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2. Fluorescent Neuronal Cells v2: Multi-Task, Multi-Format Annotations for Deep Learning in Microscopy

Author

Clissa, Luca, Macaluso, Antonio, Morelli, Roberto, Occhinegro, Alessandra, Piscitiello, Emiliana, Taddei, Ludovico, Luppi, Marco, Amici, Roberto, Cerri, Matteo, Hitrec, Timna, Rinaldi, Lorenzo, and Zoccoli, Antonio

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

Fluorescent Neuronal Cells v2 is a collection of fluorescence microscopy images and the corresponding ground-truth annotations, designed to foster innovative research in the domains of Life Sciences and Deep Learning. This dataset encompasses three image collections in which rodent neuronal cells' nuclei and cytoplasm are stained with diverse markers to highlight their anatomical or functional characteristics. Alongside the images, we provide ground-truth annotations for several learning tasks, including semantic segmentation, object detection, and counting. The contribution is two-fold. First, given the variety of annotations and their accessible formats, we envision our work facilitating methodological advancements in computer vision approaches for segmentation, detection, feature learning, unsupervised and self-supervised learning, transfer learning, and related areas. Second, by enabling extensive exploration and benchmarking, we hope Fluorescent Neuronal Cells v2 will catalyze breakthroughs in fluorescence microscopy analysis and promote cutting-edge discoveries in life sciences. The data are available at: https://amsacta.unibo.it/id/eprint/7347, Comment: 11 pages; 5 figures; 2 tables

Published
2023

7. Activation of orexin-A (hypocretin-1) receptors in the Raphe Pallidus at different ambient temperatures in the rat: effects on thermoregulation, cardiovascular control, sleep, and feeding behavior.

Author

Hitrec, Timna, Del Vecchio, Flavia, Alberti, Luca, Luppi, Marco, Martelli, Davide, Occhinegro, Alessandra, Piscitiello, Emiliana, Taddei, Ludovico, Tupone, Domenico, Amici, Roberto, and Cerri, Matteo

Subjects
AUTONOMIC nervous system, TEMPERATURE effect, BLOOD pressure, WAKEFULNESS, BODY temperature regulation
Abstract

The Raphe Pallidus (RPa) is a brainstem nucleus containing sympathetic premotor neurons that control thermogenesis and modulate cardiovascular function. It receives inputs from various hypothalamic areas, including the Lateral Hypothalamus (LH), a heterogeneous region intricately involved in several autonomic and behavioral functions. A key subpopulation of neurons in the LH expresses orexin/hypocretin, a neuropeptide which is crucially involved in the regulation of the wake-sleep states and feeding behavior. The RPa receives orexinergic projections from the LH and orexinergic signalling in the RPa has been shown to enhance thermogenesis in the anaesthetized rat, but only in the presence of an already existing thermogenic drive, without significantly affecting cardiovascular function. The present work was aimed at exploring the effects on thermoregulation and autonomic function and the possible role in the modulation of the wake-sleep states and feeding behavior of orexin injection in the RPa in the free-behaving rat. In order to assess the influence of an already present thermogenic drive on orexinergic signalling in the RPa, animals were studied at three different ambient temperatures (Ta, 10°C, 24°C, and 32°C). We found that orexin injection into the RPa variably affected the wake-sleep states, autonomic functions, motor activity, and feeding behavior, at the different Tas. In particular, in the first post-injection hour, we observed an increase in wakefulness, which was large at Ta 24°C and Ta 10°C and rather mild at Ta 32°C. Deep brain temperature was increased by orexin injection at Ta 10°C, but not at either Ta 24°C or Ta 32°C. Moreover, an increase in mean arterial blood pressure occurred at Ta 24°C, which was probably masked by the high baseline levels at Ta 10°C and was completely absent at Ta 32°C. Finally, an enhancement in feeding behavior was observed at Ta 24°C and 10°C only. In accordance with what observed in anaesthetized rats, orexinergic signalling in the RPa seems to be ineffective in the absence of any thermogenic drive. Moreover, the effects observed on the wake-sleep states and feeding behavior introduce the RPa as a novel player in the central neural network promoting wakefulness and feeding. [ABSTRACT FROM AUTHOR]

