1,178 results on '"Antenucci, A"'
Search Results
2. Changes in kynurenine metabolites in the gray and white matter of the dorsolateral prefrontal cortex of individuals affected by schizophrenia
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Antenucci, Nico, D’Errico, Giovanna, Fazio, Francesco, Nicoletti, Ferdinando, Bruno, Valeria, and Battaglia, Giuseppe
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- 2024
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3. A comparative study on semen quality and cryopreservation ability in Italian native chicken breeds
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Michele Di Iorio, Stefano Paolo Marelli, Emanuele Antenucci, Manuela Madeddu, Luisa Zaniboni, Silvia Belcredito, Giusy Rusco, Achille Schiavone, Dominga Soglia, Mauro Penasa, Cesare Castellini, Arianna Buccioni, Margherita Marzoni, Lucia Maiuro, Nicolaia Iaffaldano, and Silvia Cerolini
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italian chicken breeds ,fresh semen quality ,cryopreservation sensitivity ,breed-specific differences ,reproductive success ,Animal culture ,SF1-1100 - Abstract
This study provides a comparative assessment of fresh semen quality and sensitivity to cryopreservation in several Italian chicken breeds. The research involved 145 roosters from 13 breeds. The results showed a wide variability in all the parameters considered among the different breeds, especially in the quantitative variables of fresh semen, such as volume and concentration. For the qualitative characteristics (sperm membrane integrity and motility parameters), the variability across breeds was more pronounced for frozen than fresh semen. Interestingly, apart from total motility in fresh semen, breed had a significant effect on all semen quality parameters in both fresh and thawed ejaculates. Considering the overall qualitative characteristics, the Robusta maculata, Siciliana, and Mericanel della Brianza breeds produced ejaculates with better semen quality compared to other Italian breeds. By evaluating the main parameters of semen quality, our results underline the potential of these traits to influence the reproductive success and genetic conservation. The Bionda piemontese, Bianca di Saluzzo, Livorno bianca, Pepoi, and Siciliana breeds showed better resilience to cryopreservation, suggesting the need for breed-specific protocols to optimise semen quality after thawing. Importantly, the research highlights the central role of semen quality for both immediate fertilisation success and long-term conservation efforts. Future studies integrating OMICS technologies could elucidate molecular markers influencing breed-specific differences, helping to refine cryopreservation techniques and improve conservation strategies for indigenous Italian chicken breeds. This work contributes valuable insights to global efforts aimed at safeguarding poultry genetic diversity and sustainability.
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- 2024
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4. Reassessing the substrate specificities of the major Staphylococcus aureus peptidoglycan hydrolases lysostaphin and LytM
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Lina Antenucci, Salla Virtanen, Chandan Thapa, Minne Jartti, Ilona Pitkänen, Helena Tossavainen, and Perttu Permi
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S. aureus ,LytM ,NMR spectroscopy ,peptidoglycan hydrolases ,lysostaphin ,substrate specificity ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Orchestrated action of peptidoglycan (PG) synthetases and hydrolases is vital for bacterial growth and viability. Although the function of several PG synthetases and hydrolases is well understood, the function, regulation, and mechanism of action of PG hydrolases characterised as lysostaphin-like endopeptidases have remained elusive. Many of these M23 family members can hydrolyse glycyl-glycine peptide bonds and show lytic activity against Staphylococcus aureus whose PG contains a pentaglycine bridge, but their exact substrate specificity and hydrolysed bonds are still vaguely determined. In this work, we have employed NMR spectroscopy to study both the substrate specificity and the bond cleavage of the bactericide lysostaphin and the S. aureus PG hydrolase LytM. Yet, we provide substrate-level evidence for the functional role of these enzymes. Indeed, our results show that the substrate specificities of these structurally highly homologous enzymes are similar, but unlike observed earlier both LytM and lysostaphin prefer the D-Ala-Gly cross-linked part of mature peptidoglycan. However, we show that while lysostaphin is genuinely a glycyl-glycine hydrolase, LytM can also act as a D-alanyl-glycine endopeptidase.
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- 2024
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5. Changes in the pharyngeal and nasal microbiota in pediatric patients with adenotonsillar hypertrophy
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Federica Del Chierico, Antonia Piazzesi, Ersilia Vita Fiscarelli, Maria Vittoria Ristori, Ilaria Pirona, Alessandra Russo, Nicoletta Citerà, Gabriele Macari, Sara Santarsiero, Fabrizio Bianco, Valeria Antenucci, Valerio Damiani, Luigi Mercuri, Giovanni Carlo De Vincentis, and Lorenza Putignani
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adenotonsillar hypertrophy ,pharyngeal microbiota ,nasal microbiota ,upper airway pathobionts ,probiotics ,Microbiology ,QR1-502 - Abstract
ABSTRACT The present study aimed to investigate the pharyngeal and nasal microbiota composition in children with adenotonsillar hypertrophy (AH) and assess longitudinal alterations in both microbiota after a probiotic oral spray treatment. A cohort of 57 AH patients were enrolled and randomly assigned to the probiotic and placebo groups for a 5-month treatment course. Pharyngeal and nasal swabs were collected before and after treatment and analyzed by 16S rRNA-based metataxonomics and axenic cultures for pathobiont identification. 16S rRNA sequences from pharyngeal and nasal swabs of 65 healthy children (HC) were used as microbiota reference profiles. We found that the pharyngeal and nasal microbiota of AH children were similar. When compared to HC, we observed an increase of the genera Rothia, Granulicatella, Streptococcus, Neisseria, and Haemophilus, as well as a reduction of Corynebacterium, Pseudomonas, Acinetobacter, and Moraxella in both microbiota of AH patients. After probiotic treatment, we confirmed the absence of adverse effects and a reduction of upper respiratory tract infections (URTI). Moreover, the composition of pharyngeal microbiota was positively influenced by the reduction of potential pathobionts, like Haemophilus spp., with an increase of beneficial microbial metabolic pathways. Finally, the probiotic reduced the abundance of the pathobionts Streptococcus mitis and Gemella haemolysans in relation to AH severity. In conclusion, our results highlight the alterations of the pharyngeal and nasal microbiota associated with AH. Moreover, probiotic administration conferred protection against URTI and reduced the presence of potential pathobionts in patients with AH.IMPORTANCEAdenotonsillar hypertrophy (AH) is considered the main cause of breathing disorders during sleep in children. AH patients, after significant morbidity and often multiple courses of antibiotics, often proceed to tonsillectomy and/or adenoidectomy. Given the potential risks associated with these procedures, there is a growing interest in the use of nonsurgical adjuvant therapies, such as probiotics, that could potentially reduce their need for surgical intervention. In this study, we investigated the pharyngeal and nasal microbiota in patients with AH compared with healthy children. Furthermore, we tested the effects of probiotic spray administration on both disease symptoms and microbiota profiles, to evaluate the possible use of this microbial therapy as an adjuvant for AH patients.
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- 2024
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6. A ‘double-edged’ role for type-5 metabotropic glutamate receptors in pain disclosed by light-sensitive drugs
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Serena Notartomaso, Nico Antenucci, Mariacristina Mazzitelli, Xavier Rovira, Serena Boccella, Flavia Ricciardi, Francesca Liberatore, Xavier Gomez-Santacana, Tiziana Imbriglio, Milena Cannella, Charleine Zussy, Livio Luongo, Sabatino Maione, Cyril Goudet, Giuseppe Battaglia, Amadeu Llebaria, Ferdinando Nicoletti, and Volker Neugebauer
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photopharmacology ,pain ,behavior ,neuronal activity ,metabotropic glutamate receptor ,neurotransmission ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
We used light-sensitive drugs to identify the brain region-specific role of mGlu5 metabotropic glutamate receptors in the control of pain. Optical activation of systemic JF-NP-26, a caged, normally inactive, negative allosteric modulator (NAM) of mGlu5 receptors, in cingulate, prelimbic, and infralimbic cortices and thalamus inhibited neuropathic pain hypersensitivity. Systemic treatment of alloswitch-1, an intrinsically active mGlu5 receptor NAM, caused analgesia, and the effect was reversed by light-induced drug inactivation in the prelimbic and infralimbic cortices, and thalamus. This demonstrates that mGlu5 receptor blockade in the medial prefrontal cortex and thalamus is both sufficient and necessary for the analgesic activity of mGlu5 receptor antagonists. Surprisingly, when the light was delivered in the basolateral amygdala, local activation of systemic JF-NP-26 reduced pain thresholds, whereas inactivation of alloswitch-1 enhanced analgesia. Electrophysiological analysis showed that alloswitch-1 increased excitatory synaptic responses in prelimbic pyramidal neurons evoked by stimulation of presumed BLA input, and decreased BLA-driven feedforward inhibition of amygdala output neurons. Both effects were reversed by optical silencing and reinstated by optical reactivation of alloswitch-1. These findings demonstrate for the first time that the action of mGlu5 receptors in the pain neuraxis is not homogenous, and suggest that blockade of mGlu5 receptors in the BLA may limit the overall analgesic activity of mGlu5 receptor antagonists. This could explain the suboptimal effect of mGlu5 NAMs on pain in human studies and validate photopharmacology as an important tool to determine ideal target sites for systemic drugs.
