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1. Synthesis, electronic and photophysical properties of a bisacridinium-Zn(II) porphyrin conjugate

Author

Edo-Osagie, Amy, Sánchez-Resa, Daniel, Serillon, Dylan, Bandini, Elisa, Gourlaouen, Christophe, Jacquot de Rouville, Henri-Pierre, Ventura, Barbara, and Heitz, Valérie

Subjects
Acridinium, Porphyrin, Electron transfer, Electrochemistry, Transient absorption spectroscopy, Calculated spectra, Biochemistry, QD415-436, Physical and theoretical chemistry, QD450-801, Mathematics, QA1-939
Abstract

The synthesis of a novel bisacridinium-Zn(II) porphyrin is reported and its properties investigated via electrochemical, photophysical and computational studies. Cyclic voltammetry studies revealed a two-electron oxidation of the Zn(II) porphyrin and the simultaneous one electron reductions of the two acridiniums. Using absorption, emission and ultrafast transient absorption spectroscopies, the near total fluorescence quenching observed following excitation of either the acridinium or Zn(II) porphyrin units was assigned to ultrafast electron transfer (${\le }0.3$ ps) leading to a reduced acridinium and an oxidized porphyrin unit in the bisacridinium-Zn(II) porphyrin conjugate. In addition, computational studies were found to complement experimental results, with calculations revealing two near degenerate HOMOs for the porphyrin.

Published
2021
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2. Rhizophagus intraradices and Azospirillum brasilense improve growth of herbaceous plants and soil biological activity in revegetation of a recovering coal-mining area

Author

Meyer, Edenilson, Stoffel, Shantau Camargo Gomes, de Almeida, Anna Flávia Neri, do Amaral Scarsanella, Juliana, Vieira, André Steiner, Ventura, Barbara Santos, Canei, Andressa Danielli, Bortolini, Juliana Gress, de Faria, Sergio Miana, Soares, Cláudio Roberto Fonseca Sousa, and Lovato, Paulo Emílio

Published
2024
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4. Recovering the Imperfect: Cell Segmentation in the Presence of Dynamically Localized Proteins

Author

Çiçek, Özgün, Marrakchi, Yassine, Antwi, Enoch Boasiako, Di Ventura, Barbara, and Brox, Thomas

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Deploying off-the-shelf segmentation networks on biomedical data has become common practice, yet if structures of interest in an image sequence are visible only temporarily, existing frame-by-frame methods fail. In this paper, we provide a solution to segmentation of imperfect data through time based on temporal propagation and uncertainty estimation. We integrate uncertainty estimation into Mask R-CNN network and propagate motion-corrected segmentation masks from frames with low uncertainty to those frames with high uncertainty to handle temporary loss of signal for segmentation. We demonstrate the value of this approach over frame-by-frame segmentation and regular temporal propagation on data from human embryonic kidney (HEK293T) cells transiently transfected with a fluorescent protein that moves in and out of the nucleus over time. The method presented here will empower microscopic experiments aimed at understanding molecular and cellular function., Comment: Accepted at MICCAI Workshop on Medical Image Learning with Less Labels and Imperfect Data, 2020

Published
2020
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5. A historical perspective of biomedical explainable AI research

Author

Malinverno, Luca, Barros, Vesna, Ghisoni, Francesco, Visonà, Giovanni, Kern, Roman, Nickel, Philip J., Ventura, Barbara Elvira, Šimić, Ilija, Stryeck, Sarah, Manni, Francesca, Ferri, Cesar, Jean-Quartier, Claire, Genga, Laura, Schweikert, Gabriele, Lovrić, Mario, and Rosen-Zvi, Michal

Published
2023
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8. Ultrafast Near‐Infrared Luminescence from Cyclometalated Iridium(III) Complexes with Indirubin as Ancillary Ligand.

