Provably efficient machine learning for quantum many-body problems

Classical machine learning (ML) provides a potentially powerful approach to solving challenging quantum many-body problems in physics and chemistry. However, the advantages of ML over more traditional methods have not been firmly established. In this work, we prove that classical ML algorithms can efficiently predict ground state properties of gapped Hamiltonians in finite spatial dimensions, after learning from data obtained by measuring other Hamiltonians in the same quantum phase of matter. In contrast, under widely accepted complexity theory assumptions, classical algorithms that do not learn from data cannot achieve the same guarantee. We also prove that classical ML algorithms can efficiently classify a wide range of quantum phases of matter. Our arguments are based on the concept of a classical shadow, a succinct classical description of a many-body quantum state that can be constructed in feasible quantum experiments and be used to predict many properties of the state. Extensive numerical experiments corroborate our theoretical results in a variety of scenarios, including Rydberg atom systems, 2D random Heisenberg models, symmetry-protected topological phases, and topologically ordered phases.Comment: 10 pages, 12 figures + 57 page appendi

Fruit Metabolism and Metabolomics

Over the past ten years, metabolomics strategies have allowed the relative or absolute quantitation of metabolite levels for the study of various biological questions in plant sciences. For fruit studies, in particular, they have participated in the identification of the genes underpinning fruit development and ripening. This book proposes examples of the current use of metabolomics studies of fruit for basic research or practical applications. It includes articles about several tropical and temperate fruit species. The studies concern fruit biochemical phenotyping, fruit metabolism during development and after harvest, including primary and specialized metabolisms, or bioactive compounds involved in fruit growth and environmental responses. The analytical strategies used are based mostly on liquid or gas chromatography coupled with mass spectrometry, but also on nuclear magnetic resonance and near-infrared spectroscopy. The effect of genotype, stages of development, or fruit tissue type on metabolomic profiles and corresponding metabolism regulations are addressed for fruit metabolism studies. The interest in combining other omics with metabolomics is also exemplified

Genetics and metabolomics of elite athletes: Genome-wide association study and Metabolomics profiling of elite athletes

AIM: The outstanding performance of elite athletes is a product of a complex interaction between genetic and environmental factors. The aims of this study was to compare differences in genetic and metabolic profiles among different classes of elite athletes and to identify genetically-influenced metabolic profiles (metabotypes) underlying these differences. METHODS: Genome-wide association study (GWAS) was conducted in 1259 elite athlete samples using Drug core BeadChip arrays, followed by non-targeted metabolomics of 692 serum samples. Genotype distribution, differences in metabolic levels and genetically-influenced metabotypes were compared between high and moderate endurance and power sports as well as among sports with different cardiovascular demands (CVD). RESULTS: Out of 341385 SNPs, two novel associations are reported for endurance status including rs56330321 in ATP2B2 (p=1.47E-7) and rs2635438 in SYNE1 (p=2.54E-7). A meta-analysis confirmed the association of rs56330321 and rs2635438 with endurance athlete status at GWAS level of significance. Metabolomics analysis of 740 metabolites was performed in in 191 (discovery cohort) and 500 (replication cohort) elite athletes. These studies revealed changes in various metabolites involved in steroid biosynthesis, fatty acid oxidation, oxidative stress response, xenobiotics and various mediators of cell signaling among different groups of endurance, power and CVD athletes. By combining GWAS with metabolomics profiling data (mGWAS), 19 common variant metabolic quantitative trait loci (mQTLs) were identified, of which 5 were novel. When focusing on metabolites associated with endurance, power and CVD, 4 common variant mQTLs were found, of which one novel mQTL linking 4-androsten-3alpha,17alpha-diol monosulfate and SULT2A1 involved in steroid sulfation was identified in association with endurance. CONCLUSIONS: GWAS, metabolomics and mGWAS of elite athletes identified novel markers associated with elite athletic performance with a potential application in biomarker discovery in relation to elite athletic performance

