworks, density functional theory and ab initio methods, elucidate our findings. A detailed comparison with our experimental results exposes deficiencies of nuclear models, establishing a benchmark for future theoretical developments., Comment: 12 pages, 6 figures, 4 tables; text-identical to Nature Physics article (2024)

Published
2023
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4. Isotope Shifts of Radium Monofluoride Molecules

Author

Udrescu, S. M., Brinson, A. J., Ruiz, R. F. Garcia, Gaul, K., Berger, R., Billowes, J., Binnersley, C. L., Bissell, M. L., Breier, A. A., Chrysalidis, K., Cocolios, T. E., Cooper, B. S., Flanagan, K. T., Giesen, T. F., de Groote, R. P., Franchoo, S., Gustafsson, F. P., Isaev, T. A., Koszorus, A., Neyens, G., Perrett, H. A., Ricketts, C. M., Rothe, S., Vernon, A. R., Wendt, K. D. A., Wienholtz, F., Wilkins, S. G., and Yang, X. F.

Subjects
Nuclear Experiment, Nuclear Theory, Physics - Atomic Physics
Abstract

Isotope shifts of $^{223-226,228}$Ra$^{19}$F were measured for different vibrational levels in the electronic transition $A^{2}{}{\Pi}_{1/2}\leftarrow X^{2}{}{\Sigma}^{+}$. The observed isotope shifts demonstrate the particularly high sensitivity of radium monofluoride to nuclear size effects, offering a stringent test of models describing the electronic density within the radium nucleus. Ab initio quantum chemical calculations are in excellent agreement with experimental observations. These results highlight some of the unique opportunities that short-lived molecules could offer in nuclear structure and in fundamental symmetry studies., Comment: The paper was accepted for publication as a Letter in Physical Review Letters

Published
2021
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5. Charge radii of exotic potassium isotopes challenge nuclear theory and the magic character of $N = 32$

Author

Koszorús, Á., Yang, X. F., Jiang, W. G., Novario, S. J., Bai, S. W., Billowes, J., Binnersley, C. L., Bissell, M. L., Cocolios, T. E., Cooper, B. S., de Groote, R. P., Ekström, A., Flanagan, K. T., Forssén, C., Franchoo, S., Ruiz, R. F. Garcia, Gustafsson, F. P., Hagen, G., Jansen, G. R., Kanellakopoulos, A., Kortelainen, M., Nazarewicz, W., Neyens, G., Papenbrock, T., Reinhard, P. -G., Sahoo, B. K., Ricketts, C. M., Vernon, A. R., and Wilkins, S. G.

Subjects
Nuclear Experiment, Nuclear Theory, Physics - Atomic Physics
Abstract

Nuclear charge radii are sensitive probes of different aspects of the nucleon-nucleon interaction and the bulk properties of nuclear matter; thus, they provide a stringent test and challenge for nuclear theory. The calcium region has been of particular interest, as experimental evidence has suggested a new magic number at $N = 32$ [1-3], while the unexpectedly large increases in the charge radii [4,5] open new questions about the evolution of nuclear size in neutron-rich systems. By combining the collinear resonance ionization spectroscopy method with $\beta$-decay detection, we were able to extend the charge radii measurement of potassium ($Z =19$) isotopes up to the exotic $^{52}$K ($t_{1/2}$ = 110 ms), produced in minute quantities. Our work provides the first charge radii measurement beyond $N = 32$ in the region, revealing no signature of the magic character at this neutron number. The results are interpreted with two state-of-the-art nuclear theories. For the first time, a long sequence of isotopes could be calculated with coupled-cluster calculations based on newly developed nuclear interactions. The strong increase in the charge radii beyond $N = 28$ is not well captured by these calculations, but is well reproduced by Fayans nuclear density functional theory, which, however, overestimates the odd-even staggering effect. These findings highlight our limited understanding on the nuclear size of neutron-rich systems, and expose pressing problems that are present in some of the best current models of nuclear theory., Comment: submitted version; revision accepted in Nature Physics

Published
2020
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6. Laser spectroscopy of indium Rydberg atom bunches by electric field ionization

Author

Vernon, A. R., Ricketts, C. M., Billowes, J., Cocolios, T. E., Cooper, B. S., Flanagan, K. T., Ruiz, R. F. Garcia, Gustafsson, F. P., Neyens, G., Perrett, H. A., Sahoo, B. K., Wang, Q., Waso, F. J., and Yang, X. F.

Subjects
Physics - Atomic Physics
Abstract

This work reports on the application of a novel electric field-ionization setup for high-resolution laser spectroscopy measurements on bunched fast atomic beams in a collinear geometry. In combination with multi-step resonant excitation to Rydberg states using pulsed lasers, the field ionization technique demonstrates increased sensitivity for isotope separation and measurement of atomic parameters over non-resonant laser ionization methods. The setup was tested at the Collinear Resonance Ionization Spectroscopy experiment at ISOLDE-CERN to perform high-resolution measurements of transitions in the indium atom from the 5s$^2$5d~$^2$D$_{5/2}$ and 5s$^2$5d~$^2$D$_{3/2}$ states to 5s$^2$($n$)p~$^2$P and 5s$^2$($n$)f~$^2$F Rydberg states, up to a principal quantum number of $n$ = 72. The extracted Rydberg level energies were used to re-evaluate the ionization potential of the indium atom to be 46670.1055(21) cm$^{-1}$. The nuclear magnetic dipole and nuclear electric quadrupole hyperfine structure constants and level isotope shifts of the 5s$^2$5d~$^2$D$_{5/2}$ and 5s$^2$5d~$^2$D$_{3/2}$ states were determined for $^{113,115}$In. The results are compared to calculations using relativistic coupled-cluster theory. A good agreement is found with the ionization potential and isotope shifts, while disagreement of hyperfine structure constants indicates an increased importance of electron correlations in these excited atomic states. With the aim of further increasing the detection sensitivity for measurements on exotic isotopes, a systematic study of the field-ionization arrangement implemented in the work was performed and an improved design was simulated and is presented. The improved design offers increased background suppression independent of the distance from field ionization to ion detection.

Published
2020
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7. Analytic Response Relativistic Coupled-Cluster Theory: The first application to indium isotope shifts

Author

Sahoo, B. K., Vernon, A. R., Ruiz, R. F. Garcia, Binnersley, C. L., Billowes, J., Bissell, M. L., Cocolios, T. E., Farooq-Smith, G. J., Flanagan, K. T., Gins, W., de Groote, R. P., Koszorus, A., Neyens, G., Lynch, K. M., Parnefjord-Gustafsson, F., Ricketts, C. M., Wendt, K. D. A, Wilkins, S. G., and Yang, X. F.

Subjects
Physics - Atomic Physics, Nuclear Experiment
Abstract

With increasing demand for accurate calculation of isotope shifts of atomic systems for fundamental and nuclear structure research, an analytic energy derivative approach is presented in the relativistic coupled-cluster theory framework to determine the atomic field shift and mass shift factors. This approach allows the determination of expectation values of atomic operators, overcoming fundamental problems that are present in existing atomic physics methods, i.e. it satisfies the Hellmann-Feynman theorem, does not involve any non-terminating series, and is free from choice of any perturbative parameter. As a proof of concept, the developed analytic response relativistic coupled-cluster theory has been applied to determine mass shift and field shift factors for different atomic states of indium. High-precision isotope-shift measurements of $^{104-127}$In were performed in the 246.8-nm (5p $^2$P$_{3/2}$ $\rightarrow$ 9s $^2$S$_{1/2}$) and 246.0-nm (5p $^2$P$_{1/2}$ $\rightarrow$ 8s $^2$S$_{1/2}$) transitions to test our theoretical results. An excellent agreement between the theoretical and measured values is found, which is known to be challenging in multi-electron atoms. The calculated atomic factors allowed an accurate determination of the nuclear charge radii of the ground and isomeric states of the $^{104-127}$In isotopes, providing an isotone-independent comparison of the absolute charge radii., Comment: Submitted

Published
2019
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8. Spectroscopy of short-lived radioactive molecules: A sensitive laboratory for new physics

Author

Ruiz, R. F. Garcia, Berger, R., Billowes, J., Binnersley, C. L., Bissell, M. L., Breier, A. A., Brinson, A. J., Chrysalidis, K., Cocolios, T., Cooper, B., Flanagan, K. T., Giesen, T. F., de Groote, R. P., Franchoo, S., Gustafsson, F. P., Isaev, T. A., Koszorus, A., Neyens, G., Perrett, H. A., Ricketts, C. M., Rothe, S., Schweikhard, L., Vernon, A. R., Wendt, K. D. A., Wienholtz, F., Wilkins, S. G., and Yang, X. F.

Subjects
Nuclear Theory, High Energy Physics - Phenomenology, High Energy Physics - Theory, Nuclear Experiment
Abstract

The study of molecular systems provides exceptional opportunities for the exploration of the fundamental laws of nature and for the search for physics beyond the Standard Model of particle physics. Measurements of molecules composed of naturally occurring nuclei have provided the most stringent upper bounds to the electron electric dipole moment to date, and offer a route to investigate the violation of fundamental symmetries with unprecedented sensitivity. Radioactive molecules - where one or more of their atoms possesses a radioactive nucleus - can contain heavy and deformed nuclei, offering superior sensitivity for EDM measurements as well as for other symmetry-violating effects. Radium monofluoride, RaF, is of particular interest as it is predicted to have an appropriate electronic structure for direct laser cooling. Furthermore, some Ra isotopes are known to be octupole deformed, thereby resulting in a large enhancement of their symmetry-violating nuclear moments. Until now,however, no experimental measurements of RaF have been performed, and their study is impeded by major experimental challenges, as no stable isotopes of radium exist. Here, we present a novel experimental approach to study short-lived radioactive molecules using the highly sensitive collinear resonance ionisation method. With this technique we have measured, for the first time, the energetically low-lying electronic states for each of the isotopically pure RaF molecules at the ISOLDE-CERN. Our results provide strong evidence of the existence of a suitable laser-cooling scheme for these molecules and constitute a pivotal step towards high-precision studies in these systems. Our findings open up new opportunities in the synthesis, manipulation and study of short-lived radioactive molecules, which will have a direct impact in many-body physics, astrophysics, nuclear structure, and fundamental physics research., Comment: Submitted

Published
2019
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9. Charge radii of exotic potassium isotopes challenge nuclear theory and the magic character of N = 32

Author

Koszorús, Á., Yang, X. F., Jiang, W. G., Novario, S. J., Bai, S. W., Billowes, J., Binnersley, C. L., Bissell, M. L., Cocolios, T. E., Cooper, B. S., de Groote, R. P., Ekström, A., Flanagan, K. T., Forssén, C., Franchoo, S., Ruiz, R. F. Garcia, Gustafsson, F. P., Hagen, G., Jansen, G. R., Kanellakopoulos, A., Kortelainen, M., Nazarewicz, W., Neyens, G., Papenbrock, T., Reinhard, P.-G., Ricketts, C. M., Sahoo, B. K., Vernon, A. R., and Wilkins, S. G.