Author

Sathyaseelan Bejoymohandas, Kochan, Ventura, Barbara, Baschieri, Andrea, Mazzanti, Andrea, Bandini, Elisa, and Monti, Filippo

Subjects
*INDIGO, *LIGANDS (Chemistry), *METAL complexes, *IRIDIUM, *ACETONITRILE
Abstract

Being a constitutional isomer of the indigo dye, indirubin has been known as a purple colourant for a long time. On the other hand, its structural and photophysical properties as ligand in metal complexes are virtually unexplored. Herein, for the first time, we utilized indirubin as ancillary chelator to develop two new heteroleptic iridium(III) complexes equipped with two 2‐phenylpyridine units as archetypical cyclometalating ligands. These new complexes display fully reversible oxidation and reduction processes, and show a panchromatic absorption extending up to 900 nm in acetonitrile solution at 298 K. Moreover, an unexpected broad and unstructured emission band is detected for both complexes in the near‐infrared region, peaking at approx. 1100 nm and having a lifetime of approx. 60 ps; such an emission is attributed to a ligand‐centred triplet excited state (3LC) located on the indirubin ligand itself, as proved by DFT calculations. These findings may pave the way for further exploration of the indirubin dye as a ligand for different types of metal centres to create efficient near‐infrared triplet emitters without the need for difficult synthetic procedures. [ABSTRACT FROM AUTHOR]

Published
2024
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11. Impact of Co–Fe Overlayers on Charge Carrier Dynamics at WO3/BiVO4 Heterojunctions: A Picosecond-to-Second Spectroscopic Analysis

Author

Vecchi, Pierpaolo, primary, Ruani, Federica, additional, Mazzanti, Michele, additional, Loague, Quentin R., additional, Mazzaro, Raffaello, additional, Boscherini, Federico, additional, Ventura, Barbara, additional, Meyer, Gerald J., additional, Armaroli, Nicola, additional, Caramori, Stefano, additional, and Pasquini, Luca, additional

Published
2024
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13. Rhizophagus intraradicesand Azospirillum brasilenseimprove growth of herbaceous plants and soil biological activity in revegetation of a recovering coal-mining area

Author

Meyer, Edenilson, Stoffel, Shantau Camargo Gomes, de Almeida, Anna Flávia Neri, do Amaral Scarsanella, Juliana, Vieira, André Steiner, Ventura, Barbara Santos, Canei, Andressa Danielli, Bortolini, Juliana Gress, de Faria, Sergio Miana, Soares, Cláudio Roberto Fonseca Sousa, and Lovato, Paulo Emílio

Abstract

We assessed, in a field experiment, the effects of arbuscular mycorrhizal fungi (Rhizophagus intraradices) and plant growth-promoting bacteria (Azospirillum brasilense) on the soil biological activity and the growth of key pioneer species used in the revegetation of coal-mining areas undergoing recovery. We applied four inoculation treatments to the pioneer plant species (Lablab purpureus, Paspalum notatum, Crotalaria juncea, Neonotonia wightii, Stylosanthes guianensis, Andropogon gayanusand Trifolium repens) used in the recovery process: NI (Control – Non-inoculated), AZO (A. brasilense), AMF (R. intraradices), and co-inoculation of AZO and AMF. On the 75th and 180th days, we measured plant dry mass, mycorrhizal colonization, N and P concentration, and accumulation in plant tissue. We collected soil to quantify glomalin content and soil enzyme activity. After 180 days, we did a phytosociological characterization of the remaining spontaneous plants.The both microorganisms, singly or co-inoculated, promoted increases in different fractions of soil glomalin, acid phosphatase activity, and fluorescein diacetate activity at 75 and 180 days. The inoculation was linked to higher plant biomass production (62-89%) and increased plant P and N accumulation by 34-75% and 70-85% at 180 days, compared with the non-inoculated treatment. Among the pioneer species sown Crotalaria junceaproduced the highest biomass at the 75th and 180th days (67% and 76% of all biomass), followed by Lablab purpureus(3% and 0.5%), while the other species failed to establish. At 180 days, we observed twenty spontaneous plant species growing in the area, primarily from the Poaceaefamily (74%). That suggests that the pioneer species present in the area do not hinder the ecological succession process. Inoculation of R. intraradicesand A. brasilense, isolated or combined, increases soil biological activity, growth, and nutrient accumulation in key pioneer plant species, indicating the potential of that technique for the recovery of lands degraded by coal mining.

