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1. MiMiC: A High-Performance Framework for Multiscale Molecular Dynamics Simulations

Author

Antalík, Andrej, Levy, Andrea, Kvedaravičiūtė, Sonata, Johnson, Sophia K., Carrasco-Busturia, David, Raghavan, Bharath, Mouvet, François, Acocella, Angela, Das, Sambit, Gavini, Vikram, Mandelli, Davide, Ippoliti, Emiliano, Meloni, Simone, Carloni, Paolo, Rothlisberger, Ursula, and Olsen, Jógvan Magnus Haugaard

Subjects
Physics - Chemical Physics
Abstract

MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an interoperable approach based on a multiple-program multiple-data (MPMD) paradigm, serving as an intermediary responsible for fast data exchange and interactions between the subsystems. The main goal of MiMiC is to avoid interfering with the underlying parallelization of the external programs, including the operability on hybrid architectures (e.g., CPU/GPU), and keep their setup and execution as close as possible to the original. At the moment, MiMiC offers an efficient implementation of electrostatic embedding QM/MM that has demonstrated unprecedented parallel scaling in simulations of large biomolecules using CPMD and GROMACS as QM and MM engines, respectively. However, as it is designed for high flexibility with general multiscale models in mind, it can be straightforwardly extended beyond QM/MM. In this article, we illustrate the software design and the features of the framework, which make it a compelling choice for multiscale simulations in the upcoming era of exascale high-performance computing.

Published
2024
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3. Larger cities host richer bee faunas, but are no refuge for species with concerning conservation status: Empirical evidence from Western Europe

Author

Arthur Fauviau, William Fiordaliso, Alessandro Fisogni, Laura Fortel, Frédéric Francis, Benoît Geslin, Nina Hautekèete, Charlène Heiniger, Olivier Lambert, Violette Le Feon, François Massol, Alice Michelot-Antalik, Denis Michez, Hugues Mouret, Grégoire Noël, Yves Piquot, Lise Ropars, Lucie Schurr, Colin Van Reeth, Vincent Zaninotto, Isabelle Dajoz, and Mickaël Henry

Subjects
Wild bees, City size, Urban green spaces, Species richness, Beta diversity, Endangered species, Ecology, QH540-549.5
Abstract

In the context of worldwide biodiversity and wild bee decline, it is increasingly important to better understand the effect of land-use changes on wild bee communities at a global scale. To do so, we studied the effect of city area and urban green spaces layout on wild bee species richness and community composition, as well as on wild bee species with an unfavorable UICN conservation status. This study was based on a large European dataset encompassing 20 cities from France, Belgium and Switzerland. We found a mean wild bee species richness in cities of 96 ± 48 (SD), showing that this species richness was highly variable among cities. The main factor positively influencing wild bee species richness in cities was the area of the city. Conversely, species richness was not significantly related to the total area of urban green spaces in a given city, measured as the spatial extent of urban parks, wastelands and other semi-natural habitats, excluding urban private gardens. Species with conservation status were quite scarce in urban environments, especially when compared to the European Red List of Bees, and we could not link their presence to either city or urban green space area. Dissimilarities in wild bee species community compositions were not associated with any of the studied characteristics of cities. We found that the dissimilarity of wild bee community composition among cities was mainly driven by the rarest species, as the most common ones were found in a majority of the cities sampled. Overall, these results emphasize that larger cities host more wild bee species, but are no refuge for the ones with concerning conservation status. Thus, stakeholders are encouraged to design their cities in favor of biodiversity to better support wild bee communities, and perhaps mitigate the established effect of the urban ecological filter.

Published
2024
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4. Drought response and urban-pollinator attractiveness of ornamental plant species

Author

Margaux Quinanzoni, David Marcolet, and Alice Michelot-Antalik

Subjects
Functional traits, Floral resources, Nectar, Pollen, Hymenoptera, Bees, Ecology, QH540-549.5
Abstract

Faced with pollinator declines, cities could serve as refuges for biodiversity conservation by managing floral resources in public green spaces. Ornamental plants could play an important role in attracting pollinators because they form part of urban floral management. However, knowledge of how their floral traits respond to drought is lacking, and it is unknown whether they will be suitable for pollinators under future climates. The main objective of this study was to determine the covariation of floral traits of ornamental plant species and effects of drought on them. To this end, in a city greenhouse we measured floral traits of eight ornamental species commonly used in urban green spaces in France. We subjected the plants to a control treatment or a drought treatment, reducing the volume and frequency of watering. We observed interspecific variability in floral traits among these species and a change in covariation between the traits pollen quantity and nectar quantity in the drought treatment. Drought influenced morphological traits related to floral display more than other floral traits, with mean decreases of 28 % in floral height, 35 % in floral area and 58 % in the number of floral units. Ornamental plants seemed attractive to different morphotypes of pollinators depending on their floral unit number, nectar sugar concentration or nectar tube depth, with most visits made by Hymenoptera. These results are expected to encourage green-space managers to select urban plants according to their functional characteristics and adapt their choice of plants to climate change.