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- 2024
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7. Changes in kynurenine metabolites in the gray and white matter of the dorsolateral prefrontal cortex of individuals affected by schizophrenia
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Nico Antenucci, Giovanna D’Errico, Francesco Fazio, Ferdinando Nicoletti, Valeria Bruno, and Giuseppe Battaglia
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Psychiatry ,RC435-571 - Abstract
Abstract Alterations in the kynurenine pathway of tryptophan metabolism have been implicated in the pathophysiology of schizophrenia. Here, we performed an in-depth analysis of all metabolites of the kynurenine pathway, i.e., tryptophan (TRY), kynurenic acid (KYNA), L-kynurenine (KYN), 3-hydroxykynurenine (3-HK), anthranylic acid (ANA), 3-hydroxyanthranylic acid (3-HANA), xanthurenic acid (XA) and quinolinic acid (QUINA), in postmortem samples of the dorsolateral prefrontal cortex (DLPFC, Brodmann area 46, 9) of individuals affected by schizophrenia and non-schizophrenic controls. The analysis was carried out in the gray and white matter. Levels of KYN, 3-HK, ANA, and 3-HANA were significantly increased in both the gray and white matter of the DLPFC of individuals affected by schizophrenia, whereas levels of TRY, KYNA, and QUINA were increased exclusively in the white matter and remained unchanged in the gray matter. These increases in kynurenine metabolites did not correlate with age, sex, duration of the disease, and duration and type of antipsychotic medication. These findings suggest that the two major branches of the kynurenine pathway, i.e., the transamination of KYN into KYNA, and hydroxylation of KYN into 3-HK are activated in the white matter of individuals affected by schizophrenia, perhaps as a result of neuroinflammation, and support the evidence that abnormalities of the white matter are consistenly associated with schizophrenia.
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- 2024
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8. Validation of the volumetric flow cytometry for bovine sperm concentration
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Alessia Gloria, Claudia Bracco, Emiliana Antenucci, and Alberto Contri
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Medicine ,Science - Abstract
Abstract Sperm concentration is a stronghold of the andrological evaluation and the production of insemination doses. The use of haemocytometers, although considered the gold standard, is difficult to apply in field conditions because it is subjective and time-consuming. The present study was designed to validate the volumetric flow cytometry (volFC) in order to estimate bovine sperm concentration, comparing it with the performances of haemocytometer, NucleoCounter, and flow cytometry with the use of fluorospheres. Compared with other methods, volFC appeared less affected by large dilution of the sample, with similar concentrations calculated in the range of dilution 1:200–1:800. Using volFc the population detected on the basis of morphological criteria and fluorescence of DNA better represents the real concentration of sperm in the sample. The volFC showed high repeatability compared with the haemocytometer (coefficient of variation 1.85% and 4.52%, respectively) and stable performances with cryopreserved samples, with negligible effects of the medium components. The present study showed that volFC is as accurate and precise as other techniques to estimate sperm concentration in bovine fresh and frozen semen, but it is less affected by operative conditions, such as sample dilution. The possibility to quantify sperm functional subpopulations by volFC could potentially implement the study of the relationship between sperm attributes and fertility.
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- 2023
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9. Leishmania profilin interacts with actin through an unusual structural mechanism to control cytoskeletal dynamics in parasites
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Vizcaíno-Castillo, Andrea, Kotila, Tommi, Kogan, Konstantin, Yanase, Ryuji, Como, Juna, Antenucci, Lina, Michelot, Alphee, Sunter, Jack D., and Lappalainen, Pekka
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- 2024
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10. Artist-driven layering and user's behaviour impact on recommendations in a playlist continuation scenario
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Antenucci, Sebastiano, Boglio, Simone, Chioso, Emanuele, Dervishaj, Ervin, Kang, Shuwen, Scarlatti, Tommaso, and Dacrema, Maurizio Ferrari
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Computer Science - Information Retrieval ,Computer Science - Machine Learning - Abstract
In this paper we provide an overview of the approach we used as team Creamy Fireflies for the ACM RecSys Challenge 2018. The competition, organized by Spotify, focuses on the problem of playlist continuation, that is suggesting which tracks the user may add to an existing playlist. The challenge addresses this issue in many use cases, from playlist cold start to playlists already composed by up to a hundred tracks. Our team proposes a solution based on a few well known models both content based and collaborative, whose predictions are aggregated via an ensembling step. Moreover by analyzing the underlying structure of the data, we propose a series of boosts to be applied on top of the final predictions and improve the recommendation quality. The proposed approach leverages well-known algorithms and is able to offer a high recommendation quality while requiring a limited amount of computational resources., Comment: Source code available here: https://github.com/MaurizioFD/spotify-recsys-challenge
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- 2020
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11. Exact results on high-dimensional linear regression via statistical physics
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Mozeika, Alexander, Sheikh, Mansoor, Aguirre-Lopez, Fabian, Antenucci, Fabrizio, and Coolen, Anthony CC
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Mathematics - Statistics Theory ,Condensed Matter - Disordered Systems and Neural Networks - Abstract
It is clear that conventional statistical inference protocols need to be revised to deal correctly with the high-dimensional data that are now common. Most recent studies aimed at achieving this revision rely on powerful approximation techniques, that call for rigorous results against which they can be tested. In this context, the simplest case of high-dimensional linear regression has acquired significant new relevance and attention. In this paper we use the statistical physics perspective on inference to derive a number of new exact results for linear regression in the high-dimensional regime., Comment: Most recent version accepted for publication in Physical Review E
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- 2020
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12. Replica analysis of overfitting in generalized linear models
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Coolen, ACC, Sheikh, M, Mozeika, A, Aguirre-Lopez, F, and Antenucci, F
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Condensed Matter - Disordered Systems and Neural Networks ,Mathematics - Statistics Theory - Abstract
Nearly all statistical inference methods were developed for the regime where the number $N$ of data samples is much larger than the data dimension $p$. Inference protocols such as maximum likelihood (ML) or maximum a posteriori probability (MAP) are unreliable if $p=O(N)$, due to overfitting. This limitation has for many disciplines with increasingly high-dimensional data become a serious bottleneck. We recently showed that in Cox regression for time-to-event data the overfitting errors are not just noise but take mostly the form of a bias, and how with the replica method from statistical physics once can model and predict this bias and the noise statistics. Here we extend our approach to arbitrary generalized linear regression models (GLM), with possibly correlated covariates. We analyse overfitting in ML/MAP inference without having to specify data types or regression models, relying only on the GLM form, and derive generic order parameter equations for the case of $L2$ priors. Second, we derive the probabilistic relationship between true and inferred regression coefficients in GLMs, and show that, for the relevant hyperparameter scaling and correlated covariates, the $L2$ regularization causes a predictable direction change of the coefficient vector. Our results, illustrated by application to linear, logistic, and Cox regression, enable one to correct ML and MAP inferences in GLMs systematically for overfitting bias, and thus extend their applicability into the hitherto forbidden regime $p=O(N)$., Comment: 45 pages, 7 figures, accepted for publication in Journal of Physics A
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- 2020
13. Validation of the volumetric flow cytometry for bovine sperm concentration
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Gloria, Alessia, Bracco, Claudia, Antenucci, Emiliana, and Contri, Alberto
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- 2023
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14. Can models for long-term decarbonization policies guarantee security of power supply? A perspective from gas and power sector coupling
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Antenucci, Andrea, del Granado, Pedro Crespo, Gjorgiev, Blazhe, and Sansavini, Giovanni
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Electrical Engineering and Systems Science - Systems and Control - Abstract