Published
2021
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11. Spectroscopy of short-lived radioactive molecules

Author

Garcia Ruiz, R. F., Berger, R., Billowes, J., Binnersley, C. L., Bissell, M. L., Breier, A. A., Brinson, A. J., Chrysalidis, K., Cocolios, T. E., Cooper, B. S., Flanagan, K. T., Giesen, T. F., de Groote, R. P., Franchoo, S., Gustafsson, F. P., Isaev, T. A., Koszorús, Á., Neyens, G., Perrett, H. A., Ricketts, C. M., Rothe, S., Schweikhard, L., Vernon, A. R., Wendt, K. D. A., Wienholtz, F., Wilkins, S. G., and Yang, X. F.

Published
2020
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13. The reactions of the molecular nitrogen doubly charged ion with neutral molecules of relevance to planetary ionospheres

Author

Ricketts, C. L.

Subjects
539.7
Abstract

Diatomic dications (e.g. C02+) have been known to exist for several decades and are believed to be important components of energised media. Molecular dications possess significant internal energy due to the Coulombic repulsion of their two positive charges, meaning that many possible reaction channels are available to dications in a collision with a neutral molecule. Modellers have recently predicted that N22+ is present in the ionosphere of Earth and Titan as well as the dications C > 22+ and 02+ in the ionosphere of Earth and CC > 22+ in the ionosphere of Mars. These recent predictions, of dications in planetary ionospheres, imply that dications, and processes involving dication-neutral collisions, may have more significance than previously thought in the upper atmospheres of planets. Therefore this thesis describes a study of the reactions between N2 dications and neutrals, potentially of relevance to the ionosphere of Earth and Titan. A position sensitive coincidence (PSCO) time-of flight (TOF) mass spectrometer is used to probe the reactivity, energetics and dynamics of the bimolecular reactions of N22 . Dication-neutrals reactions often result in a pair of singly charged ions. The PSCO experiment is used to collect these pairs of singly-charged ions in coincidence. From the position-sensitive data we extract the velocity vectors of the product ions, and if the reaction of interest involves the formation of a third, undetected, neutral species, its velocity can be determined via conservation of momentum. The electron transfer reactions between dications and neutrals have been well rationalized 2+ previously, so only the electron transfer reactions of N2 with Ne and NO are discussed in this thesis. This thesis concentrates on probing the less well rationalized, bond- forming reactions between dications and neutrals. The bond-forming reactions of N22+ with O2, CO2, H2O, C2H2, CH4, H2 and Ar have been investigated and discussed. Several new bond-forming reactions mechanisms are derived for example, the bond-forming reactions of N22+ with O2 proceed via a 'long' lived complex which dissociates via loss of a neutral and then charge separation, a mechanism which is also operating for one of the bond-forming reactions of N2 with CO2 and N2 with H2O. Additional bond-forming reactions are detected for N22+ with CO2 and H2O, which proceed via shorter lived collision complexes. The reactions of N22+ with C2H2, CH4, H2 and Ar all proceed via a variety of mechanisms involving short-lived collision complexes or H and electron stripping.

Published
2007

14. Publisher Correction: Charge radii of exotic potassium isotopes challenge nuclear theory and the magic character of N = 32

Author

Koszorús, Á., Yang, X. F., Jiang, W. G., Novario, S. J., Bai, S. W., Billowes, J., Binnersley, C. L., Bissell, M. L., Cocolios, T. E., Cooper, B. S., de Groote, R. P., Ekström, A., Flanagan, K. T., Forssén, C., Franchoo, S., Ruiz, R. F. Garcia, Gustafsson, F. P., Hagen, G., Jansen, G. R., Kanellakopoulos, A., Kortelainen, M., Nazarewicz, W., Neyens, G., Papenbrock, T., Reinhard, P.-G., Ricketts, C. M., Sahoo, B. K., Vernon, A. R., and Wilkins, S. G.

Published
2021
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15. A compact RFQ cooler buncher for CRIS experiments

Author

Cooper, B. S., A.Perrett, H., Ricketts, C. M., Read, C., Edwards, G., Flanagan, K. T., Billowes, J., Binnersley, C. L., Bissell, M. L., Cocolios, T. E., de Groote, R. P., Farooq-Smith, G. J., Ruiz, R. F. Garcia, Gins, W., Koszorus, A., Neyens, G., P-Gustafsson, F., Stroke, H. H., Vernon, A. R., Wendt, K. D. A., Wilkins, S. G., and Yang, X. F.

Published
2019
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17. Spectroscopy of short-lived radioactive molecules

Author

Garcia Ruiz, R. F., Berger, R., Billowes, J., Binnersley, C. L., Bissell, M. L., Breier, A. A., Brinson, A. J., Chrysalidis, K., Cocolios, T. E., Cooper, B. S., Flanagan, K. T., Giesen, T. F., de Groote, R. P., Franchoo, S., Gustafsson, F. P., Isaev, T. A., Koszorús, Á., Neyens, G., Perrett, H. A., Ricketts, C. M., Rothe, S., Schweikhard, L., Vernon, A. R., Wendt, K. D. A., Wienholtz, F., Wilkins, S. G., Yang, X. F., Garcia Ruiz, R. F., Berger, R., Billowes, J., Binnersley, C. L., Bissell, M. L., Breier, A. A., Brinson, A. J., Chrysalidis, K., Cocolios, T. E., Cooper, B. S., Flanagan, K. T., Giesen, T. F., de Groote, R. P., Franchoo, S., Gustafsson, F. P., Isaev, T. A., Koszorús, Á., Neyens, G., Perrett, H. A., Ricketts, C. M., Rothe, S., Schweikhard, L., Vernon, A. R., Wendt, K. D. A., Wienholtz, F., Wilkins, S. G., and Yang, X. F.

Abstract

© 2020, The Author(s). Molecular spectroscopy offers opportunities for the exploration of the fundamental laws of nature and the search for new particle physics beyond the standard model1–4. Radioactive molecules—in which one or more of the atoms possesses a radioactive nucleus—can contain heavy and deformed nuclei, offering high sensitivity for investigating parity- and time-reversal-violation effects5,6. Radium monofluoride, RaF, is of particular interest because it is predicted to have an electronic structure appropriate for laser cooling6, thus paving the way for its use in high-precision spectroscopic studies. Furthermore, the effects of symmetry-violating nuclear moments are strongly enhanced5,7–9 in molecules containing octupole-deformed radium isotopes10,11. However, the study of RaF has been impeded by the lack of stable isotopes of radium. Here we present an experimental approach to studying short-lived radioactive molecules, which allows us to measure molecules with lifetimes of just tens of milliseconds. Energetically low-lying electronic states were measured for different isotopically pure RaF molecules using collinear resonance ionisation at the ISOLDE ion-beam facility at CERN. Our results provide evidence of the existence of a suitable laser-cooling scheme for these molecules and represent a key step towards high-precision studies in these systems. Our findings will enable further studies of short-lived radioactive molecules for fundamental physics research.

Published
2022

18. Laser spectroscopy of indium Rydberg atom bunches by electric field ionization

Author

Vernon, A. R., Ricketts, C. M., Billowes, J., Cocolios, T. E., Cooper, B. S., Flanagan, K. T., Garcia Ruiz, R. F., Gustafsson, F. P., Neyens, G., Perrett, H. A., Sahoo, B. K., Wang, Q., Waso, F. J., Yang, X. F., Vernon, A. R., Ricketts, C. M., Billowes, J., Cocolios, T. E., Cooper, B. S., Flanagan, K. T., Garcia Ruiz, R. F., Gustafsson, F. P., Neyens, G., Perrett, H. A., Sahoo, B. K., Wang, Q., Waso, F. J., and Yang, X. F.

Abstract

© 2020, The Author(s). This work reports on the application of a novel electric field-ionization setup for high-resolution laser spectroscopy measurements on bunched fast atomic beams in a collinear geometry. In combination with multi-step resonant excitation to Rydberg states using pulsed lasers, the field ionization technique demonstrates increased sensitivity for isotope separation and measurement of atomic parameters over previous non-resonant laser ionization methods. The setup was tested at the Collinear Resonance Ionization Spectroscopy experiment at ISOLDE-CERN to perform high-resolution measurements of transitions in the indium atom from the 5s25d2D5/2 and 5s25d2D3/2 states to 5s 2np 2P and 5s2nf2F Rydberg states, up to a principal quantum number of n= 72. The extracted Rydberg level energies were used to re-evaluate the ionization potential of the indium atom to be 46,670.107(4)cm-1. The nuclear magnetic dipole and nuclear electric quadrupole hyperfine structure constants and level isotope shifts of the 5s25d2D5/2 and 5s25d2D3/2 states were determined for 113 , 115In. The results are compared to calculations using relativistic coupled-cluster theory. A good agreement is found with the ionization potential and isotope shifts, while disagreement of hyperfine structure constants indicates an increased importance of electron correlations in these excited atomic states. With the aim of further increasing the detection sensitivity for measurements on exotic isotopes, a systematic study of the field-ionization arrangement implemented in the work was performed at the same time and an improved design was simulated and is presented. The improved design offers increased background suppression independent of the distance from field ionization to ion detection.

Published
2022

19. Tin resonance-ionization schemes for atomic- and nuclear-structure studies

Author

Gustafsson, F. P., Ricketts, C. M., Reitsma, M. L., Garcia Ruiz, R. F., Bai, S. W., Berengut, J. C., Billowes, J., Binnersley, C. L., Borschevsky, A., Cocolios, T. E., Cooper, B. S., de Groote, R. P., Flanagan, K. T., Koszorús, Á., Neyens, G., Perrett, H. A., Vernon, A. R., Wang, Q., Wilkins, S. G., Yang, X. F., Gustafsson, F. P., Ricketts, C. M., Reitsma, M. L., Garcia Ruiz, R. F., Bai, S. W., Berengut, J. C., Billowes, J., Binnersley, C. L., Borschevsky, A., Cocolios, T. E., Cooper, B. S., de Groote, R. P., Flanagan, K. T., Koszorús, Á., Neyens, G., Perrett, H. A., Vernon, A. R., Wang, Q., Wilkins, S. G., and Yang, X. F.