Published
2024
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5. A Study of the Factors Influencing the Turnover of Slovakian Small and Medium-Sized Enterprises

Author

Karacsony, Peter, Szabo, David, Antalík, Imrich, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Montenegro, Carlos, editor, Rocha, Álvaro, editor, and Cueva Lovelle, Juan Manuel, editor

Published
2024
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7. A set of ecosystem service indicators for European grasslands based on botanical surveys

Author

Simon Taugourdeau, Frédérique Louault, Alice Michelot‐Antalik, Samir Messad, François Munoz, Denis Bastianelli, Pascal Carrère, and Sylvain Plantureux

Subjects
biodiversity conservation, ecosystem resilience, environmental modelling, forage, functional traits, meadows, Agriculture (General), S1-972, Plant culture, SB1-1110
Abstract

Abstract Background Grasslands provide a wide range of ecosystem services (ESs). However, there is currently no method for easily diagnosing the level of ESs produced. Our aim was to develop ES indicators based on botanical surveys, which are readily available data and integrative of grassland spatiotemporal variability. Methods Based on academic knowledge and expertise, we identified several simple vegetation criteria that we aggregated using a multicriteria analysis tool to construct indicators of the level of ESs provided by grasslands. In this study, the indicators were calculated from over 2000 botanical surveys spread over a wide biogeographical gradient. Results Analyses of correlation between the various indicators show that “forage supply” and “diversity conservation” were not correlated. “Forage availability” and “nitrogen availability for the vegetation” were positively linked together and negatively linked to the robustness of the plant community to extreme events. A temporal approach highlights that the “biodiversity conservation” score decreased from 1970 to 2010 and that “nitrogen availability for the vegetation” was lower in 1970 and 1980 than in 2000 and 2010. Conclusions These results show that our aggregation method based on a large data set of botanical surveys could be appropriate for studying temporal dynamics of ESs.

Published
2024
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8. SC1MC-2022: A database of transition metal complexes for training ML models to predict one-site entropies and mutual information

Author

Golub, Pavlo, Beran, Pavel, Antalik, Andrej, and Brabec, Jiri

Subjects
Physics - Chemical Physics
Abstract

We introduce a new version of the database SC1MC (SC1MC-2022), obtained by extension of the recent SC1MC-2020, which includes artificial mono transition metal complexes. The database involves reference data used as inputs for training of machine learning models, one- and two-site entropies, and mutual information obtained at the DMRG level for canonical and split-localised orbitals. The purpose of this database is to obtain as much as possible information about the electronic correlation structure, which could be exploited by machine learning models to estimate these important information without a significant computational cost for any similar type of systems with some degree of transferability.

Published
2021

9. Automatic selection of active spaces for strongly correlated systems using machine learning algorithms

Author

Golub, Pavlo, Antalik, Andrej, Veis, Libor, and Brabec, Jiri

Subjects
Physics - Chemical Physics
Abstract

The active-space quantum chemical methods could provide very accurate description of strongly correlated electronic systems, which is of tremendous value for natural sciences. The proper choice of the active space is crucial, but a non-trivial task. In this article, we present the neural network (NN) based approach for automatic selection of active spaces, focused on transition metal systems. The training set has been formed from artificial systems composed from one transition metal and various ligands, on which we have performed DMRG and calculated single-site entropy. On the selected set of systems, ranging from small benchmark molecules up to larger challenging systems involving two metallic centers, we demonstrate that our ML models could correctly predict the importance of orbitals with the high accuracy. Also, the ML models show a high degree of transferability on systems much larger than any complex used in training procedures.

Published
2020

11. Ground State of the Fe(II)-porphyrin Model System Corresponds to the Quintet State: A DFT and DMRG-based Tailored CC Study

Author

Antalík, Andrej, Nachtigallová, Dana, Lo, Rabindranath, Matoušek, Mikuláš, Lang, Jakub, Legeza, Örs, Pittner, Jiří, Hobza, Pavel, and Veis, Libor

Subjects
Physics - Chemical Physics
Abstract

Fe(II)-porphyrins (FeP) play an important role in many reactions relevant to material science and biological processes, due to their closely lying spin states. However, this small energetic separation also makes it challenging to establish the correct spin state ordering. Although the prevalent opinion is that these systems posses the triplet ground state, the recent experiment on Fe(II)-phthalocyanine under conditions matching those of an isolated molecule points toward the quintet ground state. We present a thorough study of FeP model by means of the density functional theory and density matrix renormalization group based tailored coupled clusters, in which we address all previously discussed correlation effects. We examine the importance of geometrical parameters, the Fe-N distances in particular, and conclude that the system possesses the quintet ground state, which is in our calculations well-separated from the triplet state.

Published
2020
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12. Near-linear Scaling in DMRG-based Tailored Coupled Clusters: An Implementation of DLPNO-TCCSD and DLPNO-TCCSD(T)

Author

Lang, Jakub, Antalík, Andrej, Veis, Libor, Brandejs, Jan, Brabec, Jiří, Legeza, Örs, and Pittner, Jiří

Subjects
Physics - Chemical Physics
Abstract

We present a new implementation of DMRG-based tailored coupled clusters method (TCCSD), which employs the domain-based local pair natural orbital approach (DLPNO-TCCSD). Compared to the previous LPNO version of the method, the new implementation is more accurate, offers more favorable scaling and provides more consistent behavior across the variety of systems. On top of the singles and doubles, we include the perturbative triples correction (T), which is able to retrieve even more dynamic correlation. The methods were tested on three systems: tetramethyleneethane, oxo-Mn(Salen) and Iron(II)-porphyrin model. The first two were revisited to assess the performance with respect to LPNO-TCCSD. For oxo-Mn(Salen), we retrieved between 99.8-99.9% of the total canonical correlation energy which is the improvement of 0.2% over the LPNO version in less than 63% of the total LPNO runtime. Similar results were obtained for Iron(II)-porphyrin. When the perturbative triples correction was employed, irrespective of the active space size or system, the obtained energy differences between two spin states were within the chemical accuracy of 1 kcal/mol using the default DLPNO settings., Comment: Updated version: 15 pages. arXiv admin note: text overlap with arXiv:1905.06833

