Universality classes in directed sandpile models

We perform large scale numerical simulations of a directed version of the two-state stochastic sandpile model. Numerical results show that this stochastic model defines a new universality class with respect to the Abelian directed sandpile. The physical origin of the different critical behavior has to be ascribed to the presence of multiple topplings in the stochastic model. These results provide new insights onto the long debated question of universality in abelian and stochastic sandpiles.Comment: 5 pages, RevTex, includes 9 EPS figures. Minor english corrections. One reference adde

Crack roughness and avalanche precursors in the random fuse model

We analyze the scaling of the crack roughness and of avalanche precursors in the two dimensional random fuse model by numerical simulations, employing large system sizes and extensive sample averaging. We find that the crack roughness exhibits anomalous scaling, as recently observed in experiments. The roughness exponents ($\zeta$, $\zeta_{loc}$) and the global width distributions are found to be universal with respect to the lattice geometry. Failure is preceded by avalanche precursors whose distribution follows a power law up to a cutoff size. While the characteristic avalanche size scales as $s_0 \sim L^D$, with a universal fractal dimension $D$, the distribution exponent $\tau$ differs slightly for triangular and diamond lattices and, in both cases, it is larger than the mean-field (fiber bundle) value $\tau=5/2$

Corrections to scaling in the forest-fire model

We present a systematic study of corrections to scaling in the self-organized critical forest-fire model. The analysis of the steady-state condition for the density of trees allows us to pinpoint the presence of these corrections, which take the form of subdominant exponents modifying the standard finite-size scaling form. Applying an extended version of the moment analysis technique, we find the scaling region of the model and compute the first non-trivial corrections to scaling.Comment: RevTeX, 7 pages, 7 eps figure

Analysis of 22 mutations within milk protein genes in Italian Friesian cattle

The bovine milk protein caseins, αS1-CN, β-CN, αS2-CN, and κ-CN are codified by four well characterized genes, named CSN1S1, CSN2, CSN1S2, and CSN3 respectively and clustered in a region of 250-kb of chromosome 6. A recent revision of milk protein nomenclature considering only protein polymorphisms indicates 8 αS1-CN, 4 αS2-CN, 12 β-CN, and 11 κ-CN variants within the genus Bos. Other mutations were found in the non-coding regions of the cluster, such as the promoter regions or the 3'UTR. Many of these polymorphisms, together with others in various genes, such as the one coding for β-lactoglobulin (LGB), show important associations with different milk quality traits. Analyzing all these polymorphisms could help clarify the role of both the casein haplotype and the other polymorphisms in milk composition and cheese-making properties, and could explain which polymorphisms are really or mostly involved. The mPCR-LDR-UA approach recently developed to test simultaneously 22 SNPs in DNA regions responsible for milk protein expression was used to type 250 Italian Friesian cattle. In perfect agreement with literature, the most frequent alleles were CSN1S1*B, CSN2*A2, CSN3*A, variant 2 of CSN1S1 promoter, and variant A of Bov-A2 element. A quite balanced frequency was observed for the LGB*A and LGB*B. No CSN2*C, CSN3*C, and CSN3*H alleles were found. The CSN1S1*C, CSN2*A3, CSN2*I alleles were detected only at the heterozygous condition and at a frequency lower than 2%. The method allowed also finding some unusual intragenic haplotype, such as the Bov-A2 element-CSN3 haplotypes A-B and B-E. As to LGB one of the four SNPs tested was always homozygous for the same mutation, as already noticed. This finding confirms that this synonymous SNP is probably a sequencing mistake or a rare mutation not decisive for the LGB typing in the Italian Friesian. Reducing cost and time for typing simultaneously many SNPs, the method will be applied to a greater number of individuals and to other breeds, aiming to find out a number of animals for each haplotype sufficient for accurate statistical analysis to give a better understanding of the significance of milk protein polymorphism

Short communication: Carora cattle shows high variability at αsl-casein

The objective of this study was to analyze the genetic variability of milk proteins of the Carora, a shorthorned Bos taurus cattle breed in Venezuela and in other Southern American countries that is primarily used for milk production. A total of 184 individual milk samples were collected from Carora cattle in 5 herds in Venezuela. The milk protein genes alphas1-casein (CN) (CSN1S1), alphas2-CN (CSN2), beta-CN (CSN3), and beta-lactoglobulin (LGB) were typed at the protein level by isoelectrofocusing. It was necessary to further analyze CSN1S1 at the DNA level by a PCR-based method to distinguish CSN1S1*G from B. Increased variation was found in particular at the CSN1S1 gene, where 4 variants were identified. The predominant variant was CSN1S1*B (frequency = 0.8). The second most common CSN1S1 variant was CSN1S1*G (0.101), followed by CSN1S1*C (0.082). Moreover, a new isoelectrofocusing pattern was identified, which may result from a novel CSN1S1 variant, named CSN1S1*I, migrating at an intermediate position between CSN1S1*B and CSN1S1*C. Six cows carried the variant at the heterozygous condition. For the other loci, predominance of CSN2*A2 (0.764), CSN3*B (0.609), and LGB*B (0.592) was observed. Haplotype frequencies (AF) at the CSN1S1-CSN2-CSN3 complex were also estimated by taking association into account. Only 7 haplotypes showed AF values >0.05, accounting for a cumulative frequency of 0.944. The predominant haplotype was B-A2-B (frequency = 0.418), followed by B-A2-A (0.213). The occurrence of the G variant is at a rather high frequency, which is of interest for selection within the Carora breed because of the negative association of this variant with the synthesis of the specific protein. From a cheese-making point of view, this variant is associated with improved milk-clotting parameters but is negatively associated with cheese ripening. Thus, milk protein typing should be routinely carried out in the breed, with particular emphasis on using a DNA test to detect the CSN1S*G variant. The CSN1S*G allele is likely to have descended from the Brown Swiss, which contributed to the Carora breed and also carries this allele

Hyperbolicity Measures "Democracy" in Real-World Networks

We analyze the hyperbolicity of real-world networks, a geometric quantity that measures if a space is negatively curved. In our interpretation, a network with small hyperbolicity is "aristocratic", because it contains a small set of vertices involved in many shortest paths, so that few elements "connect" the systems, while a network with large hyperbolicity has a more "democratic" structure with a larger number of crucial elements. We prove mathematically the soundness of this interpretation, and we derive its consequences by analyzing a large dataset of real-world networks. We confirm and improve previous results on hyperbolicity, and we analyze them in the light of our interpretation. Moreover, we study (for the first time in our knowledge) the hyperbolicity of the neighborhood of a given vertex. This allows to define an "influence area" for the vertices in the graph. We show that the influence area of the highest degree vertex is small in what we define "local" networks, like most social or peer-to-peer networks. On the other hand, if the network is built in order to reach a "global" goal, as in metabolic networks or autonomous system networks, the influence area is much larger, and it can contain up to half the vertices in the graph. In conclusion, our newly introduced approach allows to distinguish the topology and the structure of various complex networks

Fluctuations and correlations in sandpile models

We perform numerical simulations of the sandpile model for non-vanishing driving fields $h$ and dissipation rates $\epsilon$. Unlike simulations