Published
2024
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10. Hibernation and Radioprotection: Gene Expression in the Liver and Testicle of Rats Irradiated under Synthetic Torpor

Author

Tinganelli, Walter, Hitrec, Timna, Romani, Fabrizio, Simoniello, Palma, Squarcio, Fabio, Stanzani, Agnese, Piscitiello, Emiliana, Marchesano, Valentina, Luppi, Marco, Sioli, Maximiliano, Helm, Alexander, Compagnone, Gaetano, Morganti, Alessio G., Amici, Roberto, Negrini, Matteo, Zoccoli, Antonio, Durante, Marco, Cerri, Matteo, Tinganelli, Walter, Hitrec, Timna, Romani, Fabrizio, Simoniello, Palma, Squarcio, Fabio, Stanzani, Agnese, Piscitiello, Emiliana, Marchesano, Valentina, Luppi, Marco, Sioli, Maximiliano, Helm, Alexander, Compagnone, Gaetano, Morganti, Alessio G., Amici, Roberto, Negrini, Matteo, Zoccoli, Antonio, Durante, Marco, and Cerri, Matteo

Abstract

Hibernation has been proposed as a tool for human space travel. In recent years, a procedure to induce a metabolic state known as "synthetic torpor" in non-hibernating mammals was successfully developed. Synthetic torpor may not only be an efficient method to spare resources and reduce psychological problems in long-term exploratory-class missions, but may also represent a countermeasure against cosmic rays. Here we show the preliminary results from an experiment in rats exposed to ionizing radiation in normothermic conditions or synthetic torpor. Animals were irradiated with 3 Gy X-rays and organs were collected 4 h after exposure. Histological analysis of liver and testicle showed a reduced toxicity in animals irradiated in torpor compared to controls irradiated at normal temperature and metabolic activity. The expression of ataxia telangiectasia mutated (ATM) in the liver was significantly downregulated in the group of animal in synthetic torpor. In the testicle, more genes involved in the DNA damage signaling were downregulated during synthetic torpor. These data show for the first time that synthetic torpor is a radioprotector in non-hibernators, similarly to natural torpor in hibernating animals. Synthetic torpor can be an effective strategy to protect humans during long term space exploration of the solar system.

Published
2024

13. Ultrasonic vocalisations during rapid eye movement sleep in the rat.

Author

Squarcio, Fabio, Hitrec, Timna, Luppi, Marco, Martelli, Davide, Occhinegro, Alessandra, Piscitiello, Emiliana, Taddei, Ludovico, Tupone, Domenico, Amici, Roberto, and Cerri, Matteo

Subjects
NON-REM sleep, RAPID eye movement sleep, SLEEP deprivation, ULTRASONICS, EYE movements
Abstract

Summary: Rats are known to use a 22‐kHz ultrasonic vocalisation as a distress call to warn of danger to other members of their group. We monitored 22‐kHz ultrasonic vocalisation emissions in rats (lean and obese) as part of a sleep deprivation study to detect the eventual presence of stress during the procedure. Unexpectedly, we detected ultrasonic vocalisation emission during rapid eye movement (REM) sleep, but not during non‐REM (NREM) sleep, in all the rats. The event occurs during the expiratory phase and can take place singularly or as a train. No difference was detected in the number or duration of these events in lean versus obese rats, during the light versus the dark period, and after sleep deprivation. As far as we know, this is the first report showing that rats can vocalise during REM sleep. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Corrigendum: Synthetic torpor triggers a regulated mechanism in the rat brain, favoring the reversibility of Tau protein hyperphosphorylation

Author

Squarcio, Fabio, primary, Hitrec, Timna, additional, Piscitiello, Emiliana, additional, Cerri, Matteo, additional, Giovannini, Catia, additional, Martelli, Davide, additional, Occhinegro, Alessandra, additional, Taddei, Ludovico, additional, Tupone, Domenico, additional, Amici, Roberto, additional, and Luppi, Marco, additional

Published
2023
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19. Back to Earth

Author

Cerri, Matteo, primary, Bereiter-Hahn, Jürgen, additional, Heldmaier, Gerhard, additional, Choukér, Alexander, additional, and Summerer, Leopold, additional

Published
2023
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20. Synthetic torpor triggers a regulated mechanism in the rat brain, favoring the reversibility of Tau protein hyperphosphorylation

Author

Squarcio, Fabio, primary, Hitrec, Timna, additional, Piscitiello, Emiliana, additional, Cerri, Matteo, additional, Giovannini, Catia, additional, Martelli, Davide, additional, Occhinegro, Alessandra, additional, Taddei, Ludovico, additional, Tupone, Domenico, additional, Amici, Roberto, additional, and Luppi, Marco, additional

Published
2023
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21. Molecular changes induced by a centrally-induced state of synthetic torpor in multiple organs:a new strategy for radioprotection.