Published
2019
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13. Towards the Efficient Local Tailored Coupled Cluster Approximation and the Peculiar Case of Oxo-Mn(Salen)

Author

Antalík, Andrej, Veis, Libor, Brabec, Jiří, Legeza, Örs, and Pittner, Jiří

Subjects
Physics - Chemical Physics, Quantum Physics
Abstract

We introduce a new implementation of the coupled cluster method tailored by matrix product states wave functions (DMRG-TCCSD), which employs the local pair natural orbital approach (LPNO). By exploiting locality in the coupled cluster stage of the calculation, we were able to remove some of the limitations that hindered the application of the canonical version of the method to larger systems and/or with larger basis sets. We assessed the accuracy of the approximation using two systems: tetramethyleneethane (TME) and oxo-Mn(Salen). Using the default cut-off parameters, we were able to recover over 99.7% and 99.8% of canonical correlation energy for the triplet and singlet state of TME respectively. In case of oxo-Mn(Salen), we found out that the amount of retrieved canonical correlation energy depends on the size of the active space (CAS) - we retrieved over 99.6% for the larger 27 orbital CAS and over 99.8% for the smaller 22 orbital CAS. The use of LPNO-TCCSD allowed us to perform these calculations up to quadruple-$\zeta$ basis set amounting to 1178 basis functions. Moreover, we examined dependance of the ground state of oxo-Mn(Salen) on CAS composition. We found out that the inclusion of 4d$_{xy}$ orbital plays an important role in stabilizing the singlet state at the DMRG-CASSCF level via double-shell effect. However, by including dynamic correlation the ground state was found to be triplet regardless of the size of the basis set or composition of CAS, which is in agreement with previous findings by canonical DMRG-TCCSD in smaller basis.

Published
2019
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17. Numerical and Theoretical Aspects of the DMRG-TCC Method Exemplified by the Nitrogen Dimer

Author

Faulstich, Fabian M., Máté, Mihály, Laestadius, Andre, Csirik, Mihály András, Veis, Libor, Antalik, Andrej, Brabec, Jiří, Schneider, Reinhold, Pittner, Jiří, Kvaal, Simen, and Legeza, Örs

Subjects
Physics - Chemical Physics, Condensed Matter - Strongly Correlated Electrons, Physics - Atomic Physics, Physics - Computational Physics, Quantum Physics
Abstract

In this article, we investigate the numerical and theoretical aspects of the coupled-cluster method tailored by matrix-product states. We investigate chemical properties of the used method, such as energy size extensivity and the equivalence of linked and unlinked formulation. The existing mathematical analysis is here elaborated in a quantum chemical framework. In particular, we highlight the use of a so-called CAS-ext gap describing the basis splitting between the complete active space and the external part. Moreover, the behavior of the energy error as a function of the optimal basis splitting is discussed. We show numerical investigations on the robustness with respect to the bond dimensions of the single orbital entropy and the mutual information, which are quantities that are used to choose the complete active space. Furthermore, we extend the mathematical analysis with a numerical study on the complete active space dependence of the error.

Published
2018
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18. A large-scale dataset reveals taxonomic and functional specificities of wild bee communities in urban habitats of Western Europe

Author

Arthur Fauviau, Mathilde Baude, Nicolas Bazin, William Fiordaliso, Alessandro Fisogni, Laura Fortel, Joseph Garrigue, Benoît Geslin, Jérémie Goulnik, Laurent Guilbaud, Nina Hautekèete, Charlène Heiniger, Michael Kuhlmann, Olivier Lambert, Dominique Langlois, Violette Le Féon, Carlos Lopez Vaamonde, Grégory Maillet, François Massol, Nadia Michel, Alice Michelot-Antalik, Denis Michez, Hugues Mouret, Yves Piquot, Simon G. Potts, Stuart Roberts, Lise Ropars, Lucie Schurr, Colin Van Reeth, Irène Villalta, Vincent Zaninotto, Isabelle Dajoz, and Mickaël Henry

Subjects
Medicine, Science
Abstract

Abstract Wild bees are declining, mainly due to the expansion of urban habitats that have led to land-use changes. Effects of urbanization on wild bee communities are still unclear, as shown by contrasting reports on their species and functional diversities in urban habitats. To address this current controversy, we built a large dataset, merging 16 surveys carried out in 3 countries of Western Europe during the past decades, and tested whether urbanization influences local wild bee taxonomic and functional community composition. These surveys encompassed a range of urbanization levels, that were quantified using two complementary metrics: the proportion of impervious surfaces and the human population density. Urban expansion, when measured as a proportion of impervious surfaces, but not as human population density, was significantly and negatively correlated with wild bee community species richness. Taxonomic dissimilarity of the bee community was independent of both urbanization metrics. However, occurrence rates of functional traits revealed significant differences between lightly and highly urbanized communities, for both urbanization metrics. With higher human population density, probabilities of occurrence of above-ground nesters, generalist and small species increased. With higher soil sealing, probabilities of occurrence of above-ground nesters, generalists and social bees increased as well. Overall, these results, based on a large European dataset, suggest that urbanization can have negative impacts on wild bee diversity. They further identify some traits favored in urban environments, showing that several wild bee species can thrive in cities.