The assessment of adequacy and security of the energy system requires the detailed knowledge of physical and operational characteristics. In contrast, studies concerning energy transitions employ stylized models that oftentimes ignore the technical properties but have a lasting influence on long-term energy policies. This paper investigates the gap between energy system planning and operational models by linking these two perspectives: (1) a long-term investment model with low spatial resolution and high level of aggregation, and (2) a spatially resolved system security model that captures the interdependences between the backbone of the electric power sector, i.e., the electricity and the gas infrastructures. We assess EU decarbonization pathways of the electricity sector towards 2050 by integrating the investment decisions of the long-term planning model and the safety performance of the resulting system operations via the security assessment model. In a large RES deployment scenario, we investigate two flexibility options: gas power plants and cross-country transmission expansion. Using the integrated model, we analyze how the adequacy and security of supply under extreme short-term operational conditions impact the long-term planning of the energy system and the investment decision-making. We provide country specific recommendations for UK. Results indicate weaknesses in the gas-electricity system and suggest improvements on capacity allocation., Comment: 23 pages, 7 figures, 3 tables, 50 references
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- 2019
15. Self-starting nonlinear mode-locking in random lasers
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Antenucci, Fabrizio, Lerario, Giovanni, Fernandéz, Blanca Silva, De Giorgi, Milena, Ballarini, Dario, Sanvitto, Daniele, and Leuzzi, Luca
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Physics - Optics ,Condensed Matter - Disordered Systems and Neural Networks ,Physics - Data Analysis, Statistics and Probability - Abstract
In ultra-fast multi-mode lasers, mode-locking is implemented by means of ad hoc devices, like saturable absorbers or modulators, allowing for very short pulses. This comes about because of nonlinear interactions induced among modes at different, well equispaced, frequencies. Theory predicts that the same locking of modes would occur in random lasers but, in absence of any device, its detection is unfeasible so far. Because of the general interest in the phenomenology and understanding of random lasers and, moreover, because it is a first example of self-starting mode-locking we devise and test a way to measure such peculiar non-linear coupling. Through a detailed analysis of multi-mode correlations we provide clear evidence for the occurrence of nonlinear mode-coupling in the cavity-less random laser made of a powder of GaAs crystals and its self-starting mode-locking nature. The behavior of multi-point correlations among intensity peaks is tested against the nonlinear frequency matching condition equivalent to the one underlying phase-locking in ordered ultrafast lasers. Non-trivially large multi-point correlations are clearly observed for spatially overlapping resonances and turn out to sensitively depend on the frequency matching being satisfied, eventually demonstrating the occurrence of non-linear mode-locked mode-coupling., Comment: 13 pages, 8 figures, 1 table
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- 2019
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16. Glassiness and Lack of Equipartition in Random Lasers: the common roots of Ergodicity Breaking in Disordered and Non-linear Systems
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Gradenigo, Giacomo, Antenucci, Fabrizio, and Leuzzi, Luca
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Condensed Matter - Statistical Mechanics ,Condensed Matter - Disordered Systems and Neural Networks ,Physics - Optics - Abstract
We present here for the first time a unifying perspective for the lack of equipartition in non-linear ordered systems and the low temperature phase-space fragmentation in disordered systems. We demonstrate that they are just two manifestation of the same underlying phenomenon: ergodicity breaking. Inspired by recent experiments, suggesting that lasing in optically active disordered media is related to an ergodicity-breaking transition, we studied numerically a statistical mechanics model for the nonlinearly coupled light modes in a disordered medium under external pumping. Their collective behavior appears to be akin to the one displayed around the ergodicity-breaking transition in glasses, as we show measuring the glass order parameter of the replica-symmetry-breaking theory. Most remarkably, we also find that at the same critical point a breakdown of energy equipartition among light modes occurs, the typical signature of ergodicity breaking in non-linear systems as the celebrated Fermi-Pasta-Ulam model. The crucial ingredient of our system which allows us to find equipartition breakdown together with replica symmetry breaking is that the amplitudes of light modes are locally unbounded, i.e., they are only subject to a global constraint. The physics of random lasers appears thus as a unique test-bed to develop under a unifying perspective the study of ergodicity breaking in statistical disordered systems and non-linear ordered ones., Comment: 14 pages, 4 figures
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- 2019
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17. Lexis and Grammar of Mitochondrial RNA Processing in Trypanosomes
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Aphasizheva, Inna, Alfonzo, Juan, Carnes, Jason, Cestari, Igor, Cruz-Reyes, Jorge, Göringer, H Ulrich, Hajduk, Stephen, Lukeš, Julius, Madison-Antenucci, Susan, Maslov, Dmitri A, McDermott, Suzanne M, Ochsenreiter, Torsten, Read, Laurie K, Salavati, Reza, Schnaufer, Achim, Schneider, André, Simpson, Larry, Stuart, Kenneth, Yurchenko, Vyacheslav, Zhou, Z Hong, Zíková, Alena, Zhang, Liye, Zimmer, Sara, and Aphasizhev, Ruslan
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Rare Diseases ,Genetics ,Infectious Diseases ,Vector-Borne Diseases ,Good Health and Well Being ,Animals ,RNA Editing ,RNA ,Mitochondrial ,RNA ,Protozoan ,Trypanosoma brucei brucei ,RNA decay ,RNA editing ,Trypanosoma ,kinetoplast ,mitochondria ,polyadenylation ,Biological Sciences ,Agricultural and Veterinary Sciences ,Medical and Health Sciences ,Mycology & Parasitology - Abstract
Trypanosoma brucei spp. cause African human and animal trypanosomiasis, a burden on health and economy in Africa. These hemoflagellates are distinguished by a kinetoplast nucleoid containing mitochondrial DNAs of two kinds: maxicircles encoding ribosomal RNAs (rRNAs) and proteins and minicircles bearing guide RNAs (gRNAs) for mRNA editing. All RNAs are produced by a phage-type RNA polymerase as 3' extended precursors, which undergo exonucleolytic trimming. Most pre-mRNAs proceed through 3' adenylation, uridine insertion/deletion editing, and 3' A/U-tailing. The rRNAs and gRNAs are 3' uridylated. Historically, RNA editing has attracted major research effort, and recently essential pre- and postediting processing events have been discovered. Here, we classify the key players that transform primary transcripts into mature molecules and regulate their function and turnover.
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- 2020
18. Critical Assessment of the Sustainability of Deep Eutectic Solvents: A Case Study on Six Choline Chloride-Based Mixtures
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Stefano Nejrotti, Achille Antenucci, Carlotta Pontremoli, Lorenzo Gontrani, Nadia Barbero, Marilena Carbone, and Matteo Bonomo
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Chemistry ,QD1-999 - Published
- 2022
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19. Autonomic and circulatory alterations persist despite adequate resuscitation in a 5-day sepsis swine experiment
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Marta Carrara, Pietro Antenucci, Shengchen Liu, Andreas Kohler, Rupert Langer, Stephan M. Jakob, and Manuela Ferrario
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Medicine ,Science - Abstract
Abstract Autonomic and vascular failures are common phenotypes of sepsis, typically characterized by tachycardia despite corrected hypotension/hypovolemia, vasopressor resistance, increased arterial stiffness and decreased peripheral vascular resistance. In a 5-day swine experiment of polymicrobial sepsis we aimed at characterizing arterial properties and autonomic mechanisms responsible for cardiovascular homeostasis regulation, with the final goal to verify whether the resuscitation therapy in agreement with standard guidelines was successful in restoring a physiological condition of hemodynamic profile, cardiovascular interactions and autonomic control. Twenty pigs were randomized to polymicrobial sepsis and protocol-based resuscitation or to prolonged mechanical ventilation and sedation without sepsis. The animals were studied at baseline, after sepsis development, and every 24 h during the 3-days resuscitation period. Beat-to-beat carotid blood pressure (BP), carotid blood flow, and central venous pressure were continuously recorded. The two-element Windkessel model was adopted to study carotid arterial compliance, systemic vascular resistance and characteristic time constant τ. Effective arterial elastance was calculated as a simple estimate of total arterial load. Cardiac baroreflex sensitivity (BRS) and low frequency (LF) spectral power of diastolic BP were computed to assess autonomic activity. Sepsis induced significant vascular and autonomic alterations, manifested as increased arterial stiffness, decreased vascular resistance and τ constant, reduced BRS and LF power, higher arterial afterload and elevated heart rate in septic pigs compared to sham animals. This compromised condition was persistent until the end of the experiment, despite achievement of recommended resuscitation goals by administered vasopressors and fluids. Vascular and autonomic alterations persist 3 days after goal-directed resuscitation in a clinically relevant sepsis model. We hypothesize that the addition of these variables to standard clinical markers may better profile patients’ response to treatment and this could drive a more tailored therapy which could have a potential impact on long-term outcomes.
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- 2022
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20. The Immunodynamic Effect of Radiotherapy in Prostate Cancer Patients.