Author

Cerri, Matteo, Piscitiello, Emiliana <1993>, Cerri, Matteo, and Piscitiello, Emiliana <1993>

Abstract

Torpor is a successful survival strategy displayed by several mammalian species to cope with harsh environmental conditions. A complex interplay of ambient, genetic and circadian stimuli acts centrally to induce a severe suppression of metabolic rate, usually followed by an apparently undefended reduction of body temperature. Some animals, such as marmots, are able to maintain this physiological state for months (hibernation), during which torpor bouts are periodically interrupted by short interbouts of normothermia (arousals). Interestingly, torpor adaptations have been shown to be associated with a large resistance towards stressors, such as radiation: indeed, if irradiated during torpor, hibernators can tolerate higher doses of radiation, showing an increased survival rate. New insights for radiotherapy and long-term space exploration could arise from the induction of torpor in non-hibernators, like humans. The present research project is centered on synthetic torpor (ST), a hypometabolic/hypothermic condition induced in a non-hibernator, the rat, through the pharmacological inhibition of the Raphe Pallidus, a key brainstem area controlling thermogenic effectors. By exploiting this procedure, this thesis aimed at: i) providing a multiorgan description of the functional cellular adaptations to ST; ii) exploring the possibility, and the underpinning molecular mechanisms, of enhanced radioresistance induced by ST. To achieve these aims, transcriptional and histological analysis have been performed in multiple organs of synthetic torpid rats and normothermic rats, either exposed or not exposed to 3 Gy total body of X-rays. The results showed that: i) similarly to natural torpor, ST induction leads to the activation of survival and stress resistance responses, which allow the organs to successfully adapt to the new homeostasis; ii) ST provides tissue protection against radiation damage, probably mainly through the cellular adaptations constitutively induced by ST, eve

Published
2023

24. Synthetic torpor protects rats from exposure to accelerated heavy ions

Author

Puspitasari, Anggraeini, primary, Squarcio, Fabio, additional, Quartieri, Martina, additional, Totis, Cristina, additional, Hitrec, Timna, additional, Takahashi, Akihisa, additional, Yoshida, Yukari, additional, Hanamura, Kenji, additional, Yako, Tomoko, additional, Cerri, Matteo, additional, Simoniello, Palma, additional, Durante, Marco, additional, and Tinganelli, Walter, additional

Published
2022
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25. Western-blot results from Synthetic-torpor experiments conducted in 2019-2020

Author

Squarcio, Fabio, Hitrec, Timna, Piscitiello, Emiliana, Cerri, Matteo, Occhinegro, Alessandra, Squarcio, Fabio, Hitrec, Timna, Piscitiello, Emiliana, Cerri, Matteo, and Occhinegro, Alessandra

Abstract

This dataset contains the original results for the western-blot (WB) determinations from experiments carried out in the "Physiological regulations in the wake-sleep cycle" lab, at the Department of Biomedical and Neuromotor Sciences - University of Bologna, Italy. The WB procedure, the bands acquisitions and their intensity quantifications were conducted at the “Centre for Applied Biomedical Research – CRBA” - University of Bologna, St. Orsola Hospital, Italy.