Published
2022
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19. Full configuration interaction quantum Monte Carlo benchmark and multireference coupled cluster studies of tetramethyleneethane diradical

Author

Veis, Libor, Antalík, Andrej, Legeza, Örs, Alavi, Ali, and Pittner, Jiří

Subjects
Physics - Chemical Physics, Condensed Matter - Strongly Correlated Electrons
Abstract

We have performed a FCI-quality benchmark calculation for the tetramethyleneethane molecule in cc-pVTZ basis set employing a subset of CASPT2(6,6) natural orbitals for the FCIQMC calculation. The results are in an excellent agreement with the previous large scale diffusion Monte Carlo calculations by Pozun et al. and available experimental results. Our computations verified that there is a maximum on PES of the ground singlet state ($^1\text{A}$) $45^{\circ}$ torsional angle and the corresponding vertical singlet-triplet energy gap is $0.01$ eV. We have employed this benchmark for assessment of the accuracy of MkCCSDT and DMRG-tailored CCSD (TCCSD) methods. MR MkCCSDT with CAS(2,2) model space, though giving good values for the singlet-triplet energy gap, is not able to properly describe the shape of the multireference singlet PES. Similarly, DMRG(24,25) is not able to correctly capture the shape of the singlet surface, due to the missing dynamic correlation. On the other hand, the DMRG-tailored CCSD method describes the shape of the ground singlet state with an excellent accuracy, but for the correct ordering requires computation of the zero-spin-projection component of the triplet state ($^3\text{B}_1$).

Published
2018
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22. Coupled cluster method with single and double excitations tailored by matrix product state wave functions

Author

Veis, Libor, Antalík, Andrej, Brabec, Jiří, Neese, Frank, Legeza, Örs, and Pittner, Jiří

Subjects
Physics - Chemical Physics, Quantum Physics
Abstract

In the last decade, the quantum chemical version of the density matrix renormalization group (DMRG) method has established itself as the method of choice for calculations of strongly correlated molecular systems. Despite its favourable scaling, it is in practice not suitable for computations of dynamic correlation. We present a novel method for accurate "post-DMRG" treatment of dynamic correlation based on the tailored coupled cluster (CC) theory in which the DMRG method is responsible for the proper description of non-dynamic correlation, whereas dynamic correlation is incorporated through the framework of the CC theory. We illustrate the potential of this method on prominent multireference systems, in particular N$_2$, Cr$_2$ molecules and also oxo-Mn(Salen) for which we have performed the first "post-DMRG" computations in order to shed light on the energy ordering of the lowest spin states.

Published
2016
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26. Larger cities host richer bee faunas, but are no refuge for species with concerning conservation status: Empirical evidence from Western Europe.

Author

Fauviau, Arthur, Fiordaliso, William, Fisogni, Alessandro, Fortel, Laura, Francis, Frédéric, Geslin, Benoît, Hautekèete, Nina, Heiniger, Charlène, Lambert, Olivier, Feon, Violette Le, Massol, François, Michelot-Antalik, Alice, Michez, Denis, Mouret, Hugues, Noël, Grégoire, Piquot, Yves, Ropars, Lise, Schurr, Lucie, Reeth, Colin Van, and Zaninotto, Vincent

Subjects
BEE colonies, PUBLIC spaces, CITIES & towns, WILDLIFE conservation, SPECIES diversity, GARDEN cities
Abstract

In the context of worldwide biodiversity and wild bee decline, it is increasingly important to better understand the effect of land-use changes on wild bee communities at a global scale. To do so, we studied the effect of city area and urban green spaces layout on wild bee species richness and community composition, as well as on wild bee species with an unfavorable UICN conservation status. This study was based on a large European dataset encompassing 20 cities from France, Belgium and Switzerland. We found a mean wild bee species richness in cities of 96 ± 48 (SD), showing that this species richness was highly variable among cities. The main factor positively influencing wild bee species richness in cities was the area of the city. Conversely, species richness was not significantly related to the total area of urban green spaces in a given city, measured as the spatial extent of urban parks, wastelands and other semi-natural habitats, excluding urban private gardens. Species with conservation status were quite scarce in urban environments, especially when compared to the European Red List of Bees, and we could not link their presence to either city or urban green space area. Dissimilarities in wild bee species community compositions were not associated with any of the studied characteristics of cities. We found that the dissimilarity of wild bee community composition among cities was mainly driven by the rarest species, as the most common ones were found in a majority of the cities sampled. Overall, these results emphasize that larger cities host more wild bee species, but are no refuge for the ones with concerning conservation status. Thus, stakeholders are encouraged to design their cities in favor of biodiversity to better support wild bee communities, and perhaps mitigate the established effect of the urban ecological filter. [ABSTRACT FROM AUTHOR]

Published
2024
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31. A set of ecosystem service indicators for European grasslands based on botanical surveys

Author

Taugourdeau, Simon, Louault, Frédérique, Michelot-Antalik, Alice, Messad, Samir, Munoz, François, Bastianelli, Denis, Carrère, Pascal, Plantureux, Sylvain, Taugourdeau, Simon, Louault, Frédérique, Michelot-Antalik, Alice, Messad, Samir, Munoz, François, Bastianelli, Denis, Carrère, Pascal, and Plantureux, Sylvain

Abstract

Background: Grasslands provide a wide range of ecosystem services (ESs). However, there is currently no method for easily diagnosing the level of ESs produced. Our aim was to develop ES indicators based on botanical surveys, which are readily available data and integrative of grassland spatiotemporal variability. Methods: Based on academic knowledge and expertise, we identified several simple vegetation criteria that we aggregated using a multicriteria analysis tool to construct indicators of the level of ESs provided by grasslands. In this study, the indicators were calculated from over 2000 botanical surveys spread over a wide biogeographical gradient. Results: Analyses of correlation between the various indicators show that “forage supply” and “diversity conservation” were not correlated. “Forage availability” and “nitrogen availability for the vegetation” were positively linked together and negatively linked to the robustness of the plant community to extreme events. A temporal approach highlights that the “biodiversity conservation” score decreased from 1970 to 2010 and that “nitrogen availability for the vegetation” was lower in 1970 and 1980 than in 2000 and 2010. Conclusions: These results show that our aggregation method based on a large data set of botanical surveys could be appropriate for studying temporal dynamics of ESs.

