Pubblicazioni scientifiche
Ultrasensitive detection and quantification of bovine Deltapapillomavirus in the semen of healthy horses.
Abstract BPV1, BPV2, BPV13, and BPV14 are all genotypes of bovine delta papillomaviruses (δPV), of which the first three cause infections in horses and are associated with equine sarcoids. However, BPV14 infection has never been reported in equine species. In this study, we examined 58 fresh and thawed commercial semen samples from healthy stallions. In 34 (58.6%), bovine δPV DNA was detected and quantified using droplet digital polymerase chain reaction (ddPCR). Real time quantitative PCR (qPCR) was able to identify bovine δPV DNA in 5 samples (8.6%). Of the BPV-infected semen samples, 15 were positive for BPV2 (~ 44.1%) on ddPCR and 4 (~ 11.7%) on qPCR; 12 (~ 35.3%) for BPV14 on ddPCR and 1 (~ 3%) by qPCR; 4 (~ 11.7%) for BPV1 on ddPCR, whereas qPCR failed to reveal this infection; 3 (~ 8.8%) for BPV13 on ddPCR; and BPV13 infection was not detected by qPCR. Our study showed for the first time that BPV14 is an additional infectious agent potentially responsible for infection in horses, as its transcripts were detected and quantified in some semen samples. Large-scale BPV14 screening is necessary to provide substantial data on the molecular epidemiology for a better understanding of the geographical divergence of BPV14 prevalence in different areas and how widespread BPV14 is among equids. Autori Anna Cutarelli, Francesca De Falco, Francesco Serpe, Simona Izzo, Giovanna Fusco, Cornel Catoi, Sante Roperto Rivista Scientific Report Data di pubblicazione 04/01/2025 Consulta la pubblicazione
Limiting serine availability during tumor progression promotes muscle wasting in cancer cachexia
Abstract Cancer cachexia is a multifactorial syndrome characterized by a progressive loss of body weight occurring in about 80% of cancer patients, frequently representing the leading cause of death. Dietary intervention is emerging as a promising therapeutic strategy to counteract cancer-induced wasting. Serine is the second most-consumed amino acid (AA) by cancer cells and has emerged to be strictly necessary to preserve skeletal muscle structure and functionality. Here, we demonstrate that decreased serine availability during tumor progression promotes myotubes diameter reduction in vitro and induces muscle wasting in in vivo mice models. By investigating the metabolic crosstalk between colorectal cancer cells and muscle cells, we found that incubating myotubes with conditioned media from tumor cells relying on exogenous serine consumption triggers pronounced myotubes diameter reduction. Accordingly, culturing myotubes in a serine-free medium induces fibers width reduction and suppresses the activation of the AKT-mTORC1 pathway with consequent impairment in protein synthesis, increased protein degradation, and enhanced expression of the muscle atrophy-related genes Atrogin1 and MuRF1. In addition, serine-starved conditions affect myoblast differentiation and mitochondrial oxidative metabolism, finally inducing oxidative stress in myotubes. Consistently, serine dietary deprivation strongly strengthens cancer-associated weight loss and muscle atrophy in mice models. These findings uncover serine consumption by tumor cells as a previously undisclosed driver in cancer cachexia, opening new routes for possible therapeutic approaches. Autori Erica Pranzini, Livio Muccillo, Ilaria Nesi, Alice Santi, Caterina Mancini, Giulia Lori, Massimo Genovese, Tiziano Lottini, Giuseppina Comito, Anna Caselli, Annarosa Arcangeli, Lina Sabatino, Vittorio Colantuoni, Maria Letizia Taddei, Paolo Cirri, Paolo Paoli Rivista Cell Death Discovery Data di pubblicazione 21/12/2024 Consulta la pubblicazione
Degradation of α-MnO2 in Zn-air battery gas-diffusion electrodes: An investigation based on chemical-state mapping