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Paola Nisticò, Iole Cordone, Adriana Faiella, Paola Trono, Serena Masi, Roberta Merola, Anna Antenucci, Maria Laura Foddai, Maria Consiglia Ferriero, Diana Giannarelli, Paolo Di Ridolfi, and Giuseppe Sanguineti, Radioinduced Modifications of Lymphocyte Subpopulations Involved in Resistence and Escape Mechanisms to Radiation Therapy of Localized Prostate Cancer.
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- 2021
21. A Machine Learning Predictive Model of Bloodstream Infection in Hospitalized Patients
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Rita Murri, Giulia De Angelis, Laura Antenucci, Barbara Fiori, Riccardo Rinaldi, Massimo Fantoni, Andrea Damiani, Stefano Patarnello, Maurizio Sanguinetti, Vincenzo Valentini, Brunella Posteraro, and Carlotta Masciocchi
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bloodstream infections ,machine learning ,prediction ,Medicine (General) ,R5-920 - Abstract
The aim of the study was to build a machine learning-based predictive model to discriminate between hospitalized patients at low risk and high risk of bloodstream infection (BSI). A Data Mart including all patients hospitalized between January 2016 and December 2019 with suspected BSI was built. Multivariate logistic regression was applied to develop a clinically interpretable machine learning predictive model. The model was trained on 2016–2018 data and tested on 2019 data. A feature selection based on a univariate logistic regression first selected candidate predictors of BSI. A multivariate logistic regression with stepwise feature selection in five-fold cross-validation was applied to express the risk of BSI. A total of 5660 hospitalizations (4026 and 1634 in the training and the validation subsets, respectively) were included. Eleven predictors of BSI were identified. The performance of the model in terms of AUROC was 0.74. Based on the interquartile predicted risk score, 508 (31.1%) patients were defined as being at low risk, 776 (47.5%) at medium risk, and 350 (21.4%) at high risk of BSI. Of them, 14.2% (72/508), 30.8% (239/776), and 64% (224/350) had a BSI, respectively. The performance of the predictive model of BSI is promising. Computational infrastructure and machine learning models can help clinicians identify people at low risk for BSI, ultimately supporting an antibiotic stewardship approach.
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- 2024
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22. Approximate Survey Propagation for Statistical Inference
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Antenucci, Fabrizio, Krzakala, Florent, Urbani, Pierfrancesco, and Zdeborová, Lenka
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Condensed Matter - Disordered Systems and Neural Networks ,Condensed Matter - Statistical Mechanics ,Computer Science - Information Theory ,Mathematics - Statistics Theory ,Statistics - Machine Learning - Abstract
Approximate message passing algorithm enjoyed considerable attention in the last decade. In this paper we introduce a variant of the AMP algorithm that takes into account glassy nature of the system under consideration. We coin this algorithm as the approximate survey propagation (ASP) and derive it for a class of low-rank matrix estimation problems. We derive the state evolution for the ASP algorithm and prove that it reproduces the one-step replica symmetry breaking (1RSB) fixed-point equations, well-known in physics of disordered systems. Our derivation thus gives a concrete algorithmic meaning to the 1RSB equations that is of independent interest. We characterize the performance of ASP in terms of convergence and mean-squared error as a function of the free Parisi parameter s. We conclude that when there is a model mismatch between the true generative model and the inference model, the performance of AMP rapidly degrades both in terms of MSE and of convergence, while ASP converges in a larger regime and can reach lower errors. Among other results, our analysis leads us to a striking hypothesis that whenever s (or other parameters) can be set in such a way that the Nishimori condition $M=Q>0$ is restored, then the corresponding algorithm is able to reach mean-squared error as low as the Bayes-optimal error obtained when the model and its parameters are known and exactly matched in the inference procedure., Comment: 37 pages, 14 figures
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- 2018
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23. Glassy nature of the hard phase in inference problems
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Antenucci, Fabrizio, Franz, Silvio, Urbani, Pierfrancesco, and Zdeborová, Lenka
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Condensed Matter - Disordered Systems and Neural Networks ,Condensed Matter - Statistical Mechanics ,Computer Science - Information Theory ,Mathematics - Statistics Theory ,Statistics - Machine Learning - Abstract
An algorithmically hard phase was described in a range of inference problems: even if the signal can be reconstructed with a small error from an information theoretic point of view, known algorithms fail unless the noise-to-signal ratio is sufficiently small. This hard phase is typically understood as a metastable branch of the dynamical evolution of message passing algorithms. In this work we study the metastable branch for a prototypical inference problem, the low-rank matrix factorization, that presents a hard phase. We show that for noise-to-signal ratios that are below the information theoretic threshold, the posterior measure is composed of an exponential number of metastable glassy states and we compute their entropy, called the complexity. We show that this glassiness extends even slightly below the algorithmic threshold below which the well-known approximate message passing (AMP) algorithm is able to closely reconstruct the signal. Counter-intuitively, we find that the performance of the AMP algorithm is not improved by taking into account the glassy nature of the hard phase. This result provides further evidence that the hard phase in inference problems is algorithmically impenetrable for some deep computational reasons that remain to be uncovered., Comment: 10 pages, 3 figures
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- 2018
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24. The making of smart cities: Borders, security and value in New Town Kolkata and Cape Town
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Antenucci, Ilia
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- 2021
25. Considerations about the multidimensional evaluation of a stab wound tibial neuropathy: a case report
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Antenucci Pietro, Carlucci Domenico, Pugliatti Maura, and Lucchetta Marta
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peripheral nerve diagnosis ,nerve ultrasound ,sciatic nerve ,tibial nerve ,mononeuropathy ,Medicine (General) ,R5-920 ,Medical technology ,R855-855.5 - Abstract
We present a rare case of a traumatic lesion of the tibial fibers of the sciatic nerve with spared peroneal fibers. A 33-year-old victim of a three month earlier stabbing attack came to our attention with gait impairment and weakened left foot plantar flexion and left foot internal rotation and supination. Based upon clinical signs and neurophysiological investigations we suspected that a traumatic injury of the left tibial nerve had occurred. Ultrasound examination detected a lesion of part of the left sciatic nerve, in a different site than expected. The patient was immediately enlisted for a tailored surgical reconstruction.
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- 2023
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26. C-N, C-O and C-S Ullmann-Type Coupling Reactions of Arenediazonium o-Benzenedisulfonimides
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Achille Antenucci and Stefano Dughera
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Ullmann-type coupling ,copper catalysis ,arenediazonium salts ,Chemistry ,QD1-999 - Abstract
Arenediazonium o-benzenedisulfonimides have been used as efficient electrophilic partners in Cu(I) catalysed Ullmann-type coupling. The synthetic protocols are mild and easy, and produced either N-alkylanilines, aryl ethers, or thioethers in fairly good yields (18 positive examples, average yield 66%). o-Benzenedisulfonimide was recovered at the end of the reactions and was reused to prepare the starting salts for further reactions. It is noteworthy that diazonium salts have been used as electrophilic partners in the Ullmann-type protocol for the first time.
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- 2022
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27. Bringing rehabilitation home with an e-health platform to treat stroke patients: study protocol of a randomized clinical trial (RGS@home)
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Anna Mura, Martina Maier, Belén Rubio Ballester, Javier De la Torre Costa, Judit López-Luque, Axelle Gelineau, Stephane Mandigout, Per Hamid Ghatan, Raffaele Fiorillo, Fabrizio Antenucci, Ton Coolen, Iñigo Chivite, Antonio Callen, Hugo Landais, Olga Irina Gómez, Cristina Melero, Santiago Brandi, Marc Domenech, Jean-Christophe Daviet, Riccardo Zucca, and Paul F. M. J. Verschure
- Subjects
Randomized clinical trial ,Stroke ,Virtual reality ,Motor recovery ,Upper extremities ,Wearables ,Medicine (General) ,R5-920 - Abstract
Abstract Background There is a pressing need for scalable healthcare solutions and a shift in the rehabilitation paradigm from hospitals to homes to tackle the increase in stroke incidence while reducing the practical and economic burden for patients, hospitals, and society. Digital health technologies can contribute to addressing this challenge; however, little is known about their effectiveness in at-home settings. In response, we have designed the RGS@home study to investigate the effectiveness, acceptance, and cost of a deep tech solution called the Rehabilitation Gaming System (RGS). RGS is a cloud-based system for delivering AI-enhanced rehabilitation using virtual reality, motion capture, and wearables that can be used in the hospital and at home. The core principles of the brain theory-based RGS intervention are to deliver rehabilitation exercises in the form of embodied, goal-oriented, and task-specific action. Methods The RGS@home study is a randomized longitudinal clinical trial designed to assess whether the combination of the RGS intervention with standard care is superior to standard care alone for the functional recovery of stroke patients at the hospital and at home. The study is conducted in collaboration with hospitals in Spain, Sweden, and France and includes inpatients and outpatients at subacute and chronic stages post-stroke. The intervention duration is 3 months with assessment at baseline and after 3, 6, and 12 months. The impact of RGS is evaluated in terms of quality of life measurements, usability, and acceptance using standardized clinical scales, together with health economic analysis. So far, one-third of the patients expected to participate in the study have been recruited (N = 90, mean age 60, days after stroke ≥ 30 days). The trial will end in July 2023. Discussion We predict an improvement in the patients’ recovery, high acceptance, and reduced costs due to a soft landing from the clinic to home rehabilitation. In addition, the data provided will allow us to assess whether the prescription of therapy at home can counteract deterioration and improve quality of life while also identifying new standards for online and remote assessment, diagnostics, and intervention across European hospitals. Trial registration C linicalTrials.gov NCT04620707. Registered on November 3, 2020
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- 2022
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28. Structural basis of rapid actin dynamics in the evolutionarily divergent Leishmania parasite
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Tommi Kotila, Hugo Wioland, Muniyandi Selvaraj, Konstantin Kogan, Lina Antenucci, Antoine Jégou, Juha T. Huiskonen, Guillaume Romet-Lemonne, and Pekka Lappalainen
- Subjects
Science - Abstract
The authors report here the structure-function analysis of highly divergent actin from Leishmania parasite. The study reveals remarkably rapid dynamics of parasite actin as well as the underlying molecular basis, thus providing insight into evolution of the actin cytoskeleton.