Published
2022

29. Synthetic torpor triggers a neuroprotective and regulated mechanism in the rat brain, favoring the reversibility of Tau protein hyperphosphorylation

Author

Squarcio, Fabio, primary, Hitrec, Timna, additional, Piscitiello, Emiliana, additional, Cerri, Matteo, additional, Giovannini, Catia, additional, Martelli, Davide, additional, Occhinegro, Alessandra, additional, Taddei, Ludovico, additional, Tupone, Domenico, additional, Amici, Roberto, additional, and Luppi, Marco, additional

Published
2022
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31. Venous outflow in partial heterotopic liver transplantation with spleen replacement: Evidence of no chronic venous hypertension

Author

Ravaioli, Matteo, primary, Germinario, Giuliana, additional, Cerri, Matteo, additional, Prosperi, Enrico, additional, Fallani, Guido, additional, Vasuri, Francesco, additional, Serenari, Matteo, additional, Odaldi, Federica, additional, Maroni, Lorenzo, additional, Siniscalchi, Antonio, additional, Cescon, Matteo, additional, and Renzulli, Matteo, additional

Published
2022
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41. Symposia Abstracts

Author

Siegel, Jerome M., Murillo-Rodriguez, Eric, Xu, Man, Lin, Ling, Gerashchenko, Dmitry, Blanco-Centurion, Carlos, Shiromani, Anjelica, Nishino, Seiji, Mignot, Emmanuel, Shiromani, Priyattam J., Alam, Md Noor, John, Joshi, Wu, Ming-Fung, Boehmer, Lisa N., Lack, Leon, Harris, Jodie, Mercer, Jeremy D., Bootzin, Richard R., Lack, Leon C., Britton, Willoughby B., Fridel, Keith W., Payne, Jessica, Stevens, Sally J., Shapiro, Shauna L., Cousins, Jennifer C., Hasler, Brant P., Bailey, Elaine T., Hitt, Sabrina, Estrada, Barbara, Cameron, Michael, Velluti, Ricardo A., Voss, Ursula, Coenen, Anton M. L., Campbell, Kenneth, Gulia, Kamalesh K., Mallick, Hruda Nanda, Kumar, Velayudhan Mohan, Schmidt, Markus H., Andersen, Monica L., Velazquez-Moctezuma, Javier, Gulia, Kamalesh Kumari, Koyama, Y., Takahashi, K., Toledo, C., Kayama, Y., Iwasaki, H., Kawauchi, A., Miki, T., Schmidt, M. H., Anna, Szucs, Kotchabhakdi, Naiphinich, Kotchabhakdi, Nittaya J., Allen, Richard P., Hening, Wayne A., Walters, Arthur, Walters, Arthur S., de Valck, Elke, Quanten, Stijn, Cluydts, Raymond, Berckmans, Daniël, Weaver, Terri E., Härmä, Mikko, Grunstein, Ron, Lavie, Lena, Sharma, Anuja, Lavie, Peretz, Luppi, Pierre-Hervé, Goutagny, Romain, Verret, Laure, Gervasoni, Damien, Boissard, Romuald, Lapray, Damien, Salvert, Denise, Léger, Lucienne, Peyron, Christelle, Fort, Patrice, Mallick, Birendra N., Mccarley, Robert W., Brown, Ritchie, Thakkar, Mahesh, Naidoo, Nirinjini, Datta, Subimal, Ramesh, Vijay, Basheer, Radhika, Urade, Yoshihiro, Opp, Mark R., Adrien, Joëlle, Yamuy, J., Borde, M., Xi, M., Fung, S. J., Sampogna, S., Ramos, O., Torterolo, P., Chase, M. H., Marks, Gerald A., Saaresranta, Tarja, Mccrimmon, Donald R., Alheid, George F., Kubin, Leszek, Radulovacki, Miodrag, Murck, Harald, Auer, Dorothea, Kuenzel, Heike, Held, Katja, Antonijevic, Irina A., Steiger, Axel, Edith, Holsboer-Trachsler, Martin, Hatzinger, Ulrich, Hemmeter, Schüssler, Petra, Uhr, Manfred, Yassouridis, Alexander, Askenasy, Jean, Spencer, Kevin, Siegal, Jerome M., Kobayashi, Toshinori, Ishikawa, Tohru, Tomita, Shinichi, Yoshida, Hironori, Arakawa, Kazunari, Kutty, Bindu M., Honma, Ken-Ichi, Yamanaka, Yujiro, Miyazaki, Toshihiko, Hashimoto, Satoko, Honma, Sato, Youngstedt, S. D., Mukai, Junko, Uchida, Sunao, Dinges, David F., van Dongen, Hans P. A., Gazendam, Joost A. C., Schwab, Richard J., Parthasarathy, Sairam, Kalinchuk, Anna, Porkka-Heiskanen, Tarja, Stakofsky, Allisonb, Chee, Michael, Choo, Wei-Chieh, Chan, Wai-Yen, Chuah, Lisa, Sze, Joanna, Shen, Li-Juan, Vijayan, V. K., Monie, Robert, Edwards, Susan, Shrivastava, Deepak, Goswami, Meeta, Honig, Eveline, Cloud, Robert L., Bhuvaneshwari Bhagat, M. S. K., Selvamurthy, W., Lovering, Andrew T., Fraigne, Jimmy J., Dunin-Barkowski, Witali L., Vidruk, Edward H., Orem, John M., Panjwani, Usha, Thakur, L., Anand, J. P., Banerjee, P. K., Mckenna, James, Ward, Chris, Tartar, Jaime, Strecker, Robert, Zhan, G.-X., Serrano, F., Fenik, P., Hsu, R., Kong, L., Pratico, D., Klann, E., Veasey, S. C., Fenik, Victor B., Volgin, Denys V., Swan, Jennifer L., Davies, Richard O., Row, Barry W., Huang, Zhi-Li, Mochizuki, Takatoshi, Qu, Wei-Min, Hayaishi, Osamu, Eguchi, Naomi, Yamanaka, Akihiro, Sakurai, Takeshi, Gallopin, Thierry, Vivaldi, Ennio A., Ocampo-Garcés, Adrián, Bassi, Alejandro, Bon, Olivier Le, Amici, Roberto, Baracchi, Francesca, Capitani, Paolo, Cerri, Matteo, Dentico, Daniela, Jones, Christine Ann, Luppi, Marco, Parmeggiani, Pier Luigi, Perez, Emanuele, and Zamboni, Giovanni

