Bayesian time-varying autoregressive models of COVID-19 epidemics.

The COVID-19 pandemic has highlighted the importance of reliable statistical models which, based on the available data, can provide accurate forecasts and impact analysis of alternative policy measures. Here we propose Bayesian time-dependent Poisson autoregressive models that include time-varying coefficients to estimate the effect of policy covariates on disease counts. The model is applied to the observed series of new positive cases in Italy and in the United States. The results suggest that our proposed models are capable of capturing nonlinear growth of disease counts. We also find that policy measures and, in particular, closure policies and the distribution of vaccines, lead to a significant reduction in disease counts in both countries.

Monitoring COVID-19 contagion growth.

We present a statistical model that can be employed to monitor the time evolution of the COVID-19 contagion curve and the associated reproduction rate. The model is a Poisson autoregression of the daily new observed cases and dynamically adapt its estimates to explain the evolution of contagion in terms of a short-term and long-term dependence of case counts, allowing for a comparative evaluation of health policy measures. We have applied the model to 2020 data from the countries most hit by the virus. Our empirical findings show that the proposed model describes the evolution of contagion dynamics and determines whether contagion growth can be affected by health policies. Based on our findings, we can draw two health policy conclusions that can be useful for all countries in the world. First, policy measures aimed at reducing contagion are very useful when contagion is at its peak to reduce the reproduction rate. Second, the contagion curve should be accurately monitored over time to apply policy measures that are cost-effective.

The inheritance of mitochondrial DNA in interspecific Saccharomyces hybrids and their properties in winemaking.

The inheritance of mitochondrial DNA (mtDNA) in yeast hybrids is heteroplasmic, turning into homoplasmic after few cell cycles. Mitotype restoration is reported to be biparental and random. This study shows that mitotype restoration follows fixed schemata. We created isogenic, interspecific Saccharomyces cerevisiae × Saccharomyces uvarum hybrids through direct mating and analysed their mating frequency and mitotype. The mating frequency increased for most crosses in staggered mating. Mitotyping revealed that breeding lines with the same parental strain of S. cerevisiae and different parental strains of S. uvarum give rise to the same mitotype. According to our results, we postulate that the inheritance of mtDNA is dominated by one parental strain and that the superior mitotype is specific to each breeding line. Technological tests showed typical hybrid heterosis. Copyright © 2017 John Wiley & Sons, Ltd.

Biotechnological production of cellulose by acetic acid bacteria: current state and perspectives.

Bacterial cellulose is an attractive biopolymer for a number of applications including food, biomedical, cosmetics, and engineering fields. In addition to renewability and biodegradability, its unique structure and properties such as chemical purity, nanoscale fibrous 3D network, high water-holding capacity, high degree of polymerization, high crystallinity index, light transparency, biocompatibility, and mechanical features offer several advantages when it is used as native polymer or in composite materials. Structure and properties play a functional role in both the biofilm life cycle and biotechnological applications. Among all the cellulose-producing bacteria, acetic acid bacteria of the Komagataeibacter xylinus species play the most important role because they are considered the highest producers. Bacterial cellulose from acetic acid bacteria is widely investigated as native and modified biopolymer in functionalized materials, as well as in terms of differences arising from the static or submerged production system. In this paper, the huge amount of knowledge on basic and applied aspects of bacterial cellulose is reviewed to the aim to provide a comprehensive viewpoint on the intriguing interplay between the biological machinery of synthesis, the native structure, and the factors determining its nanostructure and applications. Since in acetic acid bacteria biofilm and cellulose production are two main phenotypes with industrial impact, new insights into biofilm production are provided.

A multi-phase approach to select new wine yeast strains with enhanced fermentative fitness and glutathione production.

The genetic improvement of winemaking yeasts is a virtually infinite process, as the design of new strains must always cope with varied and ever-evolving production contexts. Good wine yeasts must feature both good primary traits, which are related to the overall fermentative fitness of the strain, and secondary traits, which provide accessory features augmenting its technological value. In this context, the superiority of "blind," genetic improvement techniques, as those based on the direct selection of the desired phenotype without prior knowledge of the genotype, was widely proven. Blind techniques such as adaptive evolution strategies were implemented for the enhancement of many traits of interest in the winemaking field. However, these strategies usually focus on single traits: this possibly leads to genetic tradeoff phenomena, where the selection of enhanced secondary traits might lead to sub-optimal primary fermentation traits. To circumvent this phenomenon, we applied a multi-step and strongly directed genetic improvement strategy aimed at combining a strong fermentative aptitude (primary trait) with an enhanced production of glutathione (secondary trait). We exploited the random genetic recombination associated to a library of 69 monosporic clones of strain UMCC 855 (Saccharomyces cerevisiae) to search for new candidates possessing both traits. This was achieved by consecutively applying three directional selective criteria: molybdate resistance (1), fermentative aptitude (2), and glutathione production (3). The strategy brought to the selection of strain 21T2-D58, which produces a high concentration of glutathione, comparable to that of other glutathione high-producers, still with a much greater fermentative aptitude.