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- 2022
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29. Structure of SNX9 SH3 in complex with a viral ligand reveals the molecular basis of its unique specificity for alanine-containing class I SH3 motifs
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Tossavainen, Helena, Uğurlu, Hasan, Karjalainen, Mikael, Hellman, Maarit, Antenucci, Lina, Fagerlund, Riku, Saksela, Kalle, and Permi, Perttu
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- 2022
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30. Improved Pseudolikelihood Regularization and Decimation methods on Non-linearly Interacting Systems with Continuous Variables
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Marruzzo, Alessia, Tyagi, Payal, Antenucci, Fabrizio, Pagnani, Andrea, and Leuzzi, Luca
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Physics - Data Analysis, Statistics and Probability ,Condensed Matter - Disordered Systems and Neural Networks ,Condensed Matter - Statistical Mechanics - Abstract
We propose and test improvements to state-of-the-art techniques of Bayeasian statistical inference based on pseudolikelihood maximization with $\ell_1$ regularization and with decimation. In particular, we present a method to determine the best value of the regularizer parameter starting from a hypothesis testing technique. Concerning the decimation, we also analyze the worst case scenario in which there is no sharp peak in the tilded-pseudolikelihood function, firstly defined as a criterion to stop the decimation. Techniques are applied to noisy systems with non-linear dynamics, mapped onto multi-variable interacting Hamiltonian effective models for waves and phasors. Results are analyzed varying the number of available samples and the externally tunable temperature-like parameter mimicing real data noise. Eventually the behavior of inference procedures described are tested against a wrong hypothesis: non-linearly generated data are analyzed with a pairwise interacting hypothesis. Our analysis shows that, looking at the behavior of the inverse graphical problem as data size increases, the methods exposed allow to rule out a wrong hypothesis., Comment: 37 pages, 24 figures
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- 2017
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31. Reassessing the substrate specificities of the major Staphylococcus aureus peptidoglycan hydrolases lysostaphin and LytM.
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Antenucci, Lina, Virtanen, Salla, Thapa, Chandan, Jartti, Minne, Pitkänen, Ilona, Tossavainen, Helena, and Permi, Perttu
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- *
LIGASES , *BIOCHEMICAL substrates , *HYDROLASES , *PEPTIDE bonds , *ENDOPEPTIDASES , *GLYCINE receptors - Abstract
Orchestrated action of peptidoglycan (PG) synthetases and hydrolases is vital for bacterial growth and viability. Although the function of several PG synthetases and hydrolases is well understood, the function, regulation, and mechanism of action of PG hydrolases characterised as lysostaphin-like endopeptidases have remained elusive. Many of these M23 family members can hydrolyse glycyl-glycine peptide bonds and show lytic activity against Staphylococcus aureus whose PG contains a pentaglycine bridge, but their exact substrate specificity and hydrolysed bonds are still vaguely determined. In this work, we have employed NMR spectroscopy to study both the substrate specificity and the bond cleavage of the bactericide lysostaphin and the S. aureus PG hydrolase LytM. Yet, we provide substrate-level evidence for the functional role of these enzymes. Indeed, our results show that the substrate specificities of these structurally highly homologous enzymes are similar, but unlike observed earlier both LytM and lysostaphin prefer the D-Ala-Gly cross-linked part of mature peptidoglycan. However, we show that while lysostaphin is genuinely a glycyl-glycine hydrolase, LytM can also act as a D-alanyl-glycine endopeptidase. [ABSTRACT FROM AUTHOR]
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- 2024
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32. Beneficial Effects of Ginger Root Extract on Pain Behaviors, Inflammation, and Mitochondrial Function in the Colon and Different Brain Regions of Male and Female Neuropathic Rats: A Gut–Brain Axis Study.
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Santos, Julianna Maria, Deshmukh, Hemalata, Elmassry, Moamen M., Yakhnitsa, Vadim, Ji, Guangchen, Kiritoshi, Takaki, Presto, Peyton, Antenucci, Nico, Liu, Xiaobo, Neugebauer, Volker, and Shen, Chwan-Li
- Abstract
Background: Neuroinflammation and mitochondrial dysfunction have been implicated in the progression of neuropathic pain (NP) but can be mitigated by supplementation with gingerol-enriched ginger (GEG). However, the exact benefits of GEG for each sex in treating neuroinflammation and mitochondrial homeostasis in different brain regions and the colon remain to be determined. Objective: Evaluate the effects of GEG on emotional/affective pain and spontaneous pain behaviors, neuroinflammation, as well as mitochondria homeostasis in the amygdala, frontal cortex, hippocampus, and colon of male and female rats in the spinal nerve ligation (SNL) NP model. Methods: One hundred rats (fifty males and fifty females) were randomly assigned to five groups: sham + vehicle, SNL + vehicle, and SNL with three different GEG doses (200, 400, and 600 mg/kg BW) for 5 weeks. A rat grimace scale and vocalizations were used to assess spontaneous and emotional/affective pain behaviors, respectively. mRNA gene and protein expression levels for tight junction protein, neuroinflammation, mitochondria homeostasis, and oxidative stress were measured in the amygdala, frontal cortex, hippocampus, and colon using qRT-PCR and Western blot (colon). Results: GEG supplementation mitigated spontaneous pain in both male and female rats with NP while decreasing emotional/affective responses only in male NP rats. GEG supplementation increased intestinal integrity (claudin 3) and suppressed neuroinflammation [glial activation (GFAP, CD11b, IBA1) and inflammation (TNFα, NFκB, IL1β)] in the selected brain regions and colon of male and female NP rats. GEG supplementation improved mitochondrial homeostasis [increased biogenesis (TFAM, PGC1α), increased fission (FIS, DRP1), decreased fusion (MFN2, MFN1) and mitophagy (PINK1), and increased Complex III] in the selected brain regions and colon in both sexes. Some GEG dose–response effects in gene expression were observed in NP rats of both sexes. Conclusions: GEG supplementation decreased emotional/affective pain behaviors of males and females via improving gut integrity, suppressing neuroinflammation, and improving mitochondrial homeostasis in the amygdala, frontal cortex, hippocampus, and colon in both male and female SNL rats in an NP model, implicating the gut–brain axis in NP. Sex differences observed in the vocalizations assay may suggest different mechanisms of evoked NP responses in females. [ABSTRACT FROM AUTHOR]
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- 2024
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33. Cryopreserving Rabbit Semen: Impact of Varying Sperm Concentrations on Quality and the Standardization of Protocol
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Michele Di Iorio, Fabrizio Lauriola, Giusy Rusco, Emanuele Antenucci, Michele Schiavitto, and Nicolaia Iaffaldano
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rabbit semen ,sperm concentrations ,standardizing freezing protocol ,motility parameters ,Veterinary medicine ,SF600-1100 - Abstract
This study aimed to investigate the impact of sperm concentrations on the in vitro quality of cryopreserved rabbit semen. The semen pools (n = 8, from 80 donors) were split into five aliquots with final sperm concentrations of 15, 25, 35, 55, and 75 × 106 per straw. The sperm motility parameters (CASA system) and membrane integrity (flow cytometric analysis) were both evaluated at various stages of the cryopreservation process: fresh semen dilution, cooling, equilibration, and immediately after and 30 min post-thawing. The results indicated the significant influence of the sperm concentration on the total motility (TM) and progressive motility (PM), with a consistent decline in all sperm variables over the time points. Notably, the semen with a final concentration of 15 × 106 exhibited a higher TM and PM after cooling and equilibration. The post-thawing quality (TM, PM) was higher (p < 0.05) in the mid-range sperm concentrations of 25 × 106 (49.9% and 19.7%) and 35 × 106 (46.2% and 19.7%) compared to the other concentrations. This study demonstrated that the sperm concentration per straw played a significant role in specific phases of the cryopreservation process. These findings contribute valuable insights for refining and standardizing the cryopreservation protocol for rabbit semen, emphasizing the importance of the sperm concentration.