Understanding Quantum Technologies 2022

Understanding Quantum Technologies 2022 is a creative-commons ebook that provides a unique 360 degrees overview of quantum technologies from science and technology to geopolitical and societal issues. It covers quantum physics history, quantum physics 101, gate-based quantum computing, quantum computing engineering (including quantum error corrections and quantum computing energetics), quantum computing hardware (all qubit types, including quantum annealing and quantum simulation paradigms, history, science, research, implementation and vendors), quantum enabling technologies (cryogenics, control electronics, photonics, components fabs, raw materials), quantum computing algorithms, software development tools and use cases, unconventional computing (potential alternatives to quantum and classical computing), quantum telecommunications and cryptography, quantum sensing, quantum technologies around the world, quantum technologies societal impact and even quantum fake sciences. The main audience are computer science engineers, developers and IT specialists as well as quantum scientists and students who want to acquire a global view of how quantum technologies work, and particularly quantum computing. This version is an extensive update to the 2021 edition published in October 2021.Comment: 1132 pages, 920 figures, Letter forma

Metagenomics and functional genomics of bacterial symbionts of Spongia (Porifera, Dictyoceratida) specimens from the Algarvian shore (South Portugal)

Sponges are early-branched, filter-feeding metazoans that usually harbor complex microbial communities comprised of diverse “uncultivable” symbiotic bacteria. In this thesis, the functional and taxonomic features of the marine sponge microbiome are determined, using Spongia officinalis as model host organism. Emphasis is given to adaptive and functional traits of the profuse and biotechnologically-relevant alphaproteobacterial symbionts of sponges. A metagenomics-centred approach was employed to reveal microbial taxa and genomic signatures enriched in the Spongia officinalis endosymbiotic consortium, and thus likely to play pivotal roles in holobiont functioning. Further, a comparative genomics study is presented unveiling the common and specific traits of ten Alphaproteobacteria genera isolated from S. officinalis with alternative symbiont cultivation methodology. Finally, a sequence composition-dependent binning approach is employed to assemble, from metagenomic sequences, the genome of an uncultured alphaproteobacterial symbiont of S. officinalis belonging to the family Rhodospirillaceae. High abundance of polyketide and terpene synthase-, eukaryotic-like protein- (ELPs), type IV secretion system-, plasmid- and ABC transporter-encoding genes, among others, characterized the sponge microbial metagenomes. In contrast, motility and chemotaxis genes were abundant in seawater and sediment microbiomes, but nearly absent in the S. officinalis symbiotic consortium. Much higher frequencies of anti-viral CRISPR-Cas and restrictionmodification systems, along with much lower viral abundances, were observed in the spongeassociated metagenomes than in the environment and interpreted as true hallmarks of this symbiotic consortium. In line with outcomes retrieved for the whole symbiotic community, alphaproteobacterial symbionts of marine sponges likely contribute the most to host fitness through nutritional exchange, cell detoxification processes and chemical defense, the latter being theoretically promoted by both polyketide and terpenoid biosynthesis. The several alphaproteobacterial cultures retrieved in this thesis, displaying high natural product biosynthesis capacities, can now be explored in studies aiming at revealing novel biological activities and chemical structures from these symbionts.As esponjas marinhas (filo Porifera) são consideradas um dos mais simples grupos entre os metazoários em função de sua falta de organização em tecidos e órgãos verdadeiros. Porém, estes animais relativamente simples em termos de plano corporal normalmente abrigam comunidades muito complexas de microorganismos. Em função de seu surgimento basal na história evolutiva do planeta, o conhecimento a respeito deste “holobionte”, isto é, o consórcio de organismos formado pela esponja marinha hospedeira e todos os seus simbiontes microbianos, possui grande relavância ao avanço da nossa compreensão sobre as interações hospedeiro-microorganismos. Nesta tese de doutoramento, tive como objetivo a determinação das características funcionais e taxonómicas do microbioma das esponjas marinhas no contexto de seu ambiente circundante (água e sedimentos marinhos, e suas respecticvas microbiotas), dando ênfase aos traços adaptativos e funcionais de alfaproteobactérias associadas ao organismo modelo Spongia officinalis (“bath sponge”)

Molecular methods for the diagnosis and characterization of phytopathogenic fungi of quarantine concern or causing emerging plant diseases