Abstract

© 2020 authors. This paper presents high-precision spectroscopic measurements of atomic tin using five different resonance-ionization schemes performed with the collinear resonance-ionization spectroscopy technique. Isotope shifts were measured for the stable tin isotopes from the 5s25p2P0,1,23 and 1S0 to the 5s25p6sP11,P1,23 and 5s25p7s1P1 atomic levels. The magnetic dipole hyperfine constants Ahf have been extracted for six atomic levels with electron angular momentum J>0 from the hyperfine structures of nuclear spin I=1/2 tin isotopes, Sn115,117,119. State-of-the-art atomic calculations using a relativistic Fock-space coupled-cluster method and the configuration interaction approach combined with many-body perturbation theory allow accurate and reliable calculations of both field- and mass-shift factors for the studied transitions, in addition to the hyperfine magnetic fields and electric-field gradients of the atomic levels. The excellent agreement with the experimental results highlights the accuracy of modern atomic theory and establishes an important foundation for precision measurements of nuclear moments and charge radii of the most exotic isotopes of tin.

Published
2022

20. Occupational Stress in UK Higher Education Institutions: A Comparative Study of All Staff Categories

Author

Tytherleigh, M. Y., Webb, C., Cooper, C. L., and Ricketts, C.

Abstract

The higher education sector in the UK continues to experience significant change. This includes restructuring, use of short-term contracts, external scrutiny and accountability, and major reductions in funding. In line with this, reports of stress at work in higher education institutions have also increased. The study reported here was carried out using a stratified random sample of all categories of staff (academic and non-academic) from 14 UK universities and colleges. Levels of occupational stress were measured using the ASSET model. The results showed that the most significant source of stress for all higher education staff (irrespective of category of employee) was job insecurity. In comparison to the normative data, staff also reported significantly higher levels of stress relating to work relationships, control, and resources and communication, and significantly lower levels of commitment both from and to their organization. However, they also reported significantly lower levels of stress relating to work-life balance, overload and job overall, and lower levels of physical ill-health. Significant differences were identified between staff working at Old versus New universities and by category of employee. These results support the growing evidence that universities no longer provide the low stress working environments they once did.