Published
2024
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18. Aggregation index, carbon, nitrogen, and natural abundance of [sup.13]C and [sup.15]N in soil aggregates and bulk soil cultivated with onion under crop successions and rotations

Author

Giumbelli, Lucas Dupont, Loss, Arcangelo, Ventura, Barbara Santos, dos Santos, Elano, Jr., Almeida, Janaine, Piccolo, Marisa de Cassia, Mafra, Alvaro Luiz, Kurtz, Claudinei, Brunetto, Gustavo, and Comin, Jucinei Jose

Subjects
Soil quality, Cover crops -- Environmental aspects, Onions -- Environmental aspects, Crop rotation -- Environmental aspects, No-tillage -- Methods, Agricultural industry, Earth sciences
Abstract

Use of soil cover crops of different families in crop rotation or succession under no-tillage system (NTS) for onion production results in higher soil quality compared to land use systems with less plant diversity. The objective was to evaluate the effect of using different combinations of plant species from different botanical families in rotation and succession of soil cover crops in NTS for onion production on formation of macroaggregates, mesoaggregates, and microaggregates, and on total organic C (TOC) and N (TN) contents, including isotopic forms of C and N, in soil aggregates and bulk soil. The treatments (T) evaluated were maize/onion (NTS-T1); cover plants (winter)/onion (NTST2); maize/winter grasses/onion (NTS-T3); velvet bean/onion (NTS-T4); millet/cover plants (winter)/onion (NTS-T5); velvet bean/rye/onion (NTS-T6); maize/onion in conventional tillage system (CTS-T7); and intercrop cover plants (summer)/onion (NTS-T8). We evaluated macroaggregates (8.0-0.25 mm), microaggregates ( Additional keywords: conventional tillage system, macroaggregates and microaggregates, natural abundance of I5N, no-tillage system, onion production, soil cover plants. Received 26 November 2019, accepted 17 June 2020, published online 23 July 2020, Introduction Onion (Allium cepa) is a member of the Amaryllidaceae family and has wide use in human food (Souza and Lorenzi 2012). Onion is grown all over the world; China, [...]

Published
2020
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21. iNClusive: a database collecting useful information on non-canonical amino acids and their incorporation into proteins for easier genetic code expansion implementation

Author

Icking, Leon-Samuel, primary, Riedlberger, Andreas Martin, additional, Krause, Fabian, additional, Widder, Jonas, additional, Frederiksen, Anne Smedegaard, additional, Stockert, Fabian, additional, Spädt, Michael, additional, Edel, Nikita, additional, Armbruster, Daniel, additional, Forlani, Giada, additional, Franchini, Selene, additional, Kaas, Paulina, additional, Kırpat Konak, Büşra Merve, additional, Krier, Fabrice, additional, Lefebvre, Maïwenn, additional, Mazraeh, Daniel, additional, Ranniger, Jeremy, additional, Gerstenecker, Johanna, additional, Gescher, Pia, additional, Voigt, Karsten, additional, Salavei, Pavel, additional, Gensch, Nicole, additional, Di Ventura, Barbara, additional, and Öztürk, Mehmet Ali, additional

Published
2023
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30. Effects of Tillage and Cover Crops on Total Carbon and Nitrogen Stocks and Particle-Size Fractions of Soil Organic Matter under Onion Crop

Author

Kuneski, Ana Carla, primary, Loss, Arcângelo, additional, Ventura, Barbara Santos, additional, Santos, Thiago Stacowski dos, additional, Giumbelli, Lucas Dupont, additional, Lima, Andria Paula, additional, Piccolo, Marisa de Cássia, additional, Torres, José Luiz Rodrigues, additional, Brunetto, Gustavo, additional, Kurtz, Claudinei, additional, Lourenzi, Cledimar Rogério, additional, and Comin, Jucinei José, additional

Published
2023
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31. Phanerozoic tectonic and sedimentation history of the Arctic: Constraints from deep‐time low‐temperature thermochronology data of Ellesmere Island and Northwest Greenland

Author

Spiegel, Cornelia, primary, Sohi, Mohammad S., additional, Reiter, Wolfgang, additional, Meier, Katrin, additional, Ventura, Barbara, additional, Lisker, Frank, additional, Estrada, Solveig, additional, Piepjohn, Karsten, additional, Berglar, Kai, additional, Koglin, Nikola, additional, Klügel, Andreas, additional, Monien, Patrick, additional, Gerdes, Axel, additional, and Linnemann, Ulf, additional