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- 2023
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34. Characterization of a Type II L-Asparaginase from the Halotolerant Bacillus subtilis CH11
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Annsy Arredondo-Nuñez, Gisele Monteiro, Carol N. Flores-Fernández, Lina Antenucci, Perttu Permi, and Amparo Iris Zavaleta
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L-asparaginase II ,Bacillus subtilis ,saline environment ,biochemical characterization ,Science - Abstract
L-asparaginases from bacterial sources have been used in antineoplastic treatments and the food industry. A type II L-asparaginase encoded by the N-truncated gene ansZP21 of halotolerant Bacillus subtilis CH11 isolated from Chilca salterns in Peru was expressed using a heterologous system in Escherichia coli BL21 (DE3)pLysS. The recombinant protein was purified using one-step nickel affinity chromatography and exhibited an activity of 234.38 U mg−1 and a maximum catalytic activity at pH 9.0 and 60 °C. The enzyme showed a homotetrameric form with an estimated molecular weight of 155 kDa through gel filtration chromatography. The enzyme half-life at 60 °C was 3 h 48 min, and L-asparaginase retained 50% of its initial activity for 24 h at 37 °C. The activity was considerably enhanced by KCl, CaCl2, MgCl2, mercaptoethanol, and DL-dithiothreitol (p-value < 0.01). Moreover, the Vmax and Km were 145.2 µmol mL−1 min−1 and 4.75 mM, respectively. These findings evidence a promising novel type II L-asparaginase for future industrial applications.
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- 2023
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35. Growing underground: Development of thermogenesis in pups of the fossorial rodent Ctenomys talarum
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Facundo Luna, Jorge Sastre-Serra, Jordi Oliver, and C. Daniel Antenucci
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thermoregulation ,non-shivering thermogenesis ,postnatal development ,maximum metabolism ,Ctenomys ,Evolution ,QH359-425 ,Ecology ,QH540-549.5 - Abstract
In mammals, during the pup’s development and adult life, integrated requirements of all activities of the individual must conform to a sustained rate of metabolism. Thus, partitioning the available energy according to short-term priorities at a specific moment allows animals to survive and optimize long-term reproductive success. In altricial rodents, thermal balance is a key factor for survival. When no exogenous source of heat is present, altricial pups rapidly lose heat, reaching ambient temperature (Ta). Fossorial rodents showed a strong dependence on burrows, where Ta remains relatively stable within narrow ranges. Pups of the fossorial rodent Ctenomys talarum are altricial, making them an excellent model to evaluate the development of thermogenic capacity. In this study, the ontogeny of the thermogenic capacity of pups of C. talarum was evaluated. Using respirometry techniques, non-shivering thermogenesis (NST), total thermogenic capacity (cold-induced maximum metabolic rate, MMR), and resting metabolic rate (RMR) in pups until post-weaning age (day 60) were analyzed. No NST was present in pups until day 60 despite the presence of molecular markers for NST in brown adipose tissue deposits, which became functional in adults. Although pups are altricial at birth, they maintain their thermal balance behaviorally during lactation. Total thermogenic capacity became fixed at an early age, indicating an improvement in shivering thermogenesis (ST) efficiency after day 10, which might be related to the development of musculature related to digging. Before the aboveground dispersal period (~day 60), pups gradually reached adult Tb by improving ST and thermal isolation, allowing them to confront climatic fluctuations on the surface.
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- 2023
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36. Identification and Evaluation of Cryptosporidium Species from New York City Cases of Cryptosporidiosis (2015 to 2018): a Watershed Perspective
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Kerri A. Alderisio, Kimberly Mergen, Heather Moessner, and Susan Madison-Antenucci
- Subjects
Cryptosporidium ,New York City ,cryptosporidiosis ,watershed ,Microbiology ,QR1-502 - Abstract
ABSTRACT Watersheds that supply residents with drinking water have the potential for contamination with Cryptosporidium oocysts. To evaluate any potential similarities between Cryptosporidium species previously found in the New York City (NYC) watershed and those causing disease in NYC, the species were identified in stool specimens from residents with cryptosporidiosis. Genetic analysis was performed on 628 positive stool samples collected from NYC residents between 2015 and 2018 to determine the species present. A total of 547 samples yielded positive results by real-time PCR. Of these samples, 512 (93.6%) were identified to the species level, with 94.7% positive for either Cryptosporidium hominis or Cryptosporidium parvum (56.4% and 38.5%, respectively), including one coinfection. Less common Cryptosporidium species identified included C. felis, C. canis, C. ubiquitum, C. meleagridis, and a Cryptosporidium sp. chipmunk genotype. Results were evaluated and compared to species and genotypes of Cryptosporidium previously identified from stormwater collected within the NYC watershed. While there was overlap with some of the rare species found in case specimens, the prevalence and distribution of species did not suggest a connection between sources previously identified in the watershed and the species causing human cases of cryptosporidiosis in NYC residents. IMPORTANCE It is important to identify the species causing human cryptosporidiosis in a population in order to investigate possible sources or routes of contamination. Many species of Cryptosporidium are host-adapted and therefore have the potential to be tracked back to specific sources that can subsequently be managed. There has been no evidence to suggest that the water supply has ever been a source of cryptosporidiosis cases in NYC, and since 2013, the New York City Department of Environmental Protection has further reduced the risk of disease through the use of ultraviolet treatment to inactivate any Cryptosporidium present in the source water. However, as one of the largest unfiltered water supplies in the country, it is important to evaluate watershed sources for potential impacts to public health. In this unique study, species of Cryptosporidium causing disease in NYC residents were identified and compared with previously identified species from the watershed.
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- 2023
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37. Bringing rehabilitation home with an e-health platform to treat stroke patients: study protocol of a randomized clinical trial (RGS@home)
- Author
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Mura, Anna, Maier, Martina, Ballester, Belén Rubio, De la Torre Costa, Javier, López-Luque, Judit, Gelineau, Axelle, Mandigout, Stephane, Ghatan, Per Hamid, Fiorillo, Raffaele, Antenucci, Fabrizio, Coolen, Ton, Chivite, Iñigo, Callen, Antonio, Landais, Hugo, Gómez, Olga Irina, Melero, Cristina, Brandi, Santiago, Domenech, Marc, Daviet, Jean-Christophe, Zucca, Riccardo, and Verschure, Paul F. M. J.