Evaluation of fingerprinting techniques to assess genotype variation among Zygosaccharomyces strains.

Molecular typing techniques are key tools in surveillance of food spoilage yeasts, in investigations on intra-species population diversity, and in tracing selected starters during fermentation. Unlike previous works on strain typing of Zygosaccharomyces spoilage species, here Zygosaccharomyces mellis and the Zygosaccharoymces rouxii complex yeasts, which include Z. rouxii, Zygosaccharomyces sapae, and a mosaic lineage (ML) of putatively hybrids, were evaluated by three typing methods for intra- and inter-species resolution. Overall these yeasts are relevant for food fermentation and spoilage, but are quite difficult to discriminate at strain and species level as they evolved by reticulation. A pool of 76 strains from different sources were typed by M13 and (GTG)5 MSP-PCR fingerprinting and PCR-RFLP of ribosomal intergenic spacer region (IGS). We demonstrated that M13 overcame (GTG)5 fingerprinting to group Z. sapae, Z. rouxii, Z. mellis and the ML isolates in congruent distinct clusters. Even if (GTG)5 primer yielded a number of DNA fingerprints comparable with those obtained by M13 primer, it failed to discriminate Z. sapae, Z. mellis and Z. rouxii at species level. Clustering of IGS RFLP patterns obtained with three endonucleases produced groups congruent with species assignment and highlighted intra-species diversity similar to that observed by M13 fingerprinting. However, IGS PCR amplification failed for 14 ML and 6 Z. mellis strains under the experimental conditions tested here, indicating that this marker could be less easy to use in fast typing protocol. Finally, our results posit that the genetic diversity within Z. sapae and Z. mellis could be shaped by isolation source. The information generated in this study would facilitate the monitoring of these yeasts during food processing and storage, and provides preliminary evidences about Z. sapae and Z. mellis intra-species diversity.

Exploration of genetic and phenotypic diversity within Saccharomyces uvarum for driving strain improvement in winemaking.

The selection and genetic improvement of wine yeast is an ongoing process, since yeast strains should match new technologies in winemaking to satisfy evolving consumer preferences. A large genetic background is the necessary starting point for any genetic improvement programme. For this reason, we collected and characterized a large number of strains belonging to Saccharomyces uvarum. In particular, 70 strains were isolated from cold-stored must samples: they were identified and compared to S. uvarum strains originating from different collections, regarding fermentation profile, spore viability and stress response. The results demonstrate a large biodiversity among the new isolates, with particular emphasis to fermentation performances, genotypes and high spore viability, making the isolates suitable for further genetic improvement programmes. Furthermore, few of them are competitive with Saccharomyces cerevisiae and per se, suitable for wine fermentation, due to their resistance to stress, short lag phase and fermentation by-products.

Increased production of bacterial cellulose as starting point for scaled-up applications.

Bacterial cellulose is composed of an ultrafine nanofiber network and well-ordered structure; therefore, it offers several advantages when used as native polymer or in composite systems.In this study, a pool of 34 acetic acid bacteria strains belonging to Komagataeibacter xylinus were screened for their ability to produce bacterial cellulose. Bacterial cellulose layers of different thickness were observed for all the culture strains. A high-producing strain, which secreted more than 23 g/L of bacterial cellulose on the isolation broth during 10 days of static cultivation, was selected and tested in optimized culture conditions. In static conditions, the increase of cellulose yield and the reduction of by-products such as gluconic acid were observed. Dried bacterial cellulose obtained in the optimized broth was characterized to determine its microstructural, thermal, and mechanical properties. All the findings of this study support the use of bacterial cellulose produced by the selected strain for biomedical and food applications.

Differential hypersaline stress response in Zygosaccharomyces rouxii complex yeasts: a physiological and transcriptional study.