Published
2023
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33. Analysis of Slow-Cycling Variants of the Light-Inducible Nuclear Protein Export System LEXY in Mammalian Cells

Author

Forlani, Giada, Antwi, Enoch B., Weis, Daniel, Öztürk, Mehmet A., Queck, Bastian A.W., Brecht, Dominik, and Di Ventura, Barbara

Subjects
Nuclear Export Signals, Oxygen, Mammals, Phototropins, Tumor Necrosis Factor Ligand Superfamily Member 14, Light, Avena, Biomedical Engineering, Animals, Nuclear Proteins, General Medicine, Biochemistry, Genetics and Molecular Biology (miscellaneous)
Abstract

The optogenetic tool LEXY consists of the second light oxygen voltage (LOV) domain of

Published
2022

34. Synthesis of symmetric and dissymmetric star-shaped pentaarylcyclopentadienyl Ru(II) complexes containing styryl-BODIPY fragments.

Author

Dumartin, Melissa, Abid, Seifallah, Gisbert, Yohan, Saffon-Merceron, Nathalie, Gao, Sheng, Armaroli, Nicola, Ventura, Barbara, Kammerer, Claire, and Rapenne, Gwénaël

Abstract

We synthesised star-shaped ruthenium(II) complexes containing one or five styryl-BODIPY units arranged around a central trisindazolylrutheniumcyclopentadienyl fragment. A symmetric complex was obtained following a five-fold Suzuki-Miyaura reaction of the pentabrominated key precursor while desymmetrisation was next achieved via a modular synthetic approach based on sequential chemoselective Suzuki-Miyaura reactions on a key building block bearing one iodophenyl and four bromophenyl groups. [ABSTRACT FROM AUTHOR]

Published
2024
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35. Organic carbon and nitrogen contents and their fractions in soils with onion crops in different management systems

Author

Ferreira, Lucas Borges, Loss, Arcangelo, Giumbelli, Lucas Dupont, Ventura, Barbara Santos, Souza, Monique, Mafra, Alvaro Luiz, Kurtz, Claudinei, Comin, Jucinei Jose, and Brunetto, Gustavo

Subjects
Onions -- Environmental aspects, Soil carbon -- Measurement -- Analysis, Soil nitrogen -- Measurement -- Analysis, Cropping systems -- Environmental aspects, Soil research, Agricultural industry, Earth sciences
Abstract

The use of plant species in rotation or succession of crops can increase C and N contents and their fractions in the soil. The objective of this study was to evaluate the effect of using soil cover crops in succession and rotation with onion crops in different soil management systems on the total organic carbon (TOC), total nitrogen (TN), and C and N fractions in soil aggregates, and bulk soil. The experiment was implemented in April 2007 with eight treatments: succession of onion and maize in a no-tillage system (NTS) (T1); rotation of soil cover crops (winter) and biennial onion in a NTS (T2); rotation of maize, winter grasses, and onion in a NTS (T3); succession of summer legume and annual onion in a NTS (T4); rotation of summer grass, winter grasses, and annual onion in a NTS (T5); succession of summer legume, winter grass, and annual onion in a NTS (T6); succession of maize and onion in a conventional tillage system (CTS) (T7); and succession of intercrops of soil cover crops (summer), and annual onion in a NTS (T8). Undisturbed soil samples were collected in the 0.0-5.0, 5.0-10.0, and 10.0-20.0cm soil layers in July 2014, and their aggregate (8.0 to 2.0mm) and bulk soil (Additional keywords: Allium cepa L., bulk soil, green manure, no-tillage system, soil aggregates, vegetable.Received 14 June 2018, accepted 9 October 2018, published online 9 November 2018, IntroductionOnion (Allium cepa L.) is a species of the Alliaceae family, which is widely used as human food. China, India, and the United States are the largest onion producers. Brazil [...]