Abstract Here, we present an integrated ultra-high-vacuum (UHV) apparatus for the growth of complex materials and heterostructures. The specific growth technique is the Pulsed Laser Deposition (PLD) by means of a dual-laser source based on an excimer KrF ultraviolet and solid-state Nd:YAG infra-red lasers. By taking advantage of the two laser sources—both lasers can be independently used within the deposition chambers—a large number of different materials—ranging from oxides to metals, to selenides, and others—can be successfully grown in the form of thin films and heterostructures. All of the samples can be in situ transferred between the deposition chambers and the analysis chambers by using vessels and holders’ manipulators. The apparatus also offers the possibility to transfer samples to remote instrumentation under UHV conditions by means of commercially available UHV-suitcases. The dual-PLD operates for in-house research as well as user facility in combination with the Advanced Photo-electric Effect beamline at the Elettra synchrotron radiation facility in Trieste and allows synchrotron-based photo-emission as well as x-ray absorption experiments on pristine films and heterostructures. Autori Benedetto Bozzini, Alessandro Alleva, Valentina Bonanni, Regina Ciancio, George Kourousias, Francesco Guzzi, Piu Rajak, Alessandra Gianoncelli Rivista Electrochimica Acta Data di pubblicazione 20/12/2024 Consulta la pubblicazione
Raman Microscopy Identification of Secondary Spurious Phases in Molten GdSr2RuCu2O8-δ Superconductor for Photonics and Plasmonic Applications
Abstract Plasmonic and Photonics applications of superconducting materials, suggested at first by the necessity to minimize the dissipative losses of conventional metals in the high frequency ranges, are topics of growing interest in Optics. In this perspective, GdSr2RuCu2O8-δ (Gd1212) Rutheno-Cuprate Superconductor presents very promising properties, showing both superconducting and magnetically ordered phases coexisting in the same cell. To investigate its features, the fabrication of macroscopic crystallographically oriented samples is necessary. The use of melt texturing techniques has shown to be among the most effective ways to achieve the best characteristics, although the fabrication of high-quality Gd1212 samples is intrinsically difficult. To reach a better understanding of Gd1212 incongruent melting reaction, a series of bulk samples annealed at temperatures below and above the melting temperature was prepared. Raman Microscopy and Mapping performed on molten and re-solidified samples revealed the presence of different phases, corresponding to those identified in our previous studies. These observations were also confirmed by XRD, TGA-DTA, and SEM+EDS characterisations. Secondary phases formation showed a strong dependence on the temperature of the annealing treatments. Susceptibility and magnetization measurements show both superconducting and magnetic transitions and a contribution of different spurious magnetic phases as suggested by EDS. Autori Marcello Gombos, Stefano Managò, Danilo Zola, Giovanni Carapella, Oreste Tarallo, Vito Mocella, Anna Chiara De Luca, Ivo Rendina, Francesco Ruffo, Pasquale Orgiani, Regina Ciancio Rivista Accepted at the Annual Meeting of the Association for Computational Linquistics (ACL), Arxiv preprint: 2402.11655 Data di pubblicazione 31/10/2024 Consulta la pubblicazione
Ferritin adsorption onto chrysotile asbestos fibers influences the protein secondary structure
Abstract Asbestos fiber exposure triggers chronic inflammation and cancer. Asbestos fibers can adsorb different types of proteins. The mechanism of this adsorption, not yet completely understood, has been studied in detail mainly with serum albumin and was shown to induce structural changes in the bound protein. The findings of these works regarded mainly the changes of the protein structure, independently of any relation with asbestos-related diseases. For the first time, we have focused our attention to the consequences of the interaction between asbestos fibers and ferritin, a protein involved in iron metabolism, which is strongly modified in asbestos-related diseases. Even if it is known that ferritin can be adsorbed by asbestos fibers, the results of this interaction for the ferritin secondary structure has not previously been studied. One consequence of asbestos-ferritin interaction, is the formation of the so-called ferruginous/asbestos bodies (ABs). In the AB-coating material, the secondary structure of ferritin is modified, and at present, it is unclear whether or not this modification is a direct consequence of the asbestos interaction. In the present study, chrysotile asbestos, more than other asbestos fiber types tested, was found to rapidly bind holo-ferritin, and the