In the context of molecular techniques applied to Plant Pathology, this Ph.D. thesis has pursued the following major objectives: i) to develop new diagnostic protocols for fungal pathogens; ii) to study the metabolic and physiological effects determined by new and emerging fungal pathogens; iii) to contribute to develop management strategies of diseases caused by quarantine and/or emerging fungi on plant species typical of the Mediterranean region. To fulfill these objectives, the following specific studies have been developed: • “Fusarium circinatum an emergent and quarantine pathogen of pine worldwide: its detection and its interaction with Phytophthora species (P. cambivora and P. parvispora) on Pinus radiata seedlings.” This study has been developed by two different lines of research: “Transferability of PCR-based diagnostic protocols: An international collaborative case study assessing protocols targeting the quarantine pine pathogen, Fusarium circinatum.” In this study, different protocols for the molecular diagnosis of F. circinatum were compared and validated for the first time in 23 laboratories spread across Europe, South Africa and Chile, in the framework of the international collaborative study funded by COST Action FP1406 “Pine pitch canker - Strategies for management of Gibberella circinata in greenhouses and forests - PINESTRENGTH ''. The protocol tested by the Laboratory of Molecular Plant Pathology of the Department of Agriculture, Food and Environment (Di3A) of the University of Catania were: (i) Real-time PCR by Lamarche et al. 2015 and (ii) real-time PCR by Luchi et al. 2018. Results from the two tested protocols were illustrated in Ioos et al (2019), Scientific Reports 2019, 9, 8195. DOI: 10.1038 / s41598-019-44672-8. “Co-infections by Fusarium circinatum and Phytophthora spp. on Pinus radiata, a case study of complex interactions in the Pine pitch canker disease.” This study investigated i. the phenotypic response of pine to the infective process and ii. the relative expression levels of genes of plant encoding for pathogenetic-related proteins and antifungal secondary metabolites. Results obtained in this research showed that the phenotypic response of pine to the simultaneous action of the aforementioned pathogens it is manifested by an increasing of the severity of the symptoms at the early stages of the infection, allowing then to speculate that Phytophthora spp. can realistically contribute to the severity of the disease. Results from gene expression suggest that a real synergic effect as the result of the effects of both pathogens it is not clearly evident. • “Scabby canker caused by Neofusicoccum batangarum (Botryosphaeriaceae), an emergent disease of Opuntia ficus-indica in minor islands around Sicily: identification of the causal agent and characterization of both its phytotoxic metabolites and the genetic variability of its local population.” The specific objectives of this study were the following: i) determine the geographical distribution of the disease; ii) characterize N. batangarum isolates obtained from symptomatic plants of prickly pear in the smaller islands of Sicily; iii) check whether the range of potential host plants of this phytopathogenic fungus includes other Mediterranean species that could act as alternative hosts or as inoculation 'reservoir'; iv) determine the ability of N. batangarum to produce phytotoxic secondary metabolites (phytotoxins) in culture, which can play an active role in the pathogenesis of the disease; v) chemically identify the phytotoxins extracted from N. batangarum liquid filtrates and determine their phytotoxic effects on the host plant as well as on non-host plant species. In cross-pathogenicity tests, N. batangarum isolated from Opuntia ficus-indica plants was able to reproduce disease symptoms on the host plant and also infect other plant species. The fungus artificially inoculated by wounding induced cancers on several hosts. This result indicates that the pathogen has a very wide range of potential hosts. Six phytotoxins were obtained and identified from Neofusicoccum batangarum culture filtrates: (-) - (R) ‐mellein (1); (±) ‐botriisocoumarin A (2); (-) - (3R, 4R) - and (-) - (3R, 4S) ‐4 hydroxymelline (3 and 4); (-) - terpestacin (5); and (+) - 3,4 ‐ dihydro - 4,5,8 - trihydroxy - 3 - methylisocoumarin, renamed (+) - neoisocoumarin (6). All six metabolites have been shown to have phytotoxic activity on both the host and non-host plants. The most active compounds proved to