Published
2018
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40. Non-Phenomenological Description of the Time-Resolved Emission in Solution with Quantum-Classical Vibronic Approaches. Application to Coumarin C153 in Methanol

Author

Cerezo, Javier, Gao, Sheng, Armaroli, Nicola, Ingrosso, Francesca, Prampolini, Giacomo, Santoro, Fabrizio, Ventura, Barbara, and Pastore, Mariachiara

Subjects
time-resolved emission spectroscopy, force field parameterization, time-dependent density functional theory, mixed quantum chemical approaches, organic dyes, molecular dynamics, vibronic approaches
Abstract

We report a joint experimental and theoretical work on the steady-state spectroscopy and time-resolved emission of the coumarin C153 dye in methanol. The lowest energy excited state of this molecule is characterized by an intramolecular charge transfer thus leading to remarkable shifts of the time-resolved emission spectra, dictated by the methanol reorganization dynamics. We selected this system as a prototypical test case for the first application of a novel computational protocol aimed at the prediction of transient emission spectral shapes, including both vibronic and solvent effects, without applying any phenomenological broadening. It combines a recently developed quantum–classical approach, the adiabatic molecular dynamics generalized vertical Hessian method (Ad-MD|𝑔|�VH), with nonequilibrium molecular dynamics simulations. For the steady-state spectra we show that the Ad-MD|gVH approach is able to reproduce quite accurately the spectral shapes and the Stokes shift, while a ∼0.15 eV error is found on the prediction of the solvent shift going from gas phase to methanol. The spectral shape of the time-resolved emission signals is, overall, well reproduced, although the simulated spectra are slightly too broad and asymmetric at low energies with respect to experiments. As far as the spectral shift is concerned, the calculated spectra from 4 ps to 100 ps are in excellent agreement with experiments, correctly predicting the end of the solvent reorganization after about 20 ps. On the other hand, before 4 ps solvent dynamics is predicted to be too fast in the simulations and, in the sub-ps timescale, the uncertainty due to the experimental time resolution (300 fs) makes the comparison less straightforward. Finally, analysis of the reorganization of the first solvation shell surrounding the excited solute, based on atomic radial distribution functions and orientational correlations, indicates a fast solvent response (≈100 fs) characterized by the strengthening of the carbonyl–methanol hydrogen bond interactions, followed by the solvent reorientation, occurring on the ps timescale, to maximize local dipolar interactions.

Published
2023

46. Explainable AI in Biomedical Research: A Systematic Review and Meta-Analysis

Author

Malinverno, Luca, primary, Barros, Vesna, additional, Ghisoni, Francesco, additional, Visonà, Giovanni, additional, Kern, Roman, additional, Nickel, Philip, additional, Ventura, Barbara Elvira, additional, Šimić, Ilija, additional, Stryeck, Sarah, additional, Manni, Francesca, additional, Ferri, Cesar, additional, Jean-Quartier, Claire, additional, Genga, Laura, additional, Schweikert, Gabriele, additional, Lovrić, Mario, additional, and Rosen-Zvi, Michal, additional

Published
2023
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47. Cellulose acetate membranes loaded with combinations of tetraphenylporphyrin, graphene oxide and Pluronic F-127 as responsive materials with antibacterial photodynamic activity

Author

Morsi, Rania E., primary, Gentili, Denis, additional, Corticelli, Franco, additional, Morandi, Vittorio, additional, Figoli, Alberto, additional, Russo, Francesca, additional, Galiano, Francesco, additional, Gentilomi, Giovanna Angela, additional, Bonvicini, Francesca, additional, Manet, Ilse, additional, and Ventura, Barbara, additional

Published
2023
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50. Antibacterial Photodynamic Therapy in the Near-Infrared Region with a Targeting Antimicrobial Peptide Connected to a π-Extended Porphyrin

Author

Gourlot, Charly, primary, Gosset, Alexis, additional, Glattard, Elise, additional, Aisenbrey, Christopher, additional, Rangasamy, Sabarinathan, additional, Rabineau, Morgane, additional, Ouk, Tan-Sothea, additional, Sol, Vincent, additional, Lavalle, Philippe, additional, Gourlaouen, Christophe, additional, Ventura, Barbara, additional, Bechinger, Burkhard, additional, and Heitz, Valérie, additional

Published
2022
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