- Published
- 2022
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38. Structural basis of rapid actin dynamics in the evolutionarily divergent Leishmania parasite
- Author
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Kotila, Tommi, Wioland, Hugo, Selvaraj, Muniyandi, Kogan, Konstantin, Antenucci, Lina, Jégou, Antoine, Huiskonen, Juha T., Romet-Lemonne, Guillaume, and Lappalainen, Pekka
- Published
- 2022
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39. Autonomic and circulatory alterations persist despite adequate resuscitation in a 5-day sepsis swine experiment
- Author
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Carrara, Marta, Antenucci, Pietro, Liu, Shengchen, Kohler, Andreas, Langer, Rupert, Jakob, Stephan M., and Ferrario, Manuela
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- 2022
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40. Estimating upper-extremity function from kinematics in stroke patients following goal-oriented computer-based training
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Belén Rubio Ballester, Fabrizio Antenucci, Martina Maier, Anthony C. C. Coolen, and Paul F. M. J. Verschure
- Subjects
Rehabilitation ,Stroke ,Interactive feedback ,Upper extremities ,Posture monitoring ,Motion sensing ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
Abstract Introduction After a stroke, a wide range of deficits can occur with varying onset latencies. As a result, assessing impairment and recovery are enormous challenges in neurorehabilitation. Although several clinical scales are generally accepted, they are time-consuming, show high inter-rater variability, have low ecological validity, and are vulnerable to biases introduced by compensatory movements and action modifications. Alternative methods need to be developed for efficient and objective assessment. In this study, we explore the potential of computer-based body tracking systems and classification tools to estimate the motor impairment of the more affected arm in stroke patients. Methods We present a method for estimating clinical scores from movement parameters that are extracted from kinematic data recorded during unsupervised computer-based rehabilitation sessions. We identify a number of kinematic descriptors that characterise the patients’ hemiparesis (e.g., movement smoothness, work area), we implement a double-noise model and perform a multivariate regression using clinical data from 98 stroke patients who completed a total of 191 sessions with RGS. Results Our results reveal a new digital biomarker of arm function, the Total Goal-Directed Movement (TGDM), which relates to the patients work area during the execution of goal-oriented reaching movements. The model’s performance to estimate FM-UE scores reaches an accuracy of $$R^2$$ R 2 : 0.38 with an error ( $$\sigma$$ σ : 12.8). Next, we evaluate its reliability ( $$r=0.89$$ r = 0.89 for test-retest), longitudinal external validity ( $$95\%$$ 95 % true positive rate), sensitivity, and generalisation to other tasks that involve planar reaching movements ( $$R^2$$ R 2 : 0.39). The model achieves comparable accuracy also for the Chedoke Arm and Hand Activity Inventory ( $$R^2$$ R 2 : 0.40) and Barthel Index ( $$R^2$$ R 2 : 0.35). Conclusions Our results highlight the clinical value of kinematic data collected during unsupervised goal-oriented motor training with the RGS combined with data science techniques, and provide new insight into factors underlying recovery and its biomarkers.
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- 2021
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41. SHANK3 conformation regulates direct actin binding and crosstalk with Rap1 signaling
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Salomaa, Siiri I., Miihkinen, Mitro, Kremneva, Elena, Paatero, Ilkka, Lilja, Johanna, Jacquemet, Guillaume, Vuorio, Joni, Antenucci, Lina, Kogan, Konstantin, Hassani Nia, Fatemeh, Hollos, Patrik, Isomursu, Aleksi, Vattulainen, Ilpo, Coffey, Eleanor T., Kreienkamp, Hans-Jürgen, Lappalainen, Pekka, and Ivaska, Johanna
- Published
- 2021
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42. How do arenediazonium salts behave in deep eutectic solvents? A combined experimental and computational approach
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Antenucci, Achille, Bonomo, Matteo, Ghigo, Giovanni, Gontrani, Lorenzo, Barolo, Claudia, and Dughera, Stefano
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- 2021
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43. Inverse problem for multi-body interaction of nonlinear waves
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Marruzzo, Alessia, Tyagi, Payal, Antenucci, Fabrizio, Pagnani, Andrea, and Leuzzi, Luca
- Subjects
Condensed Matter - Disordered Systems and Neural Networks ,Condensed Matter - Statistical Mechanics ,Physics - Optics - Abstract
The inverse problem is studied in multi-body systems with nonlinear dynamics representing, e.g., phase-locked wave systems, standard multimode and random lasers. Using a general model for four-body interacting complex-valued variables we test two methods based on pseudolikelihood, respectively with regularization and with decimation, to determine the coupling constants from sets of measured configurations. We test statistical inference predictions for increasing number of sampled configurations and for an externally tunable {\em temperature}-like parameter mimicing real data noise and helping minimization procedures. Analyzed models with phasors and rotors are generalizations of problems of real-valued spherical problems (e.g., density fluctuations), discrete spins (Ising and vectorial Potts) or finite number of states (standard Potts): inference methods presented here can, then, be straightforward applied to a large class of inverse problems., Comment: 9 pages, 9 figures
- Published
- 2016
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44. Regularization and decimation pseudolikelihood approaches to statistical inference in $XY$-spin models
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Tyagi, Payal, Marruzzo, Alessia, Pagnani, Andrea, Antenucci, Fabrizio, and Leuzzi, Luca
- Subjects
Condensed Matter - Disordered Systems and Neural Networks ,Condensed Matter - Statistical Mechanics ,Physics - Optics - Abstract
We implement a pseudolikelyhood approach with l2-regularization as well as the recently introduced pseudolikelihood with decimation procedure to the inverse problem in continuous spin models on arbitrary networks, with arbitrarily disordered couplings. Performances of the approaches are tested against data produced by Monte Carlo numerical simulations and compared also from previously studied fully-connected mean-field-based inference techniques. The results clearly show that the best network reconstruction is obtained through the decimation scheme, that also allows to dwell the inference down to lower temperature regimes. Possible applications to phasor models for light propagation in random media are proposed and discussed., Comment: 10 pages, 12 figures
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- 2016
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45. Large‐scale production of extracellular vesicles: Report on the 'massivEVs' ISEV workshop
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Lucia Paolini, Marta Monguió‐Tortajada, Marta Costa, Fabio Antenucci, Mario Barilani, Marta Clos‐Sansalvador, André Cronemberger Andrade, Tom A. P. Driedonks, Sara Giancaterino, Stephanie M. Kronstadt, Rachel R. Mizenko, Muhammad Nawaz, Xabier Osteikoetxea, Carla Pereira, Surya Shrivastava, Anders Toftegaard Boysen, Simonides Immanuel van deWakker, Martijn J. C. vanHerwijnen, Xiaoqin Wang, Dionysios C. Watson, Mario Gimona, Maria Kaparakis‐Liaskos, Konstantin Konstantinov, Sai Kiang Lim, Nicole Meisner‐Kober, Michiel Stork, Peter Nejsum, Annalisa Radeghieri, Eva Rohde, Nicolas Touzet, Marca H. M. Wauben, Kenneth W. Witwer, Antonella Bongiovanni, and Paolo Bergese
- Subjects
EV‐based products ,extracellular vesicles ,ISEV workshop ,large‐scale production ,manufacturing ,processing ,Cytology ,QH573-671 - Abstract
Abstract Extracellular vesicles (EVs) large‐scale production is a crucial point for the translation of EVs from discovery to application of EV‐based products. In October 2021, the International Society for Extracellular Vesicles (ISEV), along with support by the FET‐OPEN projects, “The Extracellular Vesicle Foundry” (evFOUNDRY) and “Extracellular vesicles from a natural source for tailor‐made nanomaterials” (VES4US), organized a workshop entitled “massivEVs” to discuss the potential challenges for translation of EV‐based products. This report gives an overview of the topics discussed during “massivEVs”, the most important points raised, and the points of consensus reached after discussion among academia and industry representatives. Overall, the review of the existing EV manufacturing, upscaling challenges and directions for their resolution highlighted in the workshop painted an optimistic future for the expanding EV field.
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- 2022
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46. Outer Membrane Vesicles of Actinobacillus pleuropneumoniae Exert Immunomodulatory Effects on Porcine Alveolar Macrophages
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Zhuang Zhu, Fabio Antenucci, Hanne Cecilie Winther-Larsen, Kerstin Skovgaard, and Anders Miki Bojesen
- Subjects
outer membrane vesicles ,Actinobacillus pleuropneumoniae ,proteomics ,porcine alveolar macrophages ,innate immune response ,host-pathogen interaction ,Microbiology ,QR1-502 - Abstract
ABSTRACT Outer membrane vesicles (OMVs) are spontaneously released by Gram-negative bacteria, including Actinobacillus pleuropneumoniae, which causes contagious pleuropneumonia in pigs and leads to considerable economic losses in the swine industry worldwide. A. pleuropneumoniae OMVs have previously been demonstrated to contain Apx toxins and proteases, as well as antigenic proteins. Nevertheless, comprehensive characterizations of their contents and interactions with host immune cells have not been made. Understanding the protein compositions and immunomodulating ability of A. pleuropneumoniae OMVs could help illuminate their biological functions and facilitate the development of OMV-based applications. In the current investigation, we comprehensively characterized the proteome of native A. pleuropneumoniae OMVs. Moreover, we qualitatively and quantitatively compared the OMV proteomes of a wild-type strain and three mutant strains, in which relevant genes were disrupted to increase OMV production and/or produce OMVs devoid of superantigen PalA. Furthermore, the interaction between A. pleuropneumoniae OMVs and porcine alveolar macrophages was also characterized. Our results indicate that native OMVs spontaneously released by A. pleuropneumoniae MIDG2331 appeared to dampen the innate immune responses by porcine alveolar macrophages stimulated by either inactivated or live parent cells. The findings suggest that OMVs may play a role in manipulating the porcine defense during the initial phases of the A. pleuropneumoniae infection. IMPORTANCE Owing to their built-in adjuvanticity and antigenicity, bacterial outer membrane vesicles (OMVs) are gaining increasing attention as potential vaccines for both human and animal use. OMVs released by Actinobacillus pleuropneumoniae, an important respiratory pathogen in pigs, have also been investigated for vaccine development. Our previous studies have shown that A. pleuropneumoniae secretes OMVs containing multiple immunogenic proteins. However, immunization of pigs with these vesicles was not able to relieve the pig lung lesions induced by the challenge with A. pleuropneumoniae, implying the elusive roles that A. pleuropneumoniae OMVs play in host-pathogen interaction. Here, we showed that A. pleuropneumoniae secretes OMVs whose yield and protein content can be altered by the deletion of the nlpI and palA genes. Furthermore, we demonstrate that A. pleuropneumoniae OMVs dampen the immune responses in porcine alveolar macrophages stimulated by A. pleuropneumoniae cells, suggesting a novel mechanism that A. pleuropneumoniae might use to evade host defense.