The Zygosaccharomyces rouxii complex comprises three distinct lineages of halotolerant yeasts relevant in food processing and spoilage, such as Z. sapae, Z. rouxii and a mosaic group of allodiploid strains. They manifest plastic genome architecture (variation in karyotype, ploidy level and Na(+)/H(+) antiporter-encoding gene copy number), and exhibit diverse tolerances to salt concentrations. Here, we investigated accumulation of compatible osmolytes and transcriptional regulation of Na(+)/H(+) antiporter-encoding ZrSOD genes during salt exposure in strains representative for the lineages, namely Z. sapae ABT301(T) (low salt tolerant), Z. rouxii CBS 732(T) (middle salt tolerant) and allodiploid strain ATCC 42981 (high salt tolerant). Growth curve modelling in 2 M NaCl-containing media supplemented with or without yeast extract as nitrogen source indicates that moderate salt tolerance of CBS 732(T) mainly depends on nitrogen availability rather than intrinsic inhibitory effects of salt. All the strains produce glycerol and not mannitol under salt stress and use two different glycerol balance strategies. ATCC 42981 produces comparatively more glycerol than Z. sapae and Z. rouxii under standard growth conditions and better retains it intracellularly under salt injuries. Conversely, Z. sapae and Z. rouxii enhance glycerol production under salt stress and intracellularly retain glycerol less efficiently than ATCC 42981. Expression analysis shows that, in diploid Z. sapae and allodiploid ATCC 42981, transcription of gene variants ZrSOD2-22/ZrSOD2 and ZrSOD22 is constitutive and salt unresponsive.

Vinegar Functions on Health: Constituents, Sources, and Formation Mechanisms.

Vinegars are one of only a few acidic condiments throughout the world. Vinegars can mainly be considered grain vinegars and fruit vinegars, according to the raw materials used. Both grain vinegars and fruit vinegars, which are fermented by traditional methods, possess a variety of physiological functions, such as antibacteria, anti-infection, antioxidation, blood glucose control, lipid metabolism regulation, weight loss, and anticancer activities. The antibacteria and anti-infection abilities of vinegars are mainly due to the presence of organic acids, polyphenols, and melanoidins. The polyphenols and melanoidins also provide the antioxidant abilities of vinegars, which are produced from the raw materials and fermentation processes, respectively. The blood glucose control, lipid metabolism regulation, and weight loss capabilities from vinegars are mainly due to acetic acid. Besides caffeoylsophorose (inhibits disaccharidase) and ligustrazine (improves blood circulation), other functional ingredients present in vinegars provide certain health benefits as well. Regarding anticancer activities, several grain vinegars strongly inhibit the growth of some cancer cells in vivo or in vitro, but related functional ingredients remain largely unknown, except tryptophol in Japanese black soybean vinegar. Considering the discovering of various functional ingredients and clarifying their mechanisms, some vinegars could be functional foods or even medicines, depending on a number of proofs that demonstrate these constituents can cure chronic diseases such as diabetes or cardiovascular problems.

Evolved Saccharomyces cerevisiae wine strains with enhanced glutathione production obtained by an evolution-based strategy.

In winemaking, the application of glutathione (GSH) has been the subject of ever-growing interest because of its important role in limiting must and wine oxidation and in protecting various aromatic compounds. Glutathione concentration in wine is highly variable, involving as it does several factors from must, through alcoholic fermentation, to yeast strain activity. Consequently, the development of new wine yeast strains able to improve flavor stability is in great demand. To generate evolved Saccharomyces cerevisiae strains with enhanced GSH production, we have applied an evolution-based strategy that combines the sexual recombination of spores with the application of molybdate, which is toxic for the cells at high concentration, as specific selective pressure. Eight molybdate-resistant strains were selected and further screened for GSH production in synthetic grape must and in microvinification assay. By this nongenetically modified strategy, we obtained two evolved strains, Mo21T2-5 and Mo21T2-12, both able to enhance GSH content in wine with an increase of 100% and 36%, respectively, compared with the parental strain 21T2, and 120% and 50% compared with initial GSH content in the must.

Tailoring the probiotic potential of non-starter Lactobacillus strains from ripened Parmigiano Reggiano cheese by in vitro screening and principal component analysis.