Published
2005

21. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

Author

Menden M, Wang D, Mason M, Szalai B, Bulusu K, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M, Jang I, Ghazoui Z, Ahsen M, Vogel R, Neto E, Norman T, Tang E, Garnett M, Di Veroli G, Fawell S, Stolovitzky G, Guinney J, Dry J, Saez-Rodriguez J, Abante J, Abecassis B, Aben N, Aghamirzaie D, Aittokallio T, Akhtari F, Al-lazikani B, Alam T, Allam A, Allen C, de Almeida M, Altarawy D, Alves V, Amadoz A, Anchang B, Antolin A, Ash J, Aznar V, Ba-alawi W, Bagheri M, Bajic V, Ball G, Ballester P, Baptista D, Bare C, Bateson M, Bender A, Bertrand D, Wijayawardena B, Boroevich K, Bosdriesz E, Bougouffa S, Bounova G, Brouwer T, Bryant B, Calaza M, Calderone A, Calza S, Capuzzi S, Carbonell-Caballero J, Carlin D, Carter H, Castagnoli L, Celebi R, Cesareni G, Chang H, Chen G, Chen H, Cheng L, Chernomoretz A, Chicco D, Cho K, Cho S, Choi D, Choi J, Choi K, Choi M, De Cock M, Coker E, Cortes-Ciriano I, Cserzo M, Cubuk C, Curtis C, Van Daele D, Dang C, Dijkstra T, Dopazo J, Draghici S, Drosou A, Dumontier M, Ehrhart F, Eid F, ElHefnawi M, Elmarakeby H, van Engelen B, Engin H, de Esch I, Evelo C, Falcao A, Farag S, Fernandez-Lozano C, Fisch K, Flobak A, Fornari C, Foroushani A, Fotso D, Fourches D, Friend S, Frigessi A, Gao F, Gao X, Gerold J, Gestraud P, Ghosh S, Gillberg J, Godoy-Lorite A, Godynyuk L, Godzik A, Goldenberg A, Gomez-Cabrero D, Gonen M, de Graaf C, Gray H, Grechkin M, Guimera R, Guney E, Haibe-Kains B, Han Y, Hase T, He D, He L, Heath L, Hellton K, Helmer-Citterich M, Hidalgo M, Hidru D, Hill S, Hochreiter S, Hong S, Hovig E, Hsueh Y, Hu Z, Huang J, Huang R, Hunyady L, Hwang J, Hwang T, Hwang W, Hwang Y, Isayev O, Walk O, Jack J, Jahandideh S, Ji J, Jo Y, Kamola P, Kanev G, Karacosta L, Karimi M, Kaski S, Kazanov M, Khamis A, Khan S, Kiani N, Kim A, Kim J, Kim K, Kim S, Kim Y, Kirk P, Kitano H, Klambauer G, Knowles D, Ko M, Kohn-Luque A, Kooistra A, Kuenemann M, Kuiper M, Kurz C, Kwon M, van Laarhoven T, Laegreid A, Lederer S, Lee H, Lee J, Lee Y, Leppaho E, Lewis R, Li J, Li L, Liley J, Lim W, Lin C, Liu Y, Lopez Y, Low J, Lysenko A, Machado D, Madhukar N, De Maeyer D, Malpartida A, Mamitsuka H, Marabita F, Marchal K, Marttinen P, Mason D, Mazaheri A, Mehmood A, Mehreen A, Michaut M, Miller R, Mitsopoulos C, Modos D, Van Moerbeke M, Moo K, Motsinger-Reif A, Movva R, Muraru S, Muratov E, Mushthofa M, Nagarajan N, Nakken S, Nath A, Neuvial P, Newton R, Ning Z, De Niz C, Oliva B, Olsen C, Palmeri A, Panesar B, Papadopoulos S, Park J, Park S, Pawitan Y, Peluso D, Pendyala S, Peng J, Perfetto L, Pirro S, Plevritis S, Politi R, Poon H, Porta E, Prellner I, Preuer K, Pujana M, Ramnarine R, Reid J, Reyal F, Richardson S, Ricketts C, Rieswijk L, Rocha M, Rodriguez-Gonzalvez C, Roell K, Rotroff D, de Ruiter J, Rukawa P, Sadacca B, Safikhani Z, Safitri F, Sales-Pardo M, Sauer S, Schlichting M, Seoane J, Serra J, Shang M, Sharma A, Sharma H, Shen Y, Shiga M, Shin M, Shkedy Z, Shopsowitz K, Sinai S, Skola D, Smirnov P, Soerensen I, Soerensen P, Song J, Song S, Soufan O, Spitzmueller A, Steipe B, Suphavilai C, Tamayo S, Tamborero D, Tang J, Tanoli Z, Tarres-Deulofeu M, Tegner J, Thommesen L, Tonekaboni S, Tran H, De Troyer E, Truong A, Tsunoda T, Turu G, Tzeng G, Verbeke L, Videla S, Vis D, Voronkov A, Votis K, Wang A, Wang H, Wang P, Wang S, Wang W, Wang X, Wennerberg K, Wernisch L, Wessels L, van Westen G, Westerman B, White S, Willighagen E, Wurdinger T, Xie L, Xie S, Xu H, Yadav B, Yau C, Yeerna H, Yin J, Yu M, Yun S, Zakharov A, Zamichos A, Zanin M, Zeng L, Zenil H, Zhang F, Zhang P, Zhang W, Zhao H, Zhao L, Zheng W, Zoufir A, Zucknick M, AstraZeneca-Sanger Drug Combinatio, Ege Üniversitesi, Gönen, Mehmet (ORCID 0000-0002-2483-075X & YÖK ID 237468), Menden, Michael P., Wang, Dennis, Mason, Mike J., Szalai, Bence, Bulusu, Krishna C., Guan, Yuanfang, Yu, Thomas, Kang, Jaewoo, Jeon, Minji, Wolfinger, Russ, Nguyen, Tin, Zaslavskiy, Mikhail, Jang, In Sock, Ghazoui, Zara, Ahsen, Mehmet Eren, Vogel, Robert, Neto, Elias Chaibub, Norman, Thea, Tang, Eric K. Y., Garnett, Mathew J., Di Veroli, Giovanni Y., Fawell, Stephen, Stolovitzky, Gustavo, Guinney, Justin, Dry, Jonathan R., Saez-Rodriguez, Julio, Abante, Jordi, Abecassis, Barbara Schmitz, Aben, Nanne, Aghamirzaie, Delasa, Aittokallio, Tero, Akhtari, Farida S., Al-lazikani, Bissan, Alam, Tanvir, Allam, Amin, Allen, Chad, de Almeida, Mariana Pelicano, Altarawy, Doaa, Alves, Vinicius, Amadoz, Alicia, Anchang, Benedict, Antolin, Albert A., Ash, Jeremy R., Romeo Aznar, Victoria, Ba-alawi, Wail, Bagheri, Moeen, Bajic, Vladimir, Ball, Gordon, Ballester, Pedro J., Baptista, Delora, Bare, Christopher, Bateson, Mathilde, Bender, Andreas, Bertrand, Denis, Wijayawardena, Bhagya, Boroevich, Keith A., Bosdriesz, Evert, Bougouffa, Salim, Bounova, Gergana, Brouwer, Thomas, Bryant, Barbara, Calaza, Manuel, Calderone, Alberto, Calza, Stefano, Capuzzi, Stephen, Carbonell-Caballero, Jose, Carlin, Daniel, Carter, Hannah, Castagnoli, Luisa, Celebi, Remzi, Cesareni, Gianni, Chang, Hyeokyoon, Chen, Guocai, Chen, Haoran, Chen, Huiyuan, Cheng, Lijun, Chernomoretz, Ariel, Chicco, Davide, Cho, Kwang-Hyun, Cho, Sunghwan, Choi, Daeseon, Choi, Jaejoon, Choi, Kwanghun, Choi, Minsoo, De Cock, Martine, Coker, Elizabeth, Cortes-Ciriano, Isidro, Cserzo, Miklos, Cubuk, Cankut, Curtis, Christina, Van Daele, Dries, Dang, Cuong C., Dijkstra, Tjeerd, Dopazo, Joaquin, Draghici, Sorin, Drosou, Anastasios, Dumontier, Michel, Ehrhart, Friederike, Eid, Fatma-Elzahraa, ElHefnawi, Mahmoud, Elmarakeby, Haitham, van Engelen, Bo, Engin, Hatice Billur, de Esch, Iwan, Evelo, Chris, Falcao, Andre O., Farag, Sherif, Fernandez-Lozano, Carlos, Fisch, Kathleen, Flobak, Asmund, Fornari, Chiara, Foroushani, Amir B. K., Fotso, Donatien Chedom, Fourches, Denis, Friend, Stephen, Frigessi, Arnoldo, Gao, Feng, Gao, Xiaoting, Gerold, Jeffrey M., Gestraud, Pierre, Ghosh, Samik, Gillberg, Jussi, Godoy-Lorite, Antonia, Godynyuk, Lizzy, Godzik, Adam, Goldenberg, Anna, Gomez-Cabrero, David, de Graaf, Chris, Gray, Harry, Grechkin, Maxim, Guimera, Roger, Guney, Emre, Haibe-Kains, Benjamin, Han, Younghyun, Hase, Takeshi, He, Di, He, Liye, Heath, Lenwood S., Hellton, Kristoffer H., Helmer-Citterich, Manuela, Hidalgo, Marta R., Hidru, Daniel, Hill, Steven M., Hochreiter, Sepp, Hong, Seungpyo, Hovig, Eivind, Hsueh, Ya-Chih, Hu, Zhiyuan, Huang, Justin K., Huang, R. Stephanie, Hunyady, Laszlo, Hwang, Jinseub, Hwang, Tae Hyun, Hwang, Woochang, Hwang, Yongdeuk, Isayev, Olexandr, Walk, Oliver Bear Don't, Jack, John, Jahandideh, Samad, Ji, Jiadong, Jo, Yousang, Kamola, Piotr J., Kanev, Georgi K., Karacosta, Loukia, Karimi, Mostafa, Kaski, Samuel, Kazanov, Marat, Khamis, Abdullah M., Khan, Suleiman Ali, Kiani, Narsis A., Kim, Allen, Kim, Jinhan, Kim, Juntae, Kim, Kiseong, Kim, Kyung, Kim, Sunkyu, Kim, Yongsoo, Kim, Yunseong, Kirk, Paul D. W., Kitano, Hiroaki, Klambauer, Gunter, Knowles, David, Ko, Melissa, Kohn-Luque, Alvaro, Kooistra, Albert J., Kuenemann, Melaine A., Kuiper, Martin, Kurz, Christoph, Kwon, Mijin, van Laarhoven, Twan, Laegreid, Astrid, Lederer, Simone, Lee, Heewon, Lee, Jeon, Lee, Yun Woo, Leppaho, Eemeli, Lewis, Richard, Li, Jing, Li, Lang, Liley, James, Lim, Weng Khong, Lin, Chieh, Liu, Yiyi, Lopez, Yosvany, Low, Joshua, Lysenko, Artem, Machado, Daniel, Madhukar, Neel, De Maeyer, Dries, Malpartida, Ana Belen, Mamitsuka, Hiroshi, Marabita, Francesco, Marchal, Kathleen, Marttinen, Pekka, Mason, Daniel, Mazaheri, Alireza, Mehmood, Arfa, Mehreen, Ali, Michaut, Magali, Miller, Ryan A., Mitsopoulos, Costas, Modos, Dezso, Van Moerbeke, Marijke, Moo, Keagan, Motsinger-Reif, Alison, Movva, Rajiv, Muraru, Sebastian, Muratov, Eugene, Mushthofa, Mushthofa, Nagarajan, Niranjan, Nakken, Sigve, Nath, Aritro, Neuvial, Pierre, Newton, Richard, Ning, Zheng, De Niz, Carlos, Oliva, Baldo, Olsen, Catharina, Palmeri, Antonio, Panesar, Bhawan, Papadopoulos, Stavros, Park, Jaesub, Park, Seonyeong, Park, Sungjoon, Pawitan, Yudi, Peluso, Daniele, Pendyala, Sriram, Peng, Jian, Perfetto, Livia, Pirro, Stefano, Plevritis, Sylvia, Politi, Regina, Poon, Hoifung, Porta, Eduard, Prellner, Isak, Preuer, Kristina, Angel Pujana, Miguel, Ramnarine, Ricardo, Reid, John E., Reyal, Fabien, Richardson, Sylvia, Ricketts, Camir, Rieswijk, Linda, Rocha, Miguel, Rodriguez-Gonzalvez, Carmen, Roell, Kyle, Rotroff, Daniel, de Ruiter, Julian R., Rukawa, Ploy, Sadacca, Benjamin, Safikhani, Zhaleh, Safitri, Fita, Sales-Pardo, Marta, Sauer, Sebastian, Schlichting, Moritz, Seoane, Jose A., Serra, Jordi, Shang, Ming-Mei, Sharma, Alok, Sharma, Hari, Shen, Yang, Shiga, Motoki, Shin, Moonshik, Shkedy, Ziv, Shopsowitz, Kevin, Sinai, Sam, Skola, Dylan, Smirnov, Petr, Soerensen, Izel Fourie, Soerensen, Peter, Song, Je-Hoon, Song, Sang Ok, Soufan, Othman, Spitzmueller, Andreas, Steipe, Boris, Suphavilai, Chayaporn, Tamayo, Sergio Pulido, Tamborero, David, Tang, Jing, Tanoli, Zia-ur-Rehman, Tarres-Deulofeu, Marc, Tegner, Jesper, Thommesen, Liv, Tonekaboni, Seyed Ali Madani, Tran, Hong, De Troyer, Ewoud, Truong, Amy, Tsunoda, Tatsuhiko, Turu, Gabor, Tzeng, Guang-Yo, Verbeke, Lieven, Videla, Santiago, Vis, Daniel, Voronkov, Andrey, Votis, Konstantinos, Wang, Ashley, Wang, Hong-Qiang Horace, Wang, Po-Wei, Wang, Sheng, Wang, Wei, Wang, Xiaochen, Wang, Xin, Wennerberg, Krister, Wernisch, Lorenz, Wessels, Lodewyk, van Westen, Gerard J. P., Westerman, Bart A., White, Simon Richard, Willighagen, Egon, Wurdinger, Tom, Xie, Lei, Xie, Shuilian, Xu, Hua, Yadav, Bhagwan, Yau, Christopher, Yeerna, Huwate, Yin, Jia Wei, Yu, Michael, Yu, MinHwan, Yun, So Jeong, Zakharov, Alexey, Zamichos, Alexandros, Zanin, Massimiliano, Zeng, Li, Zenil, Hector, Zhang, Frederick, Zhang, Pengyue, Zhang, Wei, Zhao, Hongyu, Zhao, Lan, Zheng, Wenjin, Zoufir, Azedine, Zucknick, Manuela, College of Engineering, Department of Industrial Engineering, Institute of Data Science, RS: FSE DACS IDS, Bioinformatica, RS: NUTRIM - R1 - Obesity, diabetes and cardiovascular health, RS: FHML MaCSBio, Promovendi NTM, Tero Aittokallio / Principal Investigator, Bioinformatics, Institute for Molecular Medicine Finland, Hu, Z, Fotso, DC, Menden, M, Wang, D, Mason, M, Szalai, B, Bulusu, K, Guan, Y, Yu, T, Kang, J, Jeon, M, Wolfinger, R, Nguyen, T, Zaslavskiy, M, Abante, J, Abecassis, B, Aben, N, Aghamirzaie, D, Aittokallio, T, Akhtari, F, Al-lazikani, B, Alam, T, Allam, A, Allen, C, de Almeida, M, Altarawy, D, Alves, V, Amadoz, A, Anchang, B, Antolin, A, Ash, J, Aznar, V, Ba-alawi, W, Bagheri, M, Bajic, V, Ball, G, Ballester, P, Baptista, D, Bare, C, Bateson, M, Bender, A, Bertrand, D, Wijayawardena, B, Boroevich, K, Bosdriesz, E, Bougouffa, S, Bounova, G, Brouwer, T, Bryant, B, Calaza, M, Calderone, A, Calza, S, Capuzzi, S, Carbonell-Caballero, J, Carlin, D, Carter, H, Castagnoli, L, Celebi, R, Cesareni, G, Chang, H, Chen, G, Chen, H, Cheng, L, Chernomoretz, A, Chicco, D, Cho, K, Cho, S, Choi, D, Choi, J, Choi, K, Choi, M, Cock, M, Coker, E, Cortes-Ciriano, I, Cserzo, M, Cubuk, C, Curtis, C, Daele, D, Dang, C, Dijkstra, T, Dopazo, J, Draghici, S, Drosou, A, Dumontier, M, Ehrhart, F, Eid, F, Elhefnawi, M, Elmarakeby, H, van Engelen, B, Engin, H, de Esch, I, Evelo, C, Falcao, A, Farag, S, Fernandez-Lozano, C, Fisch, K, Flobak, A, Fornari, C, Foroushani, A, Fotso, D, Fourches, D, Friend, S, Frigessi, A, Gao, F, Gao, X, Gerold, J, Gestraud, P, Ghosh, S, Gillberg, J, Godoy-Lorite, A, Godynyuk, L, Godzik, A, Goldenberg, A, Gomez-Cabrero, D, Gonen, M, de Graaf, C, Gray, H, Grechkin, M, Guimera, R, Guney, E, Haibe-Kains, B, Han, Y, Hase, T, He, D, He, L, Heath, L, Hellton, K, Helmer-Citterich, M, Hidalgo, M, Hidru, D, Hill, S, Hochreiter, S, Hong, S, Hovig, E, Hsueh, Y, Huang, J, Huang, R, Hunyady, L, Hwang, J, Hwang, T, Hwang, W, Hwang, Y, Isayev, O, Don't Walk, O, Jack, J, Jahandideh, S, Ji, J, Jo, Y, Kamola, P, Kanev, G, Karacosta, L, Karimi, M, Kaski, S, Kazanov, M, Khamis, A, Khan, S, Kiani, N, Kim, A, Kim, J, Kim, K, Kim, S, Kim, Y, Kirk, P, Kitano, H, Klambauer, G, Knowles, D, Ko, M, Kohn-Luque, A, Kooistra, A, Kuenemann, M, Kuiper, M, Kurz, C, Kwon, M, van Laarhoven, T, Laegreid, A, Lederer, S, Lee, H, Lee, J, Lee, Y, Lepp_aho, E, Lewis, R, Li, J, Li, L, Liley, J, Lim, W, Lin, C, Liu, Y, Lopez, Y, Low, J, Lysenko, A, Machado, D, Madhukar, N, Maeyer, D, Malpartida, A, Mamitsuka, H, Marabita, F, Marchal, K, Marttinen, P, Mason, D, Mazaheri, A, Mehmood, A, Mehreen, A, Michaut, M, Miller, R, Mitsopoulos, C, Modos, D, Moerbeke, M, Moo, K, Motsinger-Reif, A, Movva, R, Muraru, S, Muratov, E, Mushthofa, M, Nagarajan, N, Nakken, S, Nath, A, Neuvial, P, Newton, R, Ning, Z, Niz, C, Oliva, B, Olsen, C, Palmeri, A, Panesar, B, Papadopoulos, S, Park, J, Park, S, Pawitan, Y, Peluso, D, Pendyala, S, Peng, J, Perfetto, L, Pirro, S, Plevritis, S, Politi, R, Poon, H, Porta, E, Prellner, I, Preuer, K, Pujana, M, Ramnarine, R, Reid, J, Reyal, F, Richardson, S, Ricketts, C, Rieswijk, L, Rocha, M, Rodriguez-Gonzalvez, C, Roell, K, Rotroff, D, de Ruiter, J, Rukawa, P, Sadacca, B, Safikhani, Z, Safitri, F, Sales-Pardo, M, Sauer, S, Schlichting, M, Seoane, J, Serra, J, Shang, M, Sharma, A, Sharma, H, Shen, Y, Shiga, M, Shin, M, Shkedy, Z, Shopsowitz, K, Sinai, S, Skola, D, Smirnov, P, Soerensen, I, Soerensen, P, Song, J, Song, S, Soufan, O, Spitzmueller, A, Steipe, B, Suphavilai, C, Tamayo, S, Tamborero, D, Tang, J, Tanoli, Z, Tarres-Deulofeu, M, Tegner, J, Thommesen, L, Tonekaboni, S, Tran, H, Troyer, E, Truong, A, Tsunoda, T, Turu, G, Tzeng, G, Verbeke, L, Videla, S, Vis, D, Voronkov, A, Votis, K, Wang, A, Wang, H, Wang, P, Wang, S, Wang, W, Wang, X, Wennerberg, K, Wernisch, L, Wessels, L, van Westen, G, Westerman, B, White, S, Willighagen, E, Wurdinger, T, Xie, L, Xie, S, Xu, H, Yadav, B, Yau, C, Yeerna, H, Yin, J, Yu, M, Yun, S, Zakharov, A, Zamichos, A, Zanin, M, Zeng, L, Zenil, H, Zhang, F, Zhang, P, Zhang, W, Zhao, H, Zhao, L, Zheng, W, Zoufir, A, Zucknick, M, Jang, I, Ghazoui, Z, Ahsen, M, Vogel, R, Neto, E, Norman, T, Tang, E, Garnett, M, Veroli, G, Fawell, S, Stolovitzky, G, Guinney, J, Dry, J, Saez-Rodriguez, J, Menden, Michael P. [0000-0003-0267-5792], Mason, Mike J. [0000-0002-5652-7739], Yu, Thomas [0000-0002-5841-0198], Kang, Jaewoo [0000-0001-6798-9106], Nguyen, Tin [0000-0001-8001-9470], Ahsen, Mehmet Eren [0000-0002-4907-0427], Stolovitzky, Gustavo [0000-0002-9618-2819], Guinney, Justin [0000-0003-1477-1888], Saez-Rodriguez, Julio [0000-0002-8552-8976], Apollo - University of Cambridge Repository, Menden, Michael P [0000-0003-0267-5792], Mason, Mike J [0000-0002-5652-7739], Pathology, CCA - Cancer biology and immunology, Medical oncology laboratory, Neurosurgery, Chemistry and Pharmaceutical Sciences, AIMMS, Medicinal chemistry, Universidade do Minho, Department of Computer Science, Professorship Marttinen P., Aalto-yliopisto, and Aalto University