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- 2022
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47. A comparative study on semen quality and cryopreservation ability in Italian native chicken breeds
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Di Iorio, Michele, Marelli, Stefano Paolo, Antenucci, Emanuele, Madeddu, Manuela, Zaniboni, Luisa, Belcredito, Silvia, Rusco, Giusy, Schiavone, Achille, Soglia, Dominga, Penasa, Mauro, Castellini, Cesare, Buccioni, Arianna, Marzoni, Margherita, Maiuro, Lucia, Iaffaldano, Nicolaia, and Cerolini, Silvia
- Abstract
AbstractThis study provides a comparative assessment of fresh semen quality and sensitivity to cryopreservation in several Italian chicken breeds. The research involved 145 roosters from 13 breeds. The results showed a wide variability in all the parameters considered among the different breeds, especially in the quantitative variables of fresh semen, such as volume and concentration. For the qualitative characteristics (sperm membrane integrity and motility parameters), the variability across breeds was more pronounced for frozen than fresh semen. Interestingly, apart from total motility in fresh semen, breed had a significant effect on all semen quality parameters in both fresh and thawed ejaculates. Considering the overall qualitative characteristics, the Robusta maculata, Siciliana, and Mericanel della Brianzabreeds produced ejaculates with better semen quality compared to other Italian breeds. By evaluating the main parameters of semen quality, our results underline the potential of these traits to influence the reproductive success and genetic conservation. The Bionda piemontese, Bianca di Saluzzo, Livorno bianca, Pepoi, and Sicilianabreeds showed better resilience to cryopreservation, suggesting the need for breed-specific protocols to optimise semen quality after thawing. Importantly, the research highlights the central role of semen quality for both immediate fertilisation success and long-term conservation efforts. Future studies integrating OMICS technologies could elucidate molecular markers influencing breed-specific differences, helping to refine cryopreservation techniques and improve conservation strategies for indigenous Italian chicken breeds. This work contributes valuable insights to global efforts aimed at safeguarding poultry genetic diversity and sustainability.
- Published
- 2024
- Full Text
- View/download PDF
48. Postfazione
- Author
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Emiliano Antenucci, Alfredo Altomonte, Arioli, Antonella, Antonella Arioli (ORCID:0000-0002-5221-1067), Emiliano Antenucci, Alfredo Altomonte, Arioli, Antonella, and Antonella Arioli (ORCID:0000-0002-5221-1067)
- Abstract
In un tempo permeato dalle "passioni tristi" diventa quantomai cruciale mettere al centro, in ambito formativo, i concetti di speranza e di resilienza. Ovvero, lo sguardo di fiduciosa attesa che chi educa dovrebbe avere nei confronti di ogni essere umano e, in particolare, nei riguardi dei giovani. La convinzione nelle loro possibilità di sviluppo, per trasmettere e incentivare un atteggiamento positivo anche nelle situazioni più difficili dell’esistenza. Così, oltre ad aiutarli a riscoprire e tirar-fuori il proprio mondo valoriale, l’adulto può al contempo promuovere un ampliamento di tale mondo valoriale, principalmente attraverso l’esempio. Non in modo coercitivo e direttivo, dunque, bensì indiretto ed esperienziale. Proprio in questo consiste il contributo più importante ed insieme complesso che si può dare alla fioritura di ogni ragazzo, nella consapevolezza che se è vero che tutti possiamo rinascere, è altrettanto vero che i fiori sbocciano laddove trovano condizioni favorevoli al proprio dispiegarsi.
- Published
- 2024
49. A Machine Learning Predictive Model of Bloodstream Infection in Hospitalized Patients
- Author
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Murri, Rita, De Angelis, Giulia, Antenucci, Laura, Fiori Alfarano, Barbara, Rinaldi, Riccardo, Fantoni, Massimo, Damiani, Andrea, Patarnello, Stefano, Sanguinetti, Maurizio, Valentini, Vincenzo, Posteraro, Brunella, Masciocchi, Carlotta, Murri, Rita (ORCID:0000-0003-4263-7854), De Angelis, Giulia (ORCID:0000-0002-7087-7399), Fiori, Barbara (ORCID:0000-0003-3318-5809), Fantoni, Massimo (ORCID:0000-0001-6913-8460), Sanguinetti, Maurizio (ORCID:0000-0002-9780-7059), Valentini, Vincenzo (ORCID:0000-0003-4637-6487), Posteraro, Brunella (ORCID:0000-0002-1663-7546), Murri, Rita, De Angelis, Giulia, Antenucci, Laura, Fiori Alfarano, Barbara, Rinaldi, Riccardo, Fantoni, Massimo, Damiani, Andrea, Patarnello, Stefano, Sanguinetti, Maurizio, Valentini, Vincenzo, Posteraro, Brunella, Masciocchi, Carlotta, Murri, Rita (ORCID:0000-0003-4263-7854), De Angelis, Giulia (ORCID:0000-0002-7087-7399), Fiori, Barbara (ORCID:0000-0003-3318-5809), Fantoni, Massimo (ORCID:0000-0001-6913-8460), Sanguinetti, Maurizio (ORCID:0000-0002-9780-7059), Valentini, Vincenzo (ORCID:0000-0003-4637-6487), and Posteraro, Brunella (ORCID:0000-0002-1663-7546)
- Abstract
The aim of the study was to build a machine learning-based predictive model to discriminate between hospitalized patients at low risk and high risk of bloodstream infection (BSI). A Data Mart including all patients hospitalized between January 2016 and December 2019 with suspected BSI was built. Multivariate logistic regression was applied to develop a clinically interpretable machine learning predictive model. The model was trained on 2016-2018 data and tested on 2019 data. A feature selection based on a univariate logistic regression first selected candidate predictors of BSI. A multivariate logistic regression with stepwise feature selection in five-fold cross-validation was applied to express the risk of BSI. A total of 5660 hospitalizations (4026 and 1634 in the training and the validation subsets, respectively) were included. Eleven predictors of BSI were identified. The performance of the model in terms of AUROC was 0.74. Based on the interquartile predicted risk score, 508 (31.1%) patients were defined as being at low risk, 776 (47.5%) at medium risk, and 350 (21.4%) at high risk of BSI. Of them, 14.2% (72/508), 30.8% (239/776), and 64% (224/350) had a BSI, respectively. The performance of the predictive model of BSI is promising. Computational infrastructure and machine learning models can help clinicians identify people at low risk for BSI, ultimately supporting an antibiotic stewardship approach.
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- 2024
50. Statistical mechanics models for multimode lasers and random lasers
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Antenucci, F., Crisanti, A., Berganza, M. Ibáñez, Marruzzo, A., and Leuzzi, L.
- Subjects
Physics - Optics ,Condensed Matter - Disordered Systems and Neural Networks ,Condensed Matter - Statistical Mechanics - Abstract
We review recent statistical mechanical approaches to multimode laser theory. The theory has proved very effective to describe standard lasers. We refer of the mean field theory for passive mode locking and developments based on Monte Carlo simulations and cavity method to study the role of the frequency matching condition. The status for a complete theory of multimode lasing in open and disordered cavities is discussed and the derivation of the general statistical models in this framework is presented. When light is propagating in a disordered medium, the system can be analyzed via the replica method. For high degrees of disorder and nonlinearity, a glassy behavior is expected at the lasing threshold, providing a suggestive link between glasses and photonics. We describe in details the results for the general Hamiltonian model in mean field approximation and mention an available test for replica symmetry breaking from intensity spectra measurements. Finally, we summary some perspectives still opened for such approaches., Comment: 16 pages, 7 figures
- Published
- 2015
- Full Text
- View/download PDF
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