Non-starter lactic acid bacteria (NSLAB) inhabiting fermented food have been recently revised as source of probiotic strains. Here, we in vitro assessed the potential probiotic aptitude of a de-replicated set of NSLAB previously isolated from long ripened Parmigiano Reggiano cheeses (22 Lactobacillus rhamnosus, 18 Lactobacillus paracasei, 3 Lactobacillus casei, 2 Lactobacillus harbinensis, and 2 Lactobacillus fermentum). Most strains showed moderate to good resistance to biological barriers, including bile salts, lysozyme, and simulated gastric and pancreatic juices. Antimicrobial susceptibility tests against seven antimicrobials belonging to different categories showed that most strains are susceptible towards all the antibiotics, with the exception of vancomycin and streptomycin. The strains lost the streptomycin resistance when assayed on agar medium containing 0.5% bile salts, suggesting that detergent-like properties of cholic acids increase membrane permeability and mediate streptomycin susceptibility. No isolate showed bile salt hydrolase (BSH) activities, supporting that bile salts resistance and BSH activity are unpaired traits. Finally, NSLAB strains had moderate to high auto-aggregative and hydrophobic phenotypes, whereas two subsets of 22 and 8 strains co-aggregated with Escherichia coli and Salmonella enterica s. typhimurium, respectively. A multivariate analysis was effective to segregate one L. casei and two L. rhamnosus strains showing physiological characteristics compatible with probiotic properties.

Statistical learning models to measure the impact of COVID-19 on financial fragility.

This paper investigates the effects of the economic shock produced by the COVID-19 outbreak and diffusion on households'. Through a survey administered to Italian households, without loss of generality, we investigate changes in financial and economic decisions and the households' ability to cope with daily purchases, repay their debt obligations and face unexpected expenses. The paper also applies a statistical learning model through a synthetic indicator for the financial vulnerability of households, integrating the relevant information on the financial literacy and education of the surveyed individuals.

Unravelling genomic diversity of Zygosaccharomyces rouxii complex with a link to its life cycle.

Zygosaccharomyces rouxii and the related species Zygosaccharomyces sapae (hereafter referred to as Z. rouxii complex) are protoploid hemiascomycete yeasts relevant in the elaboration and spoilage of foodstuff. Divergence of Z. rouxii complex before whole genome duplication, leading to the genus Saccharomyces, makes these yeasts very attractive for genome evolution study. Relatively little is known, however, about the diversity in this branch at the genetic and physiological levels. In this work, we investigated Z. rouxii complex, encompassing strains that in other works have been studied separately and comparing them in a comprehensive way. We showed that the majority of strains are unusually heterogeneous in their ribosomal DNA, a signal of relaxation of concerted evolution. Further analysis showed that they have hypervariable karyotypes, different levels of ploidy, and that housekeeping markers vary both in copy number and sequence. Overall, the results provide compelling evidence that the strains considered in this study are a complex of haploid, aneuploid and diploid mosaic lineages. The reproductive mode and life cycle of Zygosaccharomyces could lead to this unsuspected diversity.

Zygosaccharomyces sapae sp. nov., isolated from Italian traditional balsamic vinegar.

Fourteen yeast isolates were recovered from two traditional balsamic vinegar (TBV) samples collected in the provinces of Modena and Reggio Emilia, Italy. Microsatellite-primed-PCR (MSP-PCR) was used to de-replicate the isolate collection into two representative strains, ABT301(T) and ABT601. Phylogenetic analysis based on the D1/D2 domains of the 26S rRNA gene indicated that these strains represented a distinct species of the genus Zygosaccharomyces, closely related to Zygosaccharomyces rouxii and Zygosaccharomyces mellis. Physiological and morphological tests supported the recognition of a novel taxon of halotolerant, osmotolerant, non-psychrotolerant and maltose-fermentation-negative yeasts showing a chain or star-shaped pattern of budding cells, which remained attached to each other. Morphological observations offered evidence of ascospore formation. A novel species, Zygosaccharomyces sapae sp. nov., is proposed to accommodate these strains, with strain ABT301(T) (= CBS 12607(T) = MUCL 54092(T)) as the type strain. Based on D1/D2 domain phylogenetic analysis, the novel strains shared the highest sequence similarity (100 %) with Zygosaccharomyces sp. strain NCYC 3042, previously isolated from sugar [James, S. A., Bond, C. J., Stratford, M. & Roberts, I. N. (2005). FEMS Yeast Res 5, 747-755]. However, based on phylogenetic (internal transcribed spacers, ITS), PCR fingerprinting and physiological analyses, marked differences were observed between the novel species and strain NCYC 3042, and these results are discussed in more detail.

