Dynamics and nonequilibrium states in the Hamiltonian mean-field model: A closer look

We critically revisit the evidence for the existence of quasistationary states in the globally coupled XY (or Hamiltonian mean-field) model. A slow-relaxation regime at long times is clearly revealed by numerical realizations of the model, but no traces of quasistationarity are found during the earlier stages of the evolution. We point out the nonergodic properties of this system in the short-time range, which makes a standard statistical description unsuitable. New aspects of the evolution during the nonergodic regime, and of the energy distribution function in the final approach to equilibrium, are disclosed

Pragmatic language disorder in Parkinson's disease and the potential effect of cognitive reserve

It is known that patients with Parkinson\u2019s Disease (PD) may show deficits in several areas of cognition, including speech and language abilities. One domain of particular interest is pragmatics, which refers to the capacity of using language in context for a successful communication. Several studies showed that some specific aspects of pragmatics \u2013 both in production and in comprehension \u2013 might be impaired in patients with PD. However, a clear picture of pragmatic abilities in PD is still missing, as most of the existing studies focused on specific aspects of the pragmatic competence rather than on sketching a complete pragmatic profile. Moreover, little is known on the potential role of protective factors in compensating the decline of communicative skills as the disease progresses. The present study has two aims: (1) to provide a complete picture of pragmatic abilities in patients with PD, by using a comprehensive battery (Assessment of Pragmatic Abilities and Cognitive Substrates, APACS) and by investigating the relationship with other aspects of cognitive functioning (e.g., working memory and Theory of Mind) and (2) to investigate whether Cognitive Reserve, i.e., the resilience to cognitive impairment provided by life experiences and activities, may compensate for the progressive pragmatic deficits in PD. We found that patients with PD, compared to healthy matched controls, had worse performance in discourse production and in the description of scenes, and that these impairments were tightly correlated with the severity of motor impairment, suggesting reduced intentionality of engaging in a communicative exchange. Patients with PD showed also an impairment in comprehending texts and humor, suggesting a problem in inferring from stories, which was related to general cognitive impairment. Notably, we did not find any significant difference between patients and controls in figurative language comprehension, a domain that is commonly impaired in other neurodegenerative diseases. This might be indicative of a specific profile of pragmatic impairment in patients with PD, worth of further investigation. Finally, Cognitive Reserve measures showed a high degree of association with pragmatic comprehension abilities, suggesting that the modification of life-styles could be a good candidate for compensating the possible problems in understanding the pragmatic aspects of language experienced by patients with PD

Identifying the oncogenic potential of gene fusions exploiting miRNAs

It is estimated that oncogenic gene fusions cause about 20% of human cancer morbidity. Identifying potentially oncogenic gene fusions may improve affected patients’ diagnosis and treatment. Previous approaches to this issue included exploiting specific gene-related information, such as gene function and regulation. Here we propose a model that profits from the previous findings and includes the microRNAs in the oncogenic assessment. We present ChimerDriver, a tool to classify gene fusions as oncogenic or not oncogenic. ChimerDriver is based on a specifically designed neural network and trained on genetic and post-transcriptional information to obtain a reliable classification. The designed neural network integrates information related to transcription factors, gene ontologies, microRNAs and other detailed information related to the functions of the genes involved in the fusion and the gene fusion structure. As a result, the performances on the test set reached 0.83 f1-score and 96% recall. The comparison with state-of-the-art tools returned comparable or higher results. Moreover, ChimerDriver performed well in a real-world case where 21 out of 24 validated gene fusion samples were detected by the gene fusion detection tool Starfusion. ChimerDriver integrates transcriptional and post-transcriptional information in an ad-hoc designed neural network to effectively discriminate oncogenic gene fusions from passenger ones. ChimerDriver source code is freely available at https://github.com/martalovino/ChimerDriver

Current Status of Biodiversity Assessment and Conservation of Wild Olive (Olea europaea L. subsp. europaea var. sylvestris)

