Cavity and replica methods for the spectral density of sparse symmetric random matrices

We review the problem of how to compute the spectral density of sparse symmetric random matrices, i.e. weighted adjacency matrices of undirected graphs. Starting from the Edwards-Jones formula, we illustrate the milestones of this line of research, including the pioneering work of Bray and Rodgers using replicas. We focus first on the cavity method, showing that it quickly provides the correct recursion equations both for single instances and at the ensemble level. We also describe an alternative replica solution that proves to be equivalent to the cavity method. Both the cavity and the replica derivations allow us to obtain the spectral density via the solution of an integral equation for an auxiliary probability density function. We show that this equation can be solved using a stochastic population dynamics algorithm, and we provide its implementation. In this formalism, the spectral density is naturally written in terms of a superposition of local contributions from nodes of given degree, whose role is thoroughly elucidated. This paper does not contain original material, but rather gives a pedagogical overview of the topic. It is indeed addressed to students and researchers who consider entering the field. Both the theoretical tools and the numerical algorithms are discussed in detail, highlighting conceptual subtleties and practical aspects.Comment: 52 pag., 5 fig. Typos fixed. Submission to SciPos

Variation in sequence and location of the fumonisin mycotoxin niosynthetic gene cluster in Fusarium

In Fusarium, the ability to produce fumonisins is governed by a 17-gene fumonisin biosynthetic gene (FUM) cluster. Here, we examined the cluster in F. oxysporum strain O-1890 and nine other species selected to represent a wide range of the genetic diversity within the GFSC

Lupus vasculitis: An overview

Lupus vasculitis (LV) is one of the secondary vasculitides occurring in the setting of systemic lupus erythematosus (SLE) in approximately 50% of patients. It is most commonly associated with small vessels, but medium-sized vessels can also be affected, whereas large vessel involvement is very rare. LV may involve different organ systems and present in a wide variety of clinical manifestations according to the size and site of the vessels involved. LV usually portends a poor prognosis, and a prompt diagnosis is fundamental for a good outcome. The spectrum of involvement ranges from a relatively mild disease affecting small vessels or a single organ to a multiorgan system disease with life-threatening manifestations, such as mesenteric vasculitis, pulmonary hemorrhage, or mononeuritis multiplex. Treatment depends upon the organs involved and the severity of the vasculitis process. In this review, we provide an overview of the different forms of LV, describing their clinical impact and focusing on the available treatment strategies

Embryo Culture, In Vitro Propagation, and Molecular Identification for Advanced Olive Breeding Programs

The high biodiversity of the olive tree is an important opportunity to develop sustainable plans to control Xylella fastidiosa (X) through breeding programs. Olive tree breeding activities have been limited due to various features of this species including the long time required for seed germination caused by the inhibition effect of the woody endocarp, the seed integument, and the endosperm. Starting from F1 seeds by cross-breeding, the embryo culture was compared with traditional seed germination, evaluating the effectiveness of in vitro multiplication of the plantlets for large-scale production. The isolated embryos were established on a new medium based on Rugini ‘84 macroelements, Murashige & Skoog ‘62 microelements, with Nitsch J. P. & Nitsch C. ‘69 vitamine and subcultured on Leva MSM modified. The results obtained confirmed that in vitro culture of olive embryos is a valid tool for increasing the percentage and speed of germination, helping to reduce the time of the olive breeding programs, offering the possibility to effectively propagate plantlets for further experiments

Caracterización microbiológica de polen apícola recolectado en dos períodos de cosecha

El polen apícola es el resultado del aglutinamiento del polen de las flores efectuado por las abejas mediante néctar y sustancias salivares, y transportado a la colmena en sus patas traseras. Este polen, destinado al consumo humano, se cosecha utilizando trampas ad hoc en las colmenas. Objetivo: Caracterizar microbiológica y fisicoquímicamente muestras de polen provenientes del centro-sur de la provincia de Buenos Aires, Argentina obtenidas al inicio del procesamiento

Complete mitochondrial sequences from Mesolithic Sardinia

Little is known about the genetic prehistory of Sardinia because of the scarcity of pre-Neolithic human remains. From a genetic perspective, modern Sardinians are known as genetic outliers in Europe, showing unusually high levels of internal diversity and a close relationship to early European Neolithic farmers. However, how far this peculiar genetic structure extends and how it originated was to date impossible to test. Here we present the first and oldest complete mitochondrial sequences from Sardinia, dated back to 10,000 yBP. These two individuals, while confirming a Mesolithic occupation of the island, belong to rare mtDNA lineages, which have never been found before in Mesolithic samples and that are currently present at low frequencies not only in Sardinia, but in the whole Europe. Preliminary Approximate Bayesian Computations, restricted by biased reference samples for Mesolithic Sardinia (the two typed samples) and Neolithic Europe (limited to central and north European sequences), suggest that the first inhabitants of the island have had a small or negligible contribution to the present-day Sardinian population, which mainly derives its genetic diversity from continental migration into the island by Neolithic times

Screening of Olive Biodiversity Defines Genotypes Potentially Resistant to Xylella fastidiosa

none17noThe recent outbreak of the Olive Quick Decline Syndrome (OQDS), caused by Xylella fastidiosa subsp. pauca (Xf), is dramatically altering ecosystem services in the peninsula of Salento (Apulia Region, southeastern Italy). Here we report the accomplishment of several exploratory missions in the Salento area, resulting in the identification of thirty paucisymptomatic or asymptomatic plants in olive orchards severely affected by the OQDS. The genetic profiles of such putatively resistant plants (PRPs), assessed by a selection of ten simple sequence repeat (SSR) markers, were compared with those of 141 Mediterranean cultivars. Most (23) PRPs formed a genetic cluster (K1) with 22 Italian cultivars, including ‘Leccino’ and ‘FS17’, previously reported as resistant to Xf. The remaining PRPs displayed relatedness with genetically differentiated germplasm, including a cluster of Tunisian cultivars. Markedly lower colonization levels were observed in PRPs of the cluster K1 with respect to control plants. Field evaluation of four cultivars related to PRPs allowed the definition of partial resistance in the genotypes ‘Frantoio’ and ‘Nocellara Messinese’. Some of the PRPs identified in this study might be exploited in cultivation, or as parental clones of breeding programs. In addition, our results indicate the possibility to characterize resistance to Xf in cultivars genetically related to PRPs.openPavan S.; Vergine M.; Nicoli F.; Sabella E.; Aprile A.; Negro C.; Fanelli V.; Savoia M.A.; Montilon V.; Susca L.; Delvento C.; Lotti C.; Nigro F.; Montemurro C.; Ricciardi L.; De Bellis L.; Luvisi A.Pavan, S.; Vergine, M.; Nicoli, F.; Sabella, E.; Aprile, A.; Negro, C.; Fanelli, V.; Savoia, M. A.; Montilon, V.; Susca, L.; Delvento, C.; Lotti, C.; Nigro, F.; Montemurro, C.; Ricciardi, L.; De Bellis, L.; Luvisi, A