Acetobacter pasteurianus strain AB0220: cultivability and phenotypic stability over 9 years of preservation.

Acetobacter species are members of the α-subclass of Proteobacteria, which harbors a large number of bacteria recalcitrant to cultivation. Strain AB0220 was isolated from a superficial acetification system and preserved for 9 years by short and long time methods. Under short time preservation it was estimated that 540.54 number of generations occurred, whereas in long time preservation conditions the number of generations was 17.40. Ethanol oxidation to acetic acid was stable and confirmed, as well as acetate assimilation during long time preservation. Cultivability checks showed persistence of phenotypic traits (growth on ethanol and methanol, growth on different carbon sources and cellulose production) over the extended preservation time. 16S rRNA gene sequences analysis showed 100 % of similarity with A. pasteurianus (Accession number GQ240636). Stability of subcultures related to the culture age and subcultures frequency, tested by ERIC/PCR, confirmed the suitability of long term preservation at least over a period of 9 years.

Endemic-epidemic models to understand COVID-19 spatio-temporal evolution.

We propose an endemic-epidemic model: a negative binomial space-time autoregression, which can be employed to monitor the contagion dynamics of the COVID-19 pandemic, both in time and in space. The model is exemplified through an empirical analysis of the provinces of northern Italy, heavily affected by the pandemic and characterized by similar non-pharmaceutical policy interventions.

A New Interactive Tool to Visualize and Analyze COVID-19 Data: The PERISCOPE Atlas.

Since the start of the 21st century, the world has not confronted a more serious threat to global public health than the COVID-19 pandemic. While governments initially took radical actions in response to the pandemic to avoid catastrophic collapse of their health care systems, government policies have also had numerous knock-on socioeconomic, political, behavioral and economic effects. Researchers, thus, have a unique opportunity to forward our collective understanding of the modern world and to respond to the emergency situation in a way that optimizes resources and maximizes results. The PERISCOPE project, funded by the European Commission, brings together a large number of research institutions to collect data and carry out research to understand all the impacts of the pandemic, and create predictive models that can be used to optimize intervention strategies and better face possible future health emergencies. One of the main tangible outcomes of this project is the PERISCOPE Atlas: an interactive tool that allows to visualize and analyze COVID-19-related health, economic and sociopolitical data, featuring a WebGIS and several dashboards. This paper describes the first release of the Atlas, listing the data sources used, the main functionalities and the future development.

SHAP and LIME: An Evaluation of Discriminative Power in Credit Risk.

In credit risk estimation, the most important element is obtaining a probability of default as close as possible to the effective risk. This effort quickly prompted new, powerful algorithms that reach a far higher accuracy, but at the cost of losing intelligibility, such as Gradient Boosting or ensemble methods. These models are usually referred to as "black-boxes", implying that you know the inputs and the output, but there is little way to understand what is going on under the hood. As a response to that, we have seen several different Explainable AI models flourish in recent years, with the aim of letting the user see why the black-box gave a certain output. In this context, we evaluate two very popular eXplainable AI (XAI) models in their ability to discriminate observations into groups, through the application of both unsupervised and predictive modeling to the weights these XAI models assign to features locally. The evaluation is carried out on real Small and Medium Enterprises data, obtained from official italian repositories, and may form the basis for the employment of such XAI models for post-processing features extraction.

The impact of the SARS-CoV-2 pandemic on financial markets: a seismologic approach.

This work investigates financial volatility cascades generated by SARS-CoV-2 related news using concepts developed in the field of seismology. We analyze the impact of socio-economic and political announcements, as well as of financial stimulus disclosures, on the reference stock markets of the United States, United Kingdom, Spain, France, Germany and Italy. We quantify market efficiency in processing SARS-CoV-2 related news by means of the observed Omori power-law exponents and we relate these empirical regularities to investors' behavior through the lens of a stylized Agent-Based financial market model. The analysis reveals that financial markets may underreact to the announcements by taking a finite time to re-adjust prices, thus moving against the efficient market hypothesis. We observe that this empirical regularity can be related to the speculative behavior of market participants, whose willingness to switch toward better performing investment strategies, as well as their degree of reactivity to price trend or mispricing, can induce long-lasting volatility cascades.