Subjects
Drug Resistance, 02 engineering and technology, 13, PATHWAY, Antineoplastic Combined Chemotherapy Protocols, Molecular Targeted Therapy, Càncer, lcsh:Science, media_common, Cancer, Tumor, Settore BIO/18, Settore BIO/11, Drug combinations, High-throughput screening, Drug Synergism, purl.org/becyt/ford/1.2 [https], Genomics, Machine Learning, predictions, 3. Good health, ddc, Technologie de l'environnement, contrôle de la pollution, Benchmarking, 5.1 Pharmaceuticals, Cancer treatment, Farmacogenètica, Science & Technology - Other Topics, Development of treatments and therapeutic interventions, 0210 nano-technology, Human, Drug, media_common.quotation_subject, Science, 49/23, ADAM17 Protein, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, SDG 3 - Good Health and Well-being, RESOURCE, Machine learning, Genetics, Chimie, Humans, BREAST-CANCER, CELL, 49/98, Science & Technology, Antineoplastic Combined Chemotherapy Protocol, 45, MUTATIONS, Computational Biology, Androgen receptor, Breast-cancer, Gene, Cell, Inhibition, Resistance, Pathway, Mutations, Landscape, Resource, 631/114/1305, medicine.disease, Drug synergy, 49, 030104 developmental biology, Pharmacogenetics, Mutation, Ciências Médicas::Biotecnologia Médica, lcsh:Q, 631/154/1435/2163, Biomarkers, RESISTANCE, 0301 basic medicine, ING-INF/06 - BIOINGEGNERIA ELETTRONICA E INFORMATICA, Statistical methods, Computer science, General Physics and Astronomy, Datasets as Topic, Drug resistance, purl.org/becyt/ford/1 [https], Phosphatidylinositol 3-Kinases, Biotecnologia Médica [Ciências Médicas], Neoplasms, Science and technology, Phosphoinositide-3 Kinase Inhibitors, Multidisciplinary, Biomarkers, Tumor, Cell Line, Tumor, Drug Antagonism, Drug Resistance, Neoplasm, Treatment Outcome, Pharmacogenetic, article, ANDROGEN RECEPTOR, 49/39, 631/114/2415, 021001 nanoscience & nanotechnology, 692/4028/67, Multidisciplinary Sciences, 317 Pharmacy, Patient Safety, Systems biology, 3122 Cancers, INHIBITION, Computational biology, Cell Line, medicine, LANDSCAPE, Physique, Human Genome, Data Science, General Chemistry, AstraZeneca-Sanger Drug Combination DREAM Consortium, Astronomie, GENE, Good Health and Well Being, Pharmacogenomics, Genomic, Neoplasm, 631/553, Phosphatidylinositol 3-Kinase
Abstract

PubMed: 31209238, The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca’s large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for >60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells. © 2019, The Author(s)., National Institute for Health Research, NIHR Wellcome Trust, WT: 102696, 206194 Magyar Tudományos Akadémia, MTA Bayer 668858 PrECISE AstraZeneca, We thank the Genomics of Drug Sensitivity in Cancer and COSMIC teams at the Wellcome Trust Sanger Institute for help with the preparation of the molecular data, Denes Turei for help with Omnipath, and Katjusa Koler for help with matching drug names across combination screens. We thank AstraZeneca for funding and provision of data to the DREAM Consortium to run the challenge, and funding from the European Union Horizon 2020 research (under grant agreement No 668858 PrECISE to J.S.R.), the Joint Research Center for Computational Biomedicine (which is partially funded by Bayer AG) to J.S.R., National Institute for Health Research (NIHR) Sheffield Biomedical Research Center, Premium Postdoctoral Fellowship Program of the Hungarian Academy of Sciences. M.G lab is supported by Wellcome Trust (102696 and 206194)., Competing interests: K.C.B., Z.G., G.Y.D., E.K.Y.T., S.F., and J.R.D. are AstraZeneca employees. K.C.B., Z.G., E.K.Y.T., S.F., and J.R.D. are AstraZeneca shareholders. Y.G. receives personal compensation from Eli Lilly and Company, is a shareholder of Cleerly, Inc., and Ann Arbor Algorithms, Inc. M.G. receives research funding from AstraZeneca and has performed consultancy for Sanofi. The remaining authors declare no competing interests.

Published
2019

22. Improving Student Performance through Computer-Based Assessment: Insights from Recent Research.

Author

Ricketts, C. and Wilks, S. J.

Abstract

Compared student performance on computer-based assessment to machine-graded multiple choice tests. Found that performance improved dramatically on the computer-based assessment when students were not required to scroll through the question paper. Concluded that students may be disadvantaged by the introduction of online assessment unless care is taken with the student-assessment interface. (EV)