Published
2005
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43. Two surgical techniques are better than one: RAVAS and RAPID are answers for the same issue

Author

Ravaioli, Matteo, primary, Fallani, Guido, additional, Cerri, Matteo, additional, Prosperi, Enrico, additional, Serra, Carla, additional, D’Errico, Antonia, additional, Serenari, Matteo, additional, Germinario, Giuliana, additional, Renzulli, Matteo, additional, Contedini, Federico, additional, Odaldi, Federica, additional, Maroni, Lorenzo, additional, Siniscalchi, Antonio, additional, Cescon, Matteo, additional, and Azoulay, Daniel, additional

Published
2021
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45. Loss of Snord116 impacts lateral hypothalamus, sleep, and food-related behaviors

Author

Pace, Marta, primary, Falappa, Matteo, additional, Freschi, Andrea, additional, Balzani, Edoardo, additional, Berteotti, Chiara, additional, Lo Martire, Viviana, additional, Kaveh, Fatemeh, additional, Hovig, Eivind, additional, Zoccoli, Giovanna, additional, Amici, Roberto, additional, Cerri, Matteo, additional, Urbanucci, Alfonso, additional, and Tucci, Valter, additional

Published
2020
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46. Loss of Snord116 alters cortical neuronal activity in mice: a preclinical investigation of Prader–Willi syndrome

Author

Pace, Marta, primary, Colombi, Ilaria, additional, Falappa, Matteo, additional, Freschi, Andrea, additional, Bandarabadi, Mojtaba, additional, Armirotti, Andrea, additional, Encarnación, Blanco María, additional, Adamantidis, Antoine R, additional, Amici, Roberto, additional, Cerri, Matteo, additional, Chiappalone, Michela, additional, and Tucci, Valter, additional

Published
2020
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50. Gene expression in the liver of the rat induced in synthetic torpor

Author

Hitrec, Timna, primary, Tinganelli, Walter, additional, Romani, Fabrizio, additional, Simoniello, Palma, additional, Squarcio, Fabio, additional, Piscitiello, Emiliana, additional, Marchesano, Valentina, additional, Luppi, Marco, additional, Occhinegro, Alessandra, additional, Sioli, Maximiliano, additional, Helm, Alexander, additional, Compagnone, Gaetano, additional, Morganti, Alessio G, additional, Amici, Roberto, additional, Negrini, Matteo, additional, Zoccoli, Antonio, additional, Durante, Marco, additional, and Cerri, Matteo, additional

Published
2020
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