presence of iron seemed to play a key role in this process, since iron-free apo-ferritin was adsorbed at a lower level, and iron-saturated chrysotile lost its ferritin-adsorbing capacity. To directly study the details of ferritin adsorption on asbestos fibers, High Resolution Transmission Electron Microscopy (HR-TEM) was employed together with FTIR microspectroscopy and Infrared nanoscopy, which to the best of our knowledge, have not previously been used for this purpose. Chrysotile-bound apo-ferritin underwent a significant change in secondary structure, showing a shift from a prevalent α-helix to a β-sheet conformation. Conversely, the adsorbed holo-ferritin structure appeared to be only weakly modified. These findings add a new potential mechanism to the toxic activities of asbestos: the fibers can modify the structure, and very likely, the function of adsorbed proteins. This, in relation to ferritin, could be a key mechanism in cell iron homeostasis alteration, typically reported in asbestos-related diseases. Autori Martina Zangari, Federica Piccirilli, Lisa Vaccari, Cristian Radu, Paola Zacchi, Annalisa Bernareggi, Sara Leone, Giuliano Zabucchi, Violetta Borelli Rivista Helyon Data di pubblicazione 30/10/2024 Consulta la pubblicazione
A Comprehensive Analysis of Process Energy Consumption on Multi-Socket Systems with GPUs
Abstract: Robustly estimating energy consumption in High-Performance Computing (HPC) is essential for assessing the energy footprint of modern workloads, particularly in fields such as Artificial Intelligence (AI) research, development, and deployment. The extensive use of supercomputers for AI training has heightened concerns about energy consumption and carbon emissions. Existing energy estimation tools often assume exclusive use of computing nodes, a premise that becomes problematic with the advent of supercomputers integrating microservices, as seen in initiatives like Acceleration as a Service (XaaS) and cloud computing. This work investigates the impact of executed instructions on overall power consumption, providing insights into the comprehensive behaviour of HPC systems. We introduce two novel mathematical models to estimate a process’s energy consumption based on the total node energy, process usage, and a normalised vector of the probability distribution of instruction types for CPU and GPU processes. Our approach enables energy accounting for specific processes without the need for isolation. Our models demonstrate high accuracy, predicting CPU power consumption with a mere 1.9% error. For GPU predictions, the models achieve a central relative error of 9.7%, showing a clear tendency to fit the test data accurately. These results pave the way for new tools to measure and account for energy consumption in shared supercomputing environments. Autori: Luis G. Leon-Vega, Niccolò Tosato, Stefano Cozzini Rivista: 11th Latin American High Performance Computing Conference, CARLA 2024 Data di pubblicazione: 30/09/2024 Consulta la pubblicazione
Effects of In-Air Post Deposition Annealing Process on the Oxygen Vacancy Content in Sputtered GDC Thin Films Probed via Operando XAS and Raman Spectroscopy
Abstract We investigate the ionic mobility in room-temperature RF-sputtered gadolinium doped ceria (GDC) thin films grown on industrial solid oxide fuel cell substrates as a function of the air-annealing at 800 and 1000 °C. The combination of X-ray diffraction, X-ray photoelectron spectroscopy, operando X-ray absorption spectroscopy, and Raman spectroscopy allows us to study the different Ce3+/ Ce4+ ratios induced by the post growth annealing procedure, together with the Ce valence changes induced by different gas atmosphere exposure. Our results give evidence of different kinetics as a function of the annealing temperature, with the sample annealed at 800 °C showing marked changes of the Ce oxidation state when exposed to both reducing and oxidizing gas atmospheres at moderate temperature (300 °C), while the Ce valence is weakly affected for the 1000 °C annealed sample. Raman spectra measurements allow us to trace the responses of the investigated samples to different gas atmospheres on the basis of the presence of different Gd–O bond strengths inside the lattice. These findings provide insight into the microscopic origin of the best performances already observed in SOFCs with a sputtered GDC barrier layer annealed at 800 °C and are fundamental to further improve sputtered GDC thin film performance in energy devices. Autori Nunzia Coppola, Sami Ur Rehman, Giovanni Carapella, Luca Braglia, Vincenzo Vaiano, Dario Montinaro, Veronica Granata, Sandeep Kumar Chaluvadi, Pasquale Orgiani, Piero Torelli, Luigi Maritato, Carmela Aruta, Alice Galdi Rivista ACS Applied Electronic Materials Data di pubblicazione 25/09/2024 Consulta la pubblicazione
Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction
Abstract N6-Methyladenosine (m6A) is a prevalent RNA post-transcriptional modification that plays crucial roles in RNA stability, structural dynamics, and interactions with proteins. The YT521-B (YTH) family of proteins, which are notable m6A readers, functions through its highly conserved YTH domain. Recent structural investigations and molecular dynamics (MD) simulations have shed light on the mechanism of recognition of m6A by the YTHDC1 protein. Despite advancements, using MD to predict the stabilization induced by m6A on the free energy of binding between RNA and YTH proteins remains challenging due to inaccuracy of the employed force field and limited sampling. For instance, simulations often fail to sufficiently capture the hydration dynamics of the binding pocket. This study addresses these challenges through an innovative methodology that integrates metadynamics, alchemical simulations, and force-field refinement. Importantly, our research identifies hydration of the binding pocket as giving only a minor contribution to the binding free energy and emphasizes the critical importance of precisely tuning force-field parameters to experimental data. By employing a fitting strategy built on alchemical calculations, we refine the m6A partial charge parameters, thereby enabling the simultaneous reproduction of N6 methylation on both the protein binding free energy and the thermodynamic stability of nine RNA duplexes. Our findings underscore the sensitivity of binding free energies to partial charges, highlighting the necessity for thorough parametrization and validation against experimental observations across a range of structural contexts. Autori Valerio Piomponi, Miroslav Krepl, Jiri Sponer, Giovanni Bussi Rivista The Journal of Physical Chemistry B, Vol 128, Issue 37 Data di pubblicazione 06/09/2024 Consulta la pubblicazione
Detach-ROCKET: Sequential feature selection for time series classification with random convolutional kernels
Abstract: Time Series Classification (TSC) is essential in fields like medicine, environmental science, and finance, enabling tasks such as disease diagnosis, anomaly detection, and stock price analysis. While machine learning models like Recurrent Neural Networks and InceptionTime are successful in numerous applications, they can face scalability issues due to computational requirements. Recently, ROCKET has emerged as an efficient alternative, achieving state-of-the-art performance and simplifying training by utilizing a large number of randomly generated features from the time series data. However, many of these features are redundant or non-informative, increasing computational load and compromising generalization. Here we introduce Sequential Feature Detachment (SFD) to identify and prune non-essential features in ROCKET-based models, such as ROCKET, MiniRocket, and MultiRocket. SFD estimates feature importance using model coefficients and can handle large feature sets without complex hyperparameter tuning. Testing on the UCR archive shows that SFD can produce models with better test accuracy using only 10% of the original features. We named these pruned models Detach-ROCKET. We also present an end-to-end procedure for determining an optimal balance between the number of features and model accuracy. On the largest binary UCR dataset, Detach-ROCKET improves test accuracy by 0.6% while reducing features by 98.9%. By enabling a significant reduction in model size without sacrificing accuracy, our methodology improves computational efficiency and contributes to model interpretability. We believe that Detach-ROCKET will be a valuable tool for researchers and practitioners working with time series data, who can find a user-friendly implementation of the model at https://github.com/gon-uri/detach_rocket. Autori: Gonzalo Uribarri, Federico Barone, Alessio Ansuini, Eric Fransén Rivista: Data Mining and Knowledge Discovery Data di pubblicazione: 20/08/2024 Consulta la pubblicazione