Published
2024

32. Ticagrelor in patients with diabetes and stable coronary artery disease with a history of previous percutaneous coronary intervention (THEMIS-PCI): a phase 3, placebo-controlled, randomised trial

Author

Santos, Vladimir, Jain, Ashit, Lendel, Irina, Russo, Michael, Haught, W H, Bouza, Manuel, Gogia, Harinder, Banerjee, Supratim, Kichura, George, Kantaros, Louis, Padron, Francisco, Passi, Rakesh, Stone, Jay, Pursley, Michael, D'Urso, Michael, Gardner, Timothy, Bennett, James, Nour, Khaled, Saini, Satinder, Zhang, Wenwu, Kumbhani, Dharam, Thomas, Dustin, Angiolillo, Dominick, Bertolet, Barry, Roman-Miranda, Amaury, Black, Robert, Manshadi, Ramin, Vaca, Carlos, Blanco, Antonio, Napoli, Mark, Brabham, David, Akyea-Djamson, Ayim, Desai, Pratik, Prasada, Sudhir, Khaira, Ajit, Forgosh, Leslie, Lieber, Ira, Umpierrez, Guillermo, Singal, Dinesh, Londono, Juan, Fraser, Neil, Ruiz, Jose, Vega, Damaris, Rodriguez, Lilia, Brown, Christopher, Syed, Faizullah, Aggarwala, Guarav, Eaves, William, Foster, Michael, Gupta, Dinesh, Avino, David, Asfour, Wail, Tonnessen, Glen, Zhao, Xue-Qiao, Singh, Narendra, Brockmyre, Andrew, Lepor, Norman, Shammas, Nicolas, Blick, David, Hearne, Steven, Prodafikas, John, Carell, Edgar, Izzo, Mark, Karim, Amin, Zakhary, Bosh, Atieh, Mahmoud, Leichter, Steven, Meadows, Charles, Hotchkiss, David, Abu-Fadel, Mazen, Wiseman, Alan, Bander, Jeffrey, Shah, Mahesh, Banerjee, Subhash, Ganim, Ricky, Sopko, Karen, Khan, Misal, Lloret, Ramon, Weirick, Troy, Mehta, Rajendra, Thadani, Udho, Bhargava, Anuj, Kosiborod, Mikhail, Moya, Jaynier, Staniloae, Cezar, Guerra, Yamirka D, Chhabra, Anil, Kosmicki, Douglas, Shaheen, Wassim, Mohammed, Akber, Bitters, J'Cinda, Pattanayak, Jan, Javier, Julian, Srivastava, Sunny, Phillips, Roland, Al-Amin, Jessie, Lillestol, Michael, Simpson, Patrick, Hazan, Lydie, Amin, Amit, Shah, Gopi, Korpas, Denes, Platt, Bruce, Dickert, Jim, Puente, Orlando, Hiotis, Louis, Doyle, Timothy, Rajan, Raj, Meholick, Alan, Gring, Christian, Hage-Korban, Elie, Feldman, Robert, Colfer, Harry, Butman, Samuel, Foster, Malcolm, Hart, Terence, Huling, Randall, Eshaghian, Shervin, Quintana, Ofsman, Cheung, Deanna, Handel, Franklin, Rodriguez, Mara, Suh, David, Gordon, Paul, Pressman, Gregg, Bauer, Michael, French, William, Barettella, Mark, Chatrathi, Sridhar, Suresh, Damodhar, Goldberg, Ronald, Huth, Mark, Younis, Liwa, Rahman, Aref, Mascolo, Richard, Welch, Michelle, Suneja, Randeep, Smith, Stephen, Shurmur, Scott, Agaiby, John, Jingo, Ahmad, Johnston, Janice, Beth, Mary, Vlastaris, Anthony, Kemp, Susan, Taheri, Hamid, Pereira, Edward, Deyoung, Michael, Hawa, Zafir, Smith, Ray, Galski, Thomas, Garas, Samer, Reddy, M, Sharma, Susheel, Hargrove, Joeseph, Treasure, Charles, Emerson, Ronald, Haddad, Tariq, Rohr, Kathryn, Levinson, Larry, Gaona, Raul, Uretsky, Barry, Maheshwari, Hiralal, Lee, Denny, Kinnaman, Stephanie, Singal, Robert, Geohas, Jeffrey, Gigliotti, Osvaldo, Raisinghani, Ajit, Khurana, Charanjit, Hella, Brent, Kelberman, Michael, Voyce, Steven, Singh, Sanjay, Lo, Eric, Singh, Pradeep, Goodfellow, Ross, Fischer, Stuart, Lorraine, Richard, Turner, Traci, Shanes, Jeffrey, Busch, Robert, Broker, Robert, Zaniewski, Michelle, Pounds, Kevin, Debs-Perez, Giselle, Ong, Stephen, Frandsen, Brad, Fullington, Douglas, Jaffrani, Naseem, Khan, Ahtaram, Lee, Marcus, Pouzar, Joe, Revtyak, George, Gonzalez, Julian, Nakhle, Samer, Murillo, Abel, Young, Douglas, Makam, Sashi, Syed, Mushtaq, Woolf, Kevin, Grena, Paul, Alfata, Sarab, Mahal, Sharan, Hoffman, David, Kizhakekuttu, Tinoy, Deering, Joseph, Bhavsar, Janak, Mikesell, Scott, Wilson, William, Wilson, Vance, El, Salah, Spinale, Francis, Kannarkat, Vinod, Rao, Sunder, Hanson, Lenita, Bertsch, John, Gonzalez-Ortiz, Elena, Severino, Norma, Willis, John, Schock, Joel, Bakhtari, Ladan, Gazmuri, Raul, Ansari, Saadat, Hall, Jason, Mehta, Arvind, Shealy, Neal, Zarich, Stuart, Singh, Deovrat, Vora, Kishor, Andrawis, Nabil, Molter, Darron, Maron, David, Cardona, Jose, D'Agostino, Ronald, Arshad, Tamjeed, Samaan, Rodney, Jones, David, Presser, Dale, Heath, John, Green, Sandy, Bittar, George, Henry, Sheldon, Korn, David, Schmedtje, John, Nadar, Venkatesh, Graham, Bruce, Labroo, Ajay, Clavijo, Leonardo, Roseman, Hal, Ledesma, Gilbert, Rosen, Robert, Dor, Isaac, Kirby, William, Sutton, Jennefer, Eder, Frank, Iteld, Bruce, Gomez-Cortes, Jose, Buchbinder, Maurice, Kasper, Joseph, Terrelonge, Antonio, Torres, Gustavo, Jagielo, Ted, Alvarez, Jose, Handelsman, Yehuda, Guillen, Mario, Richwine, Randall, Lewy-Alterbaum, Lorena, Corder, Clinton, Arvind, Moogali, Bolshoun, David, Mikhail, Magdy, Minton, Stephen, Alvarado, Odilon, Abbott, J, Cauthen, Brett, Welter, Ryan, Mintz, Randy, Cox, John, Quick, Annette, Weiss, Melvin, Dy, Johnny, Zebrack, James, Gandelman, Glenn, Hegde, Vinayak, Silver, Marc, DeGregorio, Michele, Lawson, William, Paa, Christopher, Bortnick, Anna, Krolick, Merrill, Sotolongo, Rodolfo, Cheirif, Jorge, Kumar, Priya, Jetty, Preetham, Patel, Ambar, Kruk, Mariusz, Kobielusz-Gembala, Iwona, Rewerska, Barbara, Madrzejewski, Adam, Milewski, Krzysztof, Cygler, Jerzy, Petryka-Mazurkiewicz, Joanna, Jastrzebski, Waldemar, Korecki, Janusz, Fil, Wojciech, 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Published
2019
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33. Viscosity and Diffusion: Crowding and Salt Effects in Protein Solutions