Oleaster (Olea europaea L. subsp. europaea var. sylvestris) is the ancestor of cultivated olive (Olea europaea L. subsp. europaea var. europaea) and it is spread through the whole Mediterranean Basin, showing an overlapping distribution with cultivated olive trees. Climate change and new emerging diseases are expected to severely affect the cultivations of olive in the future. Oleaster presents a higher genetic variability compared to the cultivated olive and some wild trees were found adapted to particularly harsh conditions; therefore, the role of oleaster in the future of olive cultivation may be crucial. Despite the great potential, only recently the need to deeply characterize and adequately preserve the wild olive resources drew the attention of researchers. In this review, we summarized the most important morphological and genetic studies performed on oleaster trees collected in different countries of the Mediterranean Basin. Moreover, we reviewed the strategies introduced so far to preserve and manage the oleaster germplasm collections, giving a future per-spective on their role in facing the future agricultural challenges posed by climatic changes and new emerging diseases

Is dental amalgam a higher risk factor rather than resin‐based restorations for systemic conditions? A systematic review

Objective: The aim of this study was to confirm the hypothesis that patients with one or more amalgam restorations have an increased risk for systemic diseases rather than patients with resin-based restorations. Data: The data search produced an initial 3568 total number of records. All titles and abstract were reviewed by five independent examiners, and only 36 records were selected for full text in depth examination. Out of these, only nine publications matched the inclusion criteria and were included in this systematic review. Sources: Electronic databases (MEDLINE, Scopus, Embase, and Web of Knowledge) were searched up to June 2019. In addition, a manual search was carried out on journals related to this topic. Study selection: All selected human clinical studies compared patients with dental amalgam restorations to patients with non-amalgam restorations on restorative material related diseases/health conditions with at least 50 patients and a reasonable follow up. The systemic effects of dental restorations were analyzed. As for any systemic effects, there was no difference between amalgam and composite restoration. Conclusions: With the limitations of the few available randomized controlled trials (RCTs) on the matter, amalgam restorations, similarly to other modern resin-based materials, were not related to an increased risk of systemic diseases or conditions. Clinical significance: On the basis of the available RCTs, amalgam restorations, if compared with resin-based fillings, do not show an increased risk for systemic diseases. There is still insufficient evidence to exclude or demonstrate any direct influence on general health. The removal of old amalgam restorations and their substitution with more modern adhesive restorations should be performed only when clinically necessary and not just for material concerns. In order to better evaluate the safety of dental amalgam compared to other more modern restorative materials, further RCTs that consider important parameters such as long and uniform follow up periods, number of restorations per patient, and sample populations representative of chronic or degenerative diseases are needed

Lecciana, a new low-vigour olive cultivar suitable for super high density orchards and for nutraceutical evoo production

Cultivar is the key factor for sustainability of the olive super high density planting system (SHD). ‘Lecciana’ is a new olive cultivar for oil production obtained in 1998 by a controlled cross between cv. Arbosana (♀) and cv. Leccino (♂) in a breeding program as part of an international research agreement between Agromillora Iberia S.L.U. and University of Bari. ‘Lecciana’ is the first olive cultivar of Italian descent suitable for SHD, featuring all the vegetative and productive traits required for efficient, sustainable olive growing intensification. Thanks to low vigor, early bearing (3rd year after planting), high yield efficiency (about 0.5 kg of fruits cm−2 of trunk section area) and good fruit size (3.5 g), ‘Lecciana’ could be planted with tree densities over 1,200 trees per hectare for an efficient continuous mechanical harvesting. High frost resistance, very low pistil abortion (3%), high fruit set (3%), oil content (over 19% fw) and, above all, good unsaturated fatty acids profile, polyphenols content (over 450 mg kg−1 ) and fruitiness median are the main distinctive characters of this new cultivar. The oils of ‘Lecciana’ fall into the category ‘nutraceutical EVOOs’ which can benefit from the specific functional health claim

Ampelographic and Molecular Characterisation of Aglianico Accessions (Vitis vinifera L.) Collected in Southern Italy

To characterise 31 different Aglianico accessions randomly collected in Southern Italy, 30 ampelographicdescriptors, 13 SSRs and 10 AFLP primer combinations were analysed. An appreciable variation ofampelographic descriptors was revealed mainly by mature leaf traits, while very few variations wererecorded for shoot and berry traits. Similarly, all SSR loci revealed molecular monomorphism and AFLPswith a very high genetic similarity (Dice coefficient) among all the accessions considered. One of the aimsof this study was to clarify the genetic assessment of Aglianico Nero and Aglianico del Vulture Nero,since they are registered as two different cultivars with distinct varietal codes at the Italian Register ofGrape Varieties. Registered Aglianico Nero and Aglianico del Vulture Nero were included in the analyses,compared and used as reference material. Our plants showed that all the accessions tested, independentfrom the biotype, and the two registered cultivars belong to the same genotype, suggesting that, as reportedby the Vitis International Variety Catalogue, a case of synonymy occurred between Aglianico Nero andAglianico del Vulture Nero. These cultivars could therefore be considered as a single cultivar. Moreover,the AFLP data revealed a partial match between morphological and molecular data, showing that theAFLP molecular method was able to discriminate between different accessions belonging to the samecultivar