Probing conformational dynamics of EGFR mutants via SEIRA spectroscopy: potential implications for tyrosine kinase inhibitor design
Abstract Missense mutations in EGFR’s catalytic domain alter its function, promoting cancer. SEIRA spectroscopy, supported by MD simulations, reveals structural differences in the compactness and hydration of helical motifs between active and inactive EGFR conformations models. These findings provide novel insights into the biophysical mechanisms driving EGFR activation and drug resistance, offering a robust method for studying emerging EGFR mutations and their structural impacts on TKIs efficacy. Autori Emiliano Laudadio, Federica Piccirilli, Henrick Vondracek, Giovanna Mobbili, Marta Stefania Semrau, Paola Storici, Roberta Galeazzi, Elena Romagnoli, Leonardo Sorci, Andrea Toma, Vincenzo Aglieri, Giovanni Birarda, Cristina Minnelli Rivista Physical Chemistry Chemical Physics (PCCP) Data di pubblicazione 19/08/2024 Consulta la pubblicazione
La0.2Sr0.25Ca0.45TiO3 Surface Reactivity with H2: A Combined Operando NEXAFS and Computational Study
Abstract A-site doped SrTiO3 is considered as a promising substitute for traditional anodic metals in solid oxide fuel cells (SOFCs). In this study, we present the reactivity of La0.2Sr0.25Ca0.45TiO3 (LCSTO), La0.2Sr0.7TiO3 (LSTO), and SrTiO3 (STO) toward H2 by operando ambient pressure NEXAFS spectroscopy and theoretical spectra simulation with FDMNES code. The samples were synthesized by MBE (molecular beam epitaxy), hydrothermal, and modified-Pechini routes. We found that the reducibility of the samples depends not only on their stoichiometry but also on the morphology, which is determined by the synthetic method. The results of these experiments give insight into the reducibility of Ti4+ in perovskites as well as the opportunity to further optimize the synthesis of these materials to obtain the best performance for SOFC applications. Autori F. Bassato, S. Mauri, L. Braglia, A. Yu. Petrov, E. Dobovičnik, F. Tavani, A. Tofoni, P. Ferrer, D. Grinter, G. Held, P. D’Angelo, P. Torelli Rivista The Journal of Physical Chemistry Letters Data di pubblicazione 13/08/2024 Consulta la pubblicazione
Molecular findings and virological assessment of bladder papillomavirus infection in cattle.
Abstract Bovine and ovine papillomaviruses (BPVs – OaPVs) are infectious agents that have an important role in bladder carcinogenesis of cattle. In an attempt to better understand territorial prevalence of papillomavirus genotypes and gain insights into their molecular pathway(s), a virological assessment of papillomavirus infection was performed on 52 bladder tumors in cattle using droplet digital polymerase chain reaction (ddPCR), an improved version of conventional PCR. ddPCR detected and quantified BPV DNA and mRNAs in all tumor samples, showing that these viruses play a determinant role in bovine bladder carcinogenesis. OaPV DNA and mRNA were detected and quantified in 45 bladder tumors. BPV14, BPV13, BPV2, OaPV2, OaPV1, and OaPV3 were the genotypes most closely related to bladder tumors. ddPCR quantified BPV1 and OaPV4 DNA and their transcripts less frequently. Western blot analysis revealed a significant overexpression of the phosphorylated platelet derived growth factor β receptor (PDGFβR) as well as the transcription factor E2F3, which modulate cell cycle progression in urothelial neoplasia. Furthermore, significant overexpression of calpain1, a Cys protease, was observed in bladder tumors related to BPVs alone and in BPV and OaPV coinfection. Calpain1 has been shown to play a role in producing free transcription factors of the E2F family, and molecular findings suggest that calpain family members work cooperatively to mutually regulate their protease activities in cattle bladder tumors. Altogether, these results showed territorial prevalence of BPV and OaPV genotypes and suggested that PDGFβR and the calpain system appeared to be molecular partners of both BPVs and OaPVs. Autori Francesca De Falco, Anna Cutarelli, Francesca Luisa Fedele, Cornel Catoi, Sante Roperto Rivista Veterinary Quarterly Data di pubblicazione 04/08/2024 Consulta la pubblicazione