Author

Heinen, Marco, Zanini, Fabio, Roosen-Runge, Felix, Fedunová, Diana, Zhang, Fajun, Hennig, Marcus, Seydel, Tilo, Schweins, Ralf, Sztucki, Michael, Antalík, Marián, Schreiber, Frank, and Nägele, Gerhard

Subjects
Condensed Matter - Soft Condensed Matter
Abstract

We report on a joint experimental-theoretical study of collective diffusion in, and static shear viscosity of solutions of bovine serum albumin (BSA) proteins, focusing on the dependence on protein and salt concentration. Data obtained from dynamic light scattering and rheometric measurements are compared to theoretical calculations based on an analytically treatable spheroid model of BSA with isotropic screened Coulomb plus hard-sphere interactions. The only input to the dynamics calculations is the static structure factor obtained from a consistent theoretical fit to a concentration series of small-angle X-ray scattering (SAXS) data. This fit is based on an integral equation scheme that combines high accuracy with low computational cost. All experimentally probed dynamic and static properties are reproduced theoretically with an at least semi-quantitative accuracy. For lower protein concentration and low salinity, both theory and experiment show a maximum in the reduced viscosity, caused by the electrostatic repulsion of proteins. The validity range of a generalized Stokes-Einstein (GSE) relation connecting viscosity, collective diffusion coefficient, and osmotic compressibility, proposed by Kholodenko and Douglas [PRE 51, 1081 (1995)] is examined. Significant violation of the GSE relation is found, both in experimental data and in theoretical models, in semi-dilute systems at physiological salinity, and under low-salt conditions for arbitrary protein concentrations.

Published
2011
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35. Drought response and urban-pollinator attractiveness of ornamental plant species.

Author

Quinanzoni, Margaux, Marcolet, David, and Michelot-Antalik, Alice

Subjects
ORNAMENTAL plants, PLANT species, DROUGHTS, DROUGHT management, PUBLIC spaces, CITIES & towns, BIODIVERSITY conservation
Abstract

Faced with pollinator declines, cities could serve as refuges for biodiversity conservation by managing floral resources in public green spaces. Ornamental plants could play an important role in attracting pollinators because they form part of urban floral management. However, knowledge of how their floral traits respond to drought is lacking, and it is unknown whether they will be suitable for pollinators under future climates. The main objective of this study was to determine the covariation of floral traits of ornamental plant species and effects of drought on them. To this end, in a city greenhouse we measured floral traits of eight ornamental species commonly used in urban green spaces in France. We subjected the plants to a control treatment or a drought treatment, reducing the volume and frequency of watering. We observed interspecific variability in floral traits among these species and a change in covariation between the traits pollen quantity and nectar quantity in the drought treatment. Drought influenced morphological traits related to floral display more than other floral traits, with mean decreases of 28 % in floral height, 35 % in floral area and 58 % in the number of floral units. Ornamental plants seemed attractive to different morphotypes of pollinators depending on their floral unit number, nectar sugar concentration or nectar tube depth, with most visits made by Hymenoptera. These results are expected to encourage green-space managers to select urban plants according to their functional characteristics and adapt their choice of plants to climate change. [ABSTRACT FROM AUTHOR]

Published
2024
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39. Relativistic Quark Model Based Description of Low Energy NN Scattering

Author

Antalik, R. and Lyubovitskij, V. E.