Aging in an infinite-range Hamiltonian system of coupled rotators

We analyze numerically the out-of-equilibrium relaxation dynamics of a long-range Hamiltonian system of $N$ fully coupled rotators. For a particular family of initial conditions, this system is known to enter a particular regime in which the dynamic behavior does not agree with thermodynamic predictions. Moreover, there is evidence that in the thermodynamic limit, when $N\to \infty$ is taken prior to $t\to \infty$, the system will never attain true equilibrium. By analyzing the scaling properties of the two-time autocorrelation function we find that, in that regime, a very complex dynamics unfolds in which {\em aging} phenomena appear. The scaling law strongly suggests that the system behaves in a complex way, relaxing towards equilibrium through intricate trajectories. The present results are obtained for conservative dynamics, where there is no thermal bath in contact with the system. This is the first time that aging is observed in such Hamiltonian systems.Comment: Figs. 2-4 modified, minor changes in text. To appear in Phys. Rev.

Production of the polyhydroxyalkanoate PHBV from ricotta cheese exhausted whey by haloferax mediterranei fermentation

In the last decade, the dairy industry underwent a rapid expansion due to the increasing demand of milk-based products, resulting in high quantity of wastewater, i.e., whey and ricotta cheese exhausted whey (RCEW). Although containing high content of nutritional compounds, dairy by-products are still disposed as waste rather being reintroduced in a new production chain, hence leading to environmental and economic issues. This study proposes a new biotechnological approach based on the combination of membrane filtration and fermentation to produce poly-hydroxyalkanoates (PHA), biodegradable bioplastics candidate as an alternative to petroleum-derived plastics. The protocol, exploiting the metabolic capability Haloferax mediterranei to synthesize PHA from RCEW carbon sources, was set up under laboratory and pilot scale conditions. A multi-step fractionation was used to recover a RCEW fraction containing 12.6% (w/v) of lactose, then subjected to an enzymatic treatment aimed at releasing glucose and galactose. Fermentation conditions (culture medium for the microorganism propagation, inoculum size, time, and temperature of incubation) were selected according to the maximization of polymer synthesis, under in-flasks experiments. The PHA production was then tested using a bioreactor system, under stable and monitored pH, temperature, and stirring conditions. The amount of the polymer recovered corresponded to 1.18 g/L. The differential scanning calorimetry (DSC) analysis revealed the poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) as the polymer synthesized, with a relatively high presence of hydroxyvalerate (HV). Identity and purity of the polymer were confirmed by attenuated total reflectance-Fourier transform infrared (ATR-FTIR) and X-ray photoelectron (XPS) spectroscopy analyses. By combining the fractionation of RCEW, one of the most abundant by-products from the agri-food industry, and the use of the halophile Hfx mediterranei, the production of PHBV with high purity and low crystallinity has successfully been optimized. The process, tested up to pilot scale conditions, may be further implemented (e.g., through fed-batch systems) and used for large-scale production of bioplastics, reducing the economical and environmental issues related the RCEW disposal

How to choose a good marker to analyze the olive germplasm (Olea europaea l.) and derived products

The olive tree (Olea europaea L.) is one of the most cultivated crops in the Mediterranean basin. Its economic importance is mainly due to the intense production of table olives and oil. Cultivated varieties are characterized by high morphological and genetic variability and present a large number of synonyms and homonyms. This necessitates the introduction of a rapid and accurate system for varietal identification. In the past, the recognition of olive cultivars was based solely on analysis of the morphological traits, however, these are highly influenced by environmental conditions. Therefore, over the years, several methods based on DNA analysis were developed, allowing a more accurate and reliable varietal identification. This review aims to investigate the evolving history of olive tree characterization approaches, starting from the earlier morphological methods to the latest technologies based on molecular markers, focusing on the main applications of each approach. Furthermore, we discuss the impact of the advent of next generation sequencing and the recent sequencing of the olive genome on the strategies used for the development of new molecular markers