be (±) ‐botriisocoumarin A (2), (-) - terpestacin (5) and (+) - neoisocoumarin (6). Results from this study are part of two scientific publications: Masi, Mt. et al., Toxins 2020, 12, 126. DOI: 10.3390 / toxins12020126 and Aloi, F. et al., Mediterranean Phytopathology 2020, 59 (2): 269-284. DOI: 10.14601 / Phyto-11225. • “Identification of Neofusicoccum parvum (Botryosphaeriaceae) as the causative agent of gummy cankers of lemon (Citrus × limon) trees.” This study was aimed at identifying the causative agent of the observed disease. Neofusicoccum parvum, in the family Botryosphaeriaceae, was identified as the causal agent of bot gummosis of lemon (Citrus x limon) trees, in the two major lemon-producing areas in Italy. Gummy cankers on trunk and scaffold branches of mature trees were the most typical disease symptoms. Neofusicoccum parvum was the sole fungus constantly and consistently isolated from the canker bark of symptomatic lemon trees. It was identified on the basis of morphological characters and the phylogenetic analysis of three loci, i. e. the internal transcribed spacer of nuclear ribosomal DNA (ITS) as well as the translation elongation factor 1-alpha (TEF1) and β-tubulin (TUB2) genes. The pathogenicity of N. parvum was demonstrated by wound inoculating two lemon cultivars, ‘Femminello 2kr’ and ‘Monachello’, as well as citrange (C. sinensis x Poncirus trifoliata) ‘Carrizo’ rootstock. In artificial inoculations, the fungus was very aggressive on lemons and weakly virulent on citrange, consistently with symptoms observed in the field as a consequence of natural infections. This is the first report of N. parvum, both in a wide and in a strict taxonomic sense, as a pathogen of lemon in Italy. • “Characterization of Alternaria species associated with heart rot of pomegranate fruit.” This study was aimed at identifying Alternaria species associated with heart rot disease of pomegranate fruit in southern Italy and characterizing their mycotoxigenic profile. A total of 42 Alternaria isolates were characterized. They were obtained from pomegranate fruits with symptom of heart rot sampled in Apulia and Sicily and grouped into six distinct morphotypes based on macro- and microscopic features. According to multi-gene phylogenetic analysis, including internal transcribed spacer (ITS), translation elongation factor 1-α (EF-1α), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and a SCAR marker (OPA10-2), 38 isolates of morphotypes 1 to 5 were identified as A. alternata, while isolates of morphotype 6, all from Sicily, clustered within the A. arborescens species complex. In particular, isolates of morphotype 1, the most numerous, clustered with the ex-type isolate of A. alternata, proving to belong to morphotype alternata. No difference in pathogenicity on pomegranate fruits was found between isolates of A. alternata and A. arborescens and among A. alternata isolates of different morphotypes. The toxigenic profile of isolates varied greatly: in vitro, all 42 isolates produced tenuazonic acid and most of them other mycotoxins including alternariol, alternariol monomethyl ether, altenuene and tentoxin. • “Shoot dieback of citrus, a new disease caused by Colletotrichum species.” This study was aimed at identifying the Colletotrichum species associated with twig and shoot dieback of citrus, a new disease occurring in the Mediterranean region and also reported as emerging in California. Overall, 119 Colletotrichum isolates were characterized. They were recovered from symptomatic trees of sweet orange, mandarin and mandarin-like during a survey of citrus groves in Albania and Sicily (southern Italy). The isolates were grouped into two distinct morphotypes. The grouping of isolates was supported by phylogenetic sequence analysis of two genetic markers, the internal transcribed spacer regions of rDNA (ITS) and β-tubulin (TUB2). The groups were identified as Colletotrichum gloeosporioides and C. karstii, respectively. The former accounted for more than 91% of isolates, while the latter was retrieved only occasionally in Sicily. Both species induced symptoms on artificially wound inoculated twigs. C. gloeosporioides was more aggressive than of C. karstii. Winds and prolonged drought were the factor predisposing to Colletotrichum twig and shoot dieback. This is the first report of C. gloeosporioides and C. karstii as causal agents of twig and shoot dieback disease in the Mediterranean region and the first report of C. gloeosporioides as a citrus pathogen in Albania