Subjects
High Energy Physics - Phenomenology, Nuclear Theory
Abstract

A description of the NN scattering is constructed starting from the $\pi, \eta, \eta'$ pseudoscalar-, the $\rho, \phi, \omega$ vector-, and the $\varepsilon(600), a_0, f_0(1400)$ scalar - meson-nucleon coupling constants, which we obtain within a relativistic quark model. Working within the Blankenbecler-Sugar-Logunov-Tavkhelidze quasipotential dynamics we thus describe the NN phase shifts in a relativistically invariant way. In this procedure we use the phenomenological form factor cutoff masses and the effective $\varepsilon$ and $\omega$ meson-nucleon coupling constants, only. The comparison of our NN phase shifts to the both empirical data and the Bonn OBEP fit shows good agreement -- the ratio of the $\chi^2$ for the present results to the $\chi^2$ for Bonn OBEP description is 1.2., Comment: 20 LaTeX pages, 2 postscript figures are available on request. Preprint IPSAS-RA-9401

Published
1994
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40. Using Matching Traits to Study the Impacts of Land-Use Intensification on Plant–Pollinator Interactions in European Grasslands: A Review

Author

Jérémie Goulnik, Sylvain Plantureux, Isabelle Dajoz, and Alice Michelot-Antalik

Subjects
pollination function, grasslands, agricultural practices, functional trait, effect trait, plant–pollinator interaction network, Science
Abstract

Permanent grasslands are suitable habitats for many plant and animal species, among which are pollinating insects that provide a wide range of ecosystem services. A global crisis in pollination ecosystem service has been highlighted in recent decades, partly the result of land-use intensification. At the grassland scale, however, the underlying mechanisms of land-use intensification that affect plant–pollinator interactions and pollination remain understudied. In this review, we first synthesise the literature to provide new insights into the relationships between land-use intensification and pollination by using matching community and interaction traits. We then identify knowledge gaps and summarise how land-use intensification of grassland influences floral traits that may in turn be associated with modifications to pollinator matching traits. Last, we summarise how these modifications may affect pollination function on permanent grasslands. Overall, land-use intensification may lead to a shift in flower colour, a decrease in mean nectar tube depth and a decrease in reward production and pollen quality at the community level. This, in turn, may generate a decrease in pollinator mouthparts length and body size, that may favour pollinators that require a low amount of floral reward. We found no study citing the effect of land-use intensification on volatile organic compounds emitted by flowers despite the importance of these molecules in pollinator community composition. Overall, our review highlighted major knowledge gaps about the effects of land-use intensification on plant–pollinator interactions, and suggests that land-use intensification could favour plants with generalised floral traits that adversely affect pollination.

Published
2021
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42. Weed flower dilemma: competitiveness with few costly flowers or ruderality with numerous cheap flowers?

Author

Léa Genty, Elena Kazakou, Aurélie Metay, Mathilde Baude, Antoine Gardarin, Alice Michelot-Antalik, Armel Sotillo, Ambroise Leroy, Juliette Crouzet, and Karim Barkaoui

Abstract

Weed species are ecological models that recently received considerable attention due to their particular strategies linked to their ruderal-competitive traits. They are known to have the potential to provide additional floral resources for insects in flower-poor agroecosystems. However, their floral traits are much more scarcely studied than those of plants found in other habitats, such as grasslands. The aim of this study was to describe the floral phenotype of weeds and to determine to what extent their floral traits match their ecological strategies as described on the basis of leaf traits. We therefore cultivated 19 forb weeds from perennial agroecosystems, previously identified in Mediterranean fields, in a greenhouse for seven months and collected data on 12 floral and 5 leaf traits. We tested whether these traits covaried and whether they exhibited an ecological strategy at the phenotype scale. We found that in matters of flower production, weed species face a trade-off: either numerous small, low-stature flowers with small quantities of pollen and nectar, or few, large, higher-held flowers with more pollen and nectar. The floral traits were found to reflect Grime’s CSR strategies: the weed species producing fewer but costlier flowers belonged to C-strategy species, whereas those producing more but less costly flowers belonged to species dominated by an R strategy These findings indicate that the potential of weeds as floral resources for insects is related to their ecological strategies, which are known to be affected by agricultural practices that filter species composition. This implies that, as for the provision of other ecosystem services, weed communities can be managed so as to select species with interesting floral traits for pollinators.