Published
2002

23. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

Author

Menden, M, Wang, D, Mason, M, Szalai, B, Bulusu, K, Guan, Y, Yu, T, Kang, J, Jeon, M, Wolfinger, R, Nguyen, T, Zaslavskiy, M, Abante, J, Abecassis, B, Aben, N, Aghamirzaie, D, Aittokallio, T, Akhtari, F, Al-lazikani, B, Alam, T, Allam, A, Allen, C, de Almeida, M, Altarawy, D, Alves, V, Amadoz, A, Anchang, B, Antolin, A, Ash, J, Aznar, V, Ba-alawi, W, Bagheri, M, Bajic, V, Ball, G, Ballester, P, Baptista, D, Bare, C, Bateson, M, Bender, A, Bertrand, D, Wijayawardena, B, Boroevich, K, Bosdriesz, E, Bougouffa, S, Bounova, G, Brouwer, T, Bryant, B, Calaza, M, Calderone, A, Calza, S, Capuzzi, S, Carbonell-Caballero, J, Carlin, D, Carter, H, Castagnoli, L, Celebi, R, Cesareni, G, Chang, H, Chen, G, Chen, H, Cheng, L, Chernomoretz, A, Chicco, D, Cho, K, Cho, S, Choi, D, Choi, J, Choi, K, Choi, M, Cock, M, Coker, E, Cortes-Ciriano, I, Cserzo, M, Cubuk, C, Curtis, C, Daele, D, Dang, C, Dijkstra, T, Dopazo, J, Draghici, S, Drosou, A, Dumontier, M, Ehrhart, F, Eid, F, Elhefnawi, M, Elmarakeby, H, van Engelen, B, Engin, H, de Esch, I, Evelo, C, Falcao, A, Farag, S, Fernandez-Lozano, C, Fisch, K, Flobak, A, Fornari, C, Foroushani, A, Fotso, D, Fourches, D, Friend, S, Frigessi, A, Gao, F, Gao, X, Gerold, J, Gestraud, P, Ghosh, S, Gillberg, J, Godoy-Lorite, A, Godynyuk, L, Godzik, A, Goldenberg, A, Gomez-Cabrero, D, Gonen, M, de Graaf, C, Gray, H, Grechkin, M, Guimera, R, Guney, E, Haibe-Kains, B, Han, Y, Hase, T, He, D, He, L, Heath, L, Hellton, K, Helmer-Citterich, M, Hidalgo, M, Hidru, D, Hill, S, Hochreiter, S, Hong, S, Hovig, E, Hsueh, Y, Hu, Z, Huang, J, Huang, R, Hunyady, L, Hwang, J, Hwang, T, Hwang, W, Hwang, Y, Isayev, O, Don't Walk, O, Jack, J, Jahandideh, S, Ji, J, Jo, Y, Kamola, P, Kanev, G, Karacosta, L, Karimi, M, Kaski, S, Kazanov, M, Khamis, A, Khan, S, Kiani, N, Kim, A, Kim, J, Kim, K, Kim, S, Kim, Y, Kirk, P, Kitano, H, Klambauer, G, Knowles, D, Ko, M, Kohn-Luque, A, Kooistra, A, Kuenemann, M, Kuiper, M, Kurz, C, Kwon, M, van Laarhoven, T, Laegreid, A, Lederer, S, Lee, H, Lee, J, Lee, Y, Lepp_aho, E, Lewis, R, Li, J, Li, L, Liley, J, Lim, W, Lin, C, Liu, Y, Lopez, Y, Low, J, Lysenko, A, Machado, D, Madhukar, N, Maeyer, D, Malpartida, A, Mamitsuka, H, Marabita, F, Marchal, K, Marttinen, P, Mason, D, Mazaheri, A, Mehmood, A, Mehreen, A, Michaut, M, Miller, R, Mitsopoulos, C, Modos, D, Moerbeke, M, Moo, K, Motsinger-Reif, A, Movva, R, Muraru, S, Muratov, E, Mushthofa, M, Nagarajan, N, Nakken, S, Nath, A, Neuvial, P, Newton, R, Ning, Z, Niz, C, Oliva, B, Olsen, C, Palmeri, A, Panesar, B, Papadopoulos, S, Park, J, Park, S, Pawitan, Y, Peluso, D, Pendyala, S, Peng, J, Perfetto, L, Pirro, S, Plevritis, S, Politi, R, Poon, H, Porta, E, Prellner, I, Preuer, K, Pujana, M, Ramnarine, R, Reid, J, Reyal, F, Richardson, S, Ricketts, C, Rieswijk, L, Rocha, M, Rodriguez-Gonzalvez, C, Roell, K, Rotroff, D, de Ruiter, J, Rukawa, P, Sadacca, B, Safikhani, Z, Safitri, F, Sales-Pardo, M, Sauer, S, Schlichting, M, Seoane, J, Serra, J, Shang, M, Sharma, A, Sharma, H, Shen, Y, Shiga, M, Shin, M, Shkedy, Z, Shopsowitz, K, Sinai, S, Skola, D, Smirnov, P, Soerensen, I, Soerensen, P, Song, J, Song, S, Soufan, O, Spitzmueller, A, Steipe, B, Suphavilai, C, Tamayo, S, Tamborero, D, Tang, J, Tanoli, Z, Tarres-Deulofeu, M, Tegner, J, Thommesen, L, Tonekaboni, S, Tran, H, Troyer, E, Truong, A, Tsunoda, T, Turu, G, Tzeng, G, Verbeke, L, Videla, S, Vis, D, Voronkov, A, Votis, K, Wang, A, Wang, H, Wang, P, Wang, S, Wang, W, Wang, X, Wennerberg, K, Wernisch, L, Wessels, L, van Westen, G, Westerman, B, White, S, Willighagen, E, Wurdinger, T, Xie, L, Xie, S, Xu, H, Yadav, B, Yau, C, Yeerna, H, Yin, J, Yu, M, Yun, S, Zakharov, A, Zamichos, A, Zanin, M, Zeng, L, Zenil, H, Zhang, F, Zhang, P, Zhang, W, Zhao, H, Zhao, L, Zheng, W, Zoufir, A, Zucknick, M, Jang, I, Ghazoui, Z, Ahsen, M, Vogel, R, Neto, E, Norman, T, Tang, E, Garnett, M, Veroli, G, Fawell, S, Stolovitzky, G, Guinney, J, Dry, J, Saez-Rodriguez, J, Menden M. P., Wang D., Mason M. J., Szalai B., Bulusu K. C., Guan Y., Yu T., Kang J., Jeon M., Wolfinger R., Nguyen T., Zaslavskiy M., Abante J., Abecassis B. S., Aben N., Aghamirzaie D., Aittokallio T., Akhtari F. S., Al-lazikani B., Alam T., Allam A., Allen C., de Almeida M. P., Altarawy D., Alves V., Amadoz A., Anchang B., Antolin A. A., Ash J. R., Aznar V. R., Ba-alawi W., Bagheri M., Bajic V., Ball G., Ballester P. J., Baptista D., Bare C., Bateson M., Bender A., Bertrand D., Wijayawardena B., Boroevich K. A., Bosdriesz E., Bougouffa S., Bounova G., Brouwer T., Bryant B., Calaza M., Calderone A., Calza S., Capuzzi S., Carbonell-Caballero J., Carlin D., Carter H., Castagnoli L., Celebi R., Cesareni G., Chang H., Chen G., Chen H., Cheng L., Chernomoretz A., Chicco D., Cho K. -H., Cho S., Choi D., Choi J., Choi K., Choi M., Cock M. D., Coker E., Cortes-Ciriano I., Cserzo M., Cubuk C., Curtis C., Daele D. V., Dang C. C., Dijkstra T., Dopazo J., Draghici S., Drosou A., Dumontier M., Ehrhart F., Eid F. -E., ElHefnawi M., Elmarakeby H., van Engelen B., Engin H. B., de Esch I., Evelo C., Falcao A. O., Farag S., Fernandez-Lozano C., Fisch K., Flobak A., Fornari C., Foroushani A. B. K., Fotso D. C., Fourches D., Friend S., Frigessi A., Gao F., Gao X., Gerold J. M., Gestraud P., Ghosh S., Gillberg J., Godoy-Lorite A., Godynyuk L., Godzik A., Goldenberg A., Gomez-Cabrero D., Gonen M., de Graaf C., Gray H., Grechkin M., Guimera R., Guney E., Haibe-Kains B., Han Y., Hase T., He D., He L., Heath L. S., Hellton K. H., Helmer-Citterich M., Hidalgo M. R., Hidru D., Hill S. M., Hochreiter S., Hong S., Hovig E., Hsueh Y. -C., Hu Z., Huang J. K., Huang R. S., Hunyady L., Hwang J., Hwang T. H., Hwang W., Hwang Y., Isayev O., Don't Walk O. B., Jack J., Jahandideh S., Ji J., Jo Y., Kamola P. J., Kanev G. K., Karacosta L., Karimi M., Kaski S., Kazanov M., Khamis A. M., Khan S. A., Kiani N. A., Kim A., Kim J., Kim K., Kim S., Kim Y., Kirk P. D. W., Kitano H., Klambauer G., Knowles D., Ko M., Kohn-Luque A., Kooistra A. J., Kuenemann M. A., Kuiper M., Kurz C., Kwon M., van Laarhoven T., Laegreid A., Lederer S., Lee H., Lee J., Lee Y. W., Lepp_aho E., Lewis R., Li J., Li L., Liley J., Lim W. K., Lin C., Liu Y., Lopez Y., Low J., Lysenko A., Machado D., Madhukar N., Maeyer D. D., Malpartida A. B., Mamitsuka H., Marabita F., Marchal K., Marttinen P., Mason D., Mazaheri A., Mehmood A., Mehreen A., Michaut M., Miller R. A., Mitsopoulos C., Modos D., Moerbeke M. V., Moo K., Motsinger-Reif A., Movva R., Muraru S., Muratov E., Mushthofa M., Nagarajan N., Nakken S., Nath A., Neuvial P., Newton R., Ning Z., Niz C. D., Oliva B., Olsen C., Palmeri A., Panesar B., Papadopoulos S., Park J., Park S., Pawitan Y., Peluso D., Pendyala S., Peng J., Perfetto L., Pirro S., Plevritis S., Politi R., Poon H., Porta E., Prellner I., Preuer K., Pujana M. A., Ramnarine R., Reid J. E., Reyal F., Richardson S., Ricketts C., Rieswijk L., Rocha M., Rodriguez-Gonzalvez C., Roell K., Rotroff D., de Ruiter J. R., Rukawa P., Sadacca B., Safikhani Z., Safitri F., Sales-Pardo M., Sauer S., Schlichting M., Seoane J. A., Serra J., Shang M. -M., Sharma A., Sharma H., Shen Y., Shiga M., Shin M., Shkedy Z., Shopsowitz K., Sinai S., Skola D., Smirnov P., Soerensen I. F., Soerensen P., Song J. -H., Song S. O., Soufan O., Spitzmueller A., Steipe B., Suphavilai C., Tamayo S. P., Tamborero D., Tang J., Tanoli Z. -U. -R., Tarres-Deulofeu M., Tegner J., Thommesen L., Tonekaboni S. A. M., Tran H., Troyer E. D., Truong A., Tsunoda T., Turu G., Tzeng G. -Y., Verbeke L., Videla S., Vis D., Voronkov A., Votis K., Wang A., Wang H. -Q. H., Wang P. -W., Wang S., Wang W., Wang X., Wennerberg K., Wernisch L., Wessels L., van Westen G. J. P., Westerman B. A., White S. R., Willighagen E., Wurdinger T., Xie L., Xie S., Xu H., Yadav B., Yau C., Yeerna H., Yin J. W., Yu M., Yu M. H., Yun S. J., Zakharov A., Zamichos A., Zanin M., Zeng L., Zenil H., Zhang F., Zhang P., Zhang W., Zhao H., Zhao L., Zheng W., Zoufir A., Zucknick M., Jang I. S., Ghazoui Z., Ahsen M. E., Vogel R., Neto E. C., Norman T., Tang E. K. Y., Garnett M. J., Veroli G. Y. D., Fawell S., Stolovitzky G., Guinney J., Dry J. R., Saez-Rodriguez J., Menden, M, Wang, D, Mason, M, Szalai, B, Bulusu, K, Guan, Y, Yu, T, Kang, J, Jeon, M, Wolfinger, R, Nguyen, T, Zaslavskiy, M, Abante, J, Abecassis, B, Aben, N, Aghamirzaie, D, Aittokallio, T, Akhtari, F, Al-lazikani, B, Alam, T, Allam, A, Allen, C, de Almeida, M, Altarawy, D, Alves, V, Amadoz, A, Anchang, B, Antolin, A, Ash, J, Aznar, V, Ba-alawi, W, Bagheri, M, Bajic, V, Ball, G, Ballester, P, Baptista, D, Bare, C, Bateson, M, Bender, A, Bertrand, D, Wijayawardena, B, Boroevich, K, Bosdriesz, E, Bougouffa, S, Bounova, G, Brouwer, T, Bryant, B, Calaza, M, Calderone, A, Calza, S, Capuzzi, S, Carbonell-Caballero, J, Carlin, D, Carter, H, Castagnoli, L, Celebi, R, Cesareni, G, Chang, H, Chen, G, Chen, H, Cheng, L, Chernomoretz, A, Chicco, D, Cho, K, Cho, S, Choi, D, Choi, J, Choi, K, Choi, M, Cock, M, Coker, E, Cortes-Ciriano, I, Cserzo, M, Cubuk, C, Curtis, C, Daele, D, Dang, C, Dijkstra, T, Dopazo, J, Draghici, S, Drosou, A, Dumontier, M, Ehrhart, F, Eid, F, Elhefnawi, M, Elmarakeby, H, van Engelen, B, Engin, H, de Esch, I, Evelo, C, Falcao, A, Farag, S, Fernandez-Lozano, C, Fisch, K, Flobak, A, Fornari, C, Foroushani, A, Fotso, D, Fourches, D, Friend, S, Frigessi, A, Gao, F, Gao, X, Gerold, J, Gestraud, P, Ghosh, S, Gillberg, J, Godoy-Lorite, A, Godynyuk, L, Godzik, A, Goldenberg, A, Gomez-Cabrero, D, Gonen, M, de Graaf, C, Gray, H, Grechkin, M, Guimera, R, Guney, E, Haibe-Kains, B, Han, Y, Hase, T, He, D, He, L, Heath, L, Hellton, K, Helmer-Citterich, M, Hidalgo, M, Hidru, D, Hill, S, Hochreiter, S, Hong, S, Hovig, E, Hsueh, Y, Hu, Z, Huang, J, Huang, R, Hunyady, L, Hwang, J, Hwang, T, Hwang, W, Hwang, Y, Isayev, O, Don't Walk, O, Jack, J, Jahandideh, S, Ji, J, Jo, Y, Kamola, P, Kanev, G, Karacosta, L, Karimi, M, Kaski, S, Kazanov, M, Khamis, A, Khan, S, Kiani, N, Kim, A, Kim, J, Kim, K, Kim, S, Kim, Y, Kirk, P, Kitano, H, Klambauer, G, Knowles, D, Ko, M, Kohn-Luque, A, Kooistra, A, Kuenemann, M, Kuiper, M, Kurz, C, Kwon, M, van Laarhoven, T, Laegreid, A, Lederer, S, Lee, H, Lee, J, Lee, Y, Lepp_aho, E, Lewis, R, Li, J, Li, L, Liley, J, Lim, W, Lin, C, Liu, Y, Lopez, Y, Low, J, Lysenko, A, Machado, D, Madhukar, N, Maeyer, D, Malpartida, A, Mamitsuka, H, Marabita, F, Marchal, K, Marttinen, P, Mason, D, Mazaheri, A, Mehmood, A, Mehreen, A, Michaut, M, Miller, R, Mitsopoulos, C, Modos, D, Moerbeke, M, Moo, K, Motsinger-Reif, A, Movva, R, Muraru, S, Muratov, E, Mushthofa, M, Nagarajan, N, Nakken, S, Nath, A, Neuvial, P, Newton, R, Ning, Z, Niz, C, Oliva, B, Olsen, C, Palmeri, A, Panesar, B, Papadopoulos, S, Park, J, Park, S, Pawitan, Y, Peluso, D, Pendyala, S, Peng, J, Perfetto, L, Pirro, S, Plevritis, S, Politi, R, Poon, H, Porta, E, Prellner, I, Preuer, K, Pujana, M, Ramnarine, R, Reid, J, Reyal, F, Richardson, S, Ricketts, C, Rieswijk, L, Rocha, M, Rodriguez-Gonzalvez, C, Roell, K, Rotroff, D, de Ruiter, J, Rukawa, P, Sadacca, B, Safikhani, Z, Safitri, F, Sales-Pardo, M, Sauer, S, Schlichting, M, Seoane, J, Serra, J, Shang, M, Sharma, A, Sharma, H, Shen, Y, Shiga, M, Shin, M, Shkedy, Z, Shopsowitz, K, Sinai, S, Skola, D, Smirnov, P, Soerensen, I, Soerensen, P, Song, J, Song, S, Soufan, O, Spitzmueller, A, Steipe, B, Suphavilai, C, Tamayo, S, Tamborero, D, Tang, J, Tanoli, Z, Tarres-Deulofeu, M, Tegner, J, Thommesen, L, Tonekaboni, S, Tran, H, Troyer, E, Truong, A, Tsunoda, T, Turu, G, Tzeng, G, Verbeke, L, Videla, S, Vis, D, Voronkov, A, Votis, K, Wang, A, Wang, H, Wang, P, Wang, S, Wang, W, Wang, X, Wennerberg, K, Wernisch, L, Wessels, L, van Westen, G, Westerman, B, White, S, Willighagen, E, Wurdinger, T, Xie, L, Xie, S, Xu, H, Yadav, B, Yau, C, Yeerna, H, Yin, J, Yu, M, Yun, S, Zakharov, A, Zamichos, A, Zanin, M, Zeng, L, Zenil, H, Zhang, F, Zhang, P, Zhang, W, Zhao, H, Zhao, L, Zheng, W, Zoufir, A, Zucknick, M, Jang, I, Ghazoui, Z, Ahsen, M, Vogel, R, Neto, E, Norman, T, Tang, E, Garnett, M, Veroli, G, Fawell, S, Stolovitzky, G, Guinney, J, Dry, J, Saez-Rodriguez, J, Menden M. P., Wang D., Mason M. J., Szalai B., Bulusu K. C., Guan Y., Yu T., Kang J., Jeon M., Wolfinger R., Nguyen T., Zaslavskiy M., Abante J., Abecassis B. S., Aben N., Aghamirzaie D., Aittokallio T., Akhtari F. S., Al-lazikani B., Alam T., Allam A., Allen C., de Almeida M. P., Altarawy D., Alves V., Amadoz A., Anchang B., Antolin A. A., Ash J. R., Aznar V. R., Ba-alawi W., Bagheri M., Bajic V., Ball G., Ballester P. J., Baptista D., Bare C., Bateson M., Bender A., Bertrand D., Wijayawardena B., Boroevich K. A., Bosdriesz E., Bougouffa S., Bounova G., Brouwer T., Bryant B., Calaza M., Calderone A., Calza S., Capuzzi S., Carbonell-Caballero J., Carlin D., Carter H., Castagnoli L., Celebi R., Cesareni G., Chang H., Chen G., Chen H., Cheng L., Chernomoretz A., Chicco D., Cho K. -H., Cho S., Choi D., Choi J., Choi K., Choi M., Cock M. D., Coker E., Cortes-Ciriano I., Cserzo M., Cubuk C., Curtis C., Daele D. V., Dang C. C., Dijkstra T., Dopazo J., Draghici S., Drosou A., Dumontier M., Ehrhart F., Eid F. -E., ElHefnawi M., Elmarakeby H., van Engelen B., Engin H. B., de Esch I., Evelo C., Falcao A. O., Farag S., Fernandez-Lozano C., Fisch K., Flobak A., Fornari C., Foroushani A. B. K., Fotso D. C., Fourches D., Friend S., Frigessi A., Gao F., Gao X., Gerold J. M., Gestraud P., Ghosh S., Gillberg J., Godoy-Lorite A., Godynyuk L., Godzik A., Goldenberg A., Gomez-Cabrero D., Gonen M., de Graaf C., Gray H., Grechkin M., Guimera R., Guney E., Haibe-Kains B., Han Y., Hase T., He D., He L., Heath L. S., Hellton K. H., Helmer-Citterich M., Hidalgo M. R., Hidru D., Hill S. M., Hochreiter S., Hong S., Hovig E., Hsueh Y. -C., Hu Z., Huang J. K., Huang R. S., Hunyady L., Hwang J., Hwang T. H., Hwang W., Hwang Y., Isayev O., Don't Walk O. B., Jack J., Jahandideh S., Ji J., Jo Y., Kamola P. J., Kanev G. K., Karacosta L., Karimi M., Kaski S., Kazanov M., Khamis A. M., Khan S. A., Kiani N. A., Kim A., Kim J., Kim K., Kim S., Kim Y., Kirk P. D. W., Kitano H., Klambauer G., Knowles D., Ko M., Kohn-Luque A., Kooistra A. J., Kuenemann M. A., Kuiper M., Kurz C., Kwon M., van Laarhoven T., Laegreid A., Lederer S., Lee H., Lee J., Lee Y. W., Lepp_aho E., Lewis R., Li J., Li L., Liley J., Lim W. K., Lin C., Liu Y., Lopez Y., Low J., Lysenko A., Machado D., Madhukar N., Maeyer D. D., Malpartida A. B., Mamitsuka H., Marabita F., Marchal K., Marttinen P., Mason D., Mazaheri A., Mehmood A., Mehreen A., Michaut M., Miller R. A., Mitsopoulos C., Modos D., Moerbeke M. V., Moo K., Motsinger-Reif A., Movva R., Muraru S., Muratov E., Mushthofa M., Nagarajan N., Nakken S., Nath A., Neuvial P., Newton R., Ning Z., Niz C. D., Oliva B., Olsen C., Palmeri A., Panesar B., Papadopoulos S., Park J., Park S., Pawitan Y., Peluso D., Pendyala S., Peng J., Perfetto L., Pirro S., Plevritis S., Politi R., Poon H., Porta E., Prellner I., Preuer K., Pujana M. A., Ramnarine R., Reid J. E., Reyal F., Richardson S., Ricketts C., Rieswijk L., Rocha M., Rodriguez-Gonzalvez C., Roell K., Rotroff D., de Ruiter J. R., Rukawa P., Sadacca B., Safikhani Z., Safitri F., Sales-Pardo M., Sauer S., Schlichting M., Seoane J. A., Serra J., Shang M. -M., Sharma A., Sharma H., Shen Y., Shiga M., Shin M., Shkedy Z., Shopsowitz K., Sinai S., Skola D., Smirnov P., Soerensen I. F., Soerensen P., Song J. -H., Song S. O., Soufan O., Spitzmueller A., Steipe B., Suphavilai C., Tamayo S. P., Tamborero D., Tang J., Tanoli Z. -U. -R., Tarres-Deulofeu M., Tegner J., Thommesen L., Tonekaboni S. A. M., Tran H., Troyer E. D., Truong A., Tsunoda T., Turu G., Tzeng G. -Y., Verbeke L., Videla S., Vis D., Voronkov A., Votis K., Wang A., Wang H. -Q. H., Wang P. -W., Wang S., Wang W., Wang X., Wennerberg K., Wernisch L., Wessels L., van Westen G. J. P., Westerman B. A., White S. R., Willighagen E., Wurdinger T., Xie L., Xie S., Xu H., Yadav B., Yau C., Yeerna H., Yin J. W., Yu M., Yu M. H., Yun S. J., Zakharov A., Zamichos A., Zanin M., Zeng L., Zenil H., Zhang F., Zhang P., Zhang W., Zhao H., Zhao L., Zheng W., Zoufir A., Zucknick M., Jang I. S., Ghazoui Z., Ahsen M. E., Vogel R., Neto E. C., Norman T., Tang E. K. Y., Garnett M. J., Veroli G. Y. D., Fawell S., Stolovitzky G., Guinney J., Dry J. R., and Saez-Rodriguez J.