Published
2023
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43. Forage nutritive value shows synergies with plant diversity in a wide range of semi-natural grassland habitats

Author

Cian Blaix, Olivier Chabrerie, Didier Alard, Manuella Catterou, Sylvain Diquelou, Thierry Dutoit, Jérôme Lacoux, Grégory Loucougaray, Alice Michelot-Antalik, Marine Pacé, Antoine Tardif, Servane Lemauviel-Lavenant, Anne Bonis, Laboratoire de Géographie Physique et Environnementale (GEOLAB), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut Sciences de l'Homme et de la Société (IR SHS UNILIM), Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecophysiologie Végétale, Agronomie et Nutritions NCS (EVA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Laboratoire des EcoSystèmes et des Sociétés en Montagne (UR LESSEM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Agronomie et Environnement (LAE), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work is a result of the SUR-PAS project ('SURveillance de l’état de conservation des habitats agro-PAStoraux pelousaires et prairiaux') funded by Le Ministère de la Transition Ecologique et Solidaire (MTES) and driven by UMS PatriNat for the Office Français de la Biodiversité (OFB), within the framework of the 'Habitats, Fauna, Flora' directive, Natura 2000 Project., and This work is a result of the SUR-PAS project ('SURveillance de l’état de conservation des habitats agro-PAStoraux pelousaires et prairiaux') funded by Le Ministère de la Transition Ecologique et Solidaire (MTES), France, and driven by UMS PatriNat for the Office Français de la Biodiversité (OFB), within the framework of the 'Habitats, Fauna, Flora' directive, Natura 2000 Project

Subjects
History, LDMC, Ecology, Polymers and Plastics, mineral content, [SDV]Life Sciences [q-bio], Evenness, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Functional diversity, Industrial and Manufacturing Engineering, permanent grasslands, Grassland conservation, Forage quality, crude protein, forage digestibility, [SDE]Environmental Sciences, Animal Science and Zoology, Natura 2000, SLA, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Business and International Management, semi-natural grasslands, Agronomy and Crop Science, Species diversity
Abstract

International audience; Assessing the relationship between grassland plant diversity and agronomic value is a major challenge to reconcile nature conservation and agricultural use of extensive grassland habitats. To do this, multiple facets of forage production must be considered such as the quantity produced and its nutritive value, commonly assessed through its digestibility, energy content, and nutrient content. The aim of this study was to analyse the effects of plant diversity and functional traits on forage productivity and nutritive value in a wide set of semi-natural grassland habitats.Forage was sampled in 202 plots located across 68 permanent extensive grasslands in eight regions of France. Species and functional diversity indices, community-weighted means (CWM) of plant functional traits, and the relative cover of main plant functional types (PFT; graminoids, forbs, and legumes) were used to describe plant communities. Forage production was evaluated by recording early standing biomass (SB), and nutritive value parameters, namely digestibility (DMD), crude protein content (CP), and average mineral content (MinAv) at the beginning of the vegetation growing season.Species richness was negatively associated with SB and MinAv. Species evenness was positively correlated with CP, DMD, and MinAv, while PFT evenness was positively correlated with CP and DMD. Forage standing biomass increased with increasing graminoid cover and decreased with increasing forb cover. A higher legume cover and specific leaf area CWM as well as a lower leaf dry matter content CWM was associated with improved forage nutritive value and had no effect on SB. Our results highlight that a better forage nutritive value can be obtained with a higher plant species evenness in permanent grassland habitats. Furthermore, in grasslands with an even distribution of plant functional types, forage nutritive value may be improved with no loss in early standing biomass.

Published
2023
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46. The N-Terminal Region of the Ryanodine Receptor Affects Channel Activation

Author

Andrea Faltinova, Nataša Tomaskova, Marián Antalik, Jozef Sevcik, and Alexandra Zahradnikova

Subjects
ryanodine receptor, domain peptide, allosteric activation, CPVT mutations, planar lipid bilayer, structural modeling, Physiology, QP1-981
Abstract

Mutations in the cardiac ryanodine receptor (RyR2), the ion channel responsible for release of calcium ions from intracellular stores into cytoplasm, are the cause of several inherited cardiac arrhythmias. At the molecular level, disease symptoms can be mimicked by domain peptides from mutation-prone regions of RyR2 that bind to RyR2 and activate it. Here we show that the domain peptide DPcpvtN2, corresponding to the central helix of the N-terminal region of RyR2, activates the RyR2 channel. Structural modeling of interaction between DPcpvtN2 and the N-terminal region of RyR2 in the closed and open conformation provided three plausible structures of the complex. Only one of them could explain the dependence of RyR2 activity on concentration of DPcpvtN2. The structure of the complex was at odds with the previously proposed “domain switch” mechanism of competition between domain peptides and ryanodine receptor domains. Likewise, in structural models of the N-terminal region, the conformational changes induced by DPcpvtN2 binding were different from those induced by mutation of central helix amino acids. The activating effect of DPcpvtN2 binding and of mutations in the central helix could be explained by their similar effect on the transition energy between the closed and open conformation of RyR2.

Published
2017
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47. A large-scale dataset reveals taxonomic and functional specificities of wild bee communities in urban habitats of Western Europe

Author

Fauviau, Arthur, primary, Baude, Mathilde, additional, Bazin, Nicolas, additional, Fiordaliso, William, additional, Fisogni, Alessandro, additional, Fortel, Laura, additional, Garrigue, Joseph, additional, Geslin, Benoît, additional, Goulnik, Jérémie, additional, Guilbaud, Laurent, additional, Hautekèete, Nina, additional, Heiniger, Charlène, additional, Kuhlmann, Michael, additional, Lambert, Olivier, additional, Langlois, Dominique, additional, Le Féon, Violette, additional, Lopez Vaamonde, Carlos, additional, Maillet, Grégory, additional, Massol, François, additional, Michel, Nadia, additional, Michelot-Antalik, Alice, additional, Michez, Denis, additional, Mouret, Hugues, additional, Piquot, Yves, additional, Potts, Simon G., additional, Roberts, Stuart, additional, Ropars, Lise, additional, Schurr, Lucie, additional, Van Reeth, Colin, additional, Villalta, Irène, additional, Zaninotto, Vincent, additional, Dajoz, Isabelle, additional, and Henry, Mickaël, additional

Published
2022
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