Abstract

The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca’s large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for >60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.

Published
2019

32. Isotope Shifts of Radium Monofluoride Molecules

Author

Udrescu, S. M., primary, Brinson, A. J., additional, Ruiz, R. F. Garcia, additional, Gaul, K., additional, Berger, R., additional, Billowes, J., additional, Binnersley, C. L., additional, Bissell, M. L., additional, Breier, A. A., additional, Chrysalidis, K., additional, Cocolios, T. E., additional, Cooper, B. S., additional, Flanagan, K. T., additional, Giesen, T. F., additional, de Groote, R. P., additional, Franchoo, S., additional, Gustafsson, F. P., additional, Isaev, T. A., additional, Koszorús, Á., additional, Neyens, G., additional, Perrett, H. A., additional, Ricketts, C. M., additional, Rothe, S., additional, Vernon, A. R., additional, Wendt, K. D. A., additional, Wienholtz, F., additional, Wilkins, S. G., additional, and Yang, X. F., additional

Published
2021
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33. Inferring Cancer Progression from Single-Cell Sequencing while Allowing Mutation Losses

Author

Ciccolella, S, Ricketts, C, Soto Gomez, M, Patterson, M, Silverbush, D, Bonizzoni, P, Hajirasouliha, I, Della Vedova, G, Ciccolella, Simone, Ricketts, Camir, Soto Gomez, Mauricio, Patterson, Murray, Silverbush, Dana, Bonizzoni, Paola, Hajirasouliha, Iman, Della Vedova, Gianluca, Ciccolella, S, Ricketts, C, Soto Gomez, M, Patterson, M, Silverbush, D, Bonizzoni, P, Hajirasouliha, I, Della Vedova, G, Ciccolella, Simone, Ricketts, Camir, Soto Gomez, Mauricio, Patterson, Murray, Silverbush, Dana, Bonizzoni, Paola, Hajirasouliha, Iman, and Della Vedova, Gianluca

Abstract

In recent years, the well-known Infinite Sites Assumption (ISA) has been a fundamental feature of computational methods devised for reconstructing tumor phylogenies and inferring cancer progressions. However, recent studies leveraging Single-Cell Sequencing (SCS) techniques have shown evidence of the widespread recurrence and, especially, loss of mutations in several tumor samples. While there exist established computational methods that infer phylogenies with mutation losses, there remain some advancements to be made.

Published
2021

39. A Comparison of the Preclinical Performance of the Echelon™+ Stapler with Thunderbird Reloads to Two Commercial Endoscopic Surgical Staplers

Author

Wang S, Hua Y, Liu J, Huang ZF, Clymer JW, Ricketts CD, and Hao J

Subjects
stapler, endoscopic, burst pressure, malformed staples, leaking, Medical technology, R855-855.5
Abstract

Shanshan Wang, Ying Hua, Jun Liu, Zhifan F Huang, Jeffrey W Clymer, Crystal D Ricketts, Jin Hao Ethicon, Inc, Cincinnati, OH, USACorrespondence: Jeffrey W Clymer, Ethicon, Inc, 4545 Creek Road, Cincinnati, OH, 45242, USA, Email jclymer@its.jnj.comBackground: Design of surgical staplers continues to advance with more consistent staple formation that can lead to higher leak pressures and lower rates of leak along the staple line. This study was performed to compare the Ethicon Echelon™+ Stapler with Thunderbird reloads to two other currently available commercial staplers, Reach Anzhi and Fulbright Lunar with corresponding reloads.Methods: The rate of malformed staples for three staplers was determined in porcine stomach (3.0– 3.3 mm thickness) via CT scanning. Staple line air leak pressures in bronchial tissue (3.0– 3.3 mm) and fluid leak pressures in colon (1.3– 1.7 mm) were measured and compared to a standard success criterion for both tissues.Results: The rate of malformed staples in gastric tissue for Echelon+ was more than 90% lower than for the two other commercial staplers (p < 0.001). In bronchus, Echelon+ had 56% higher air leak pressures than Reach Anzhi (p < 0.001) and was not significantly different from Fulbright Lunar. In colon, Echelon+ had over twice the fluid leak pressures of the comparators (p < 0.001).Conclusion: The Echelon+ Stapler with Thunderbird reloads exhibited a low rate of malformed staples, and its staple lines withstood high leak pressures in both thick and thin tissues. Clinical studies are needed to confirm that these observed benefits carry over into actual practice.Keywords: stapler, endoscopic, burst pressure, malformed staples, leaking

Published
2023

41. Teaching tools to promote active learning: case study

Author

Nirmalakhandan, N., Ricketts, C., McShannon, J., and Barrett, S.

Subjects
Engineering -- Study and teaching, Engineering -- Case studies, Software -- Usage, Education -- Methods, Education -- Case studies, Software quality, Business, Education, Engineering and manufacturing industries
Abstract

In this case study, we present a teaching approach that promotes active learning in engineering classes. Students are provided with a combination of physical, mathematical, and computer simulation models that allow them to participate, act, react, and reflect, rather than just listen to lectures, as in traditional classes. We illustrate important aspects of our pedagogy with one of 12 modules that have been implemented in an undergraduate hydraulic engineering course. Student evaluations indicate that this approach is appealing to most students. Data are presented to show that this approach has contributed to improved student learning and achievement. DOI: 10.1061/(ASCE)1052-3928(2007)133:1(31) CE Database subject headings: Physical properties; Mathematical models; Computer models; Computer software; Simulation models; Case reports; Engineering education.

Published
2007

42. Improving air-cooled condenser performance in combined cycle power plants

Author

Gadhamshetty, V., Nirmalakhandan, N., Myint, M., and Ricketts, C.

Subjects
Electric power-plants -- Energy use, Electric power-plants -- Tests, problems and exercises, Power plants -- Energy use, Power plants -- Tests, problems and exercises, Combined-cycle power plants -- Energy use, Combined-cycle power plants -- Thermal properties, Condensers (Vapors and gases) -- Evaluation, Condensers (Vapors and gases) -- Case studies, Engineering and manufacturing industries, Science and technology
Abstract

It has been recognized in recent times that air-cooled condensers (ACCs) are environmentally preferable to the traditional water-cooled condensers for rejecting heat in combined-cycle power plants (CCPPs). However, a drawback of ACCs is that their performance can decline with increasing ambient air temperature. A new approach is proposed in this paper that has the potential to alleviate this drawback of ACCs. In this approach, a chilled-water thermal energy storage system (TES) is used to precool the inflow air to the ACC whenever the ambient air temperature increases above the design air inlet temperature. The temperature of the TES system is maintained by an absorption refrigeration system (ARS) driven by low-quality waste heat from the CCPP. A process model integrating the CCPP with the ARS and the TES has been developed to optimize the volume of the TES. A 500 MW CCPP with steam turbine net output of 170.9 MW was chosen to evaluate the application of this approach for a power plant to be located in southern New Mexico. This analysis showed that a tank volume of 4,500 [m.sup.3] will be required to maintain the air temperature at the inlet to the ACC at the design value of 20[degrees]C throughout the year. Simulations under ambient air temperatures up to 40[degrees]C indicated that the proposed system is capable of maintaining the rated net power output of the plant with minimal fluctuations. Simulations also showed that TES tank volume is most sensitive to the design air inlet temperature to the ACC--an increase of this temperature by 1[degrees]C can result in at least 25% reduction in the volume. DOI: 10.1061/(ASCE)0733-9402(2006)132:2(81) CE Database subject headings: Absorption; Powerplants; Energy storage; Cooling; New Mexico.

Published
2006

43. Gaining retention and achievement for students program: a faculty development program

Author

McShannon, J., Hynes, P., Nirmalakhandan, N., Venkataramana, G., Ricketts, C., Ulery, A., and Steiner, R.

Subjects
Engineering -- Study and teaching, Engineering -- Curricula, Education -- Methods, Business, Education, Engineering and manufacturing industries
Abstract

This paper presents a unique faculty development program called Gaining Retention and Achievement for Students Program (GRASP) developed lit New Mexico State University. A fundamental assumption of GRASP is faculty are crucial to student retention and achievement, hence the primary focus on faculty. GRASP focuses on incorporating faculty's teaching behaviors which increase student retention and achievement. The program is composed of four interlaced components: assessment of student learning styles: faculty development to cultivate and implement appropriate teaching strategies: in-class observations and feedback of faculty and students' classroom behavior; and assessment of the impact on student retention and achievement. Student enrollment data is presented to demonstrate the success of GRASP in improving student retention and achievement. Faculty surveys indicate faculty changed teaching practices and intend to use program strategies in future semesters. CE Database subject headings: Teaching methods: Engineering education: Faculty: Students.

Published
2006

46. Tin resonance-ionization schemes for atomic- and nuclear-structure studies

Author

Gustafsson, F. P., primary, Ricketts, C. M., additional, Reitsma, M. L., additional, Garcia Ruiz, R. F., additional, Bai, S. W., additional, Berengut, J. C., additional, Billowes, J., additional, Binnersley, C. L., additional, Borschevsky, A., additional, Cocolios, T. E., additional, Cooper, B. S., additional, de Groote, R. P., additional, Flanagan, K. T., additional, Koszorús, Á., additional, Neyens, G., additional, Perrett, H. A., additional, Vernon, A. R., additional, Wang, Q., additional, Wilkins, S. G., additional, and Yang, X. F., additional

Published
2020
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47. Laser spectroscopy of indium Rydberg atom bunches by electric field ionization

Author

Vernon, A. R., primary, Ricketts, C. M., additional, Billowes, J., additional, Cocolios, T. E., additional, Cooper, B. S., additional, Flanagan, K. T., additional, Garcia Ruiz, R. F., additional, Gustafsson, F. P., additional, Neyens, G., additional, Perrett, H. A., additional, Sahoo, B. K., additional, Wang, Q., additional, Waso, F. J., additional, and Yang, X. F., additional

Published
2020
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48. Analytic response relativistic coupled-cluster theory: the first application to indium isotope shifts

Author

Sahoo, B K, primary, Vernon, A R, additional, Garcia Ruiz, R F, additional, Binnersley, C L, additional, Billowes, J, additional, Bissell, M L, additional, Cocolios, T E, additional, Farooq-Smith, G J, additional, Flanagan, K T, additional, Gins, W, additional, de Groote, R P, additional, Koszorús, Á, additional, Neyens, G, additional, Lynch, K M, additional, Parnefjord-Gustafsson, F, additional, Ricketts, C M, additional, Wendt, K D A, additional, Wilkins, S G, additional, and Yang, X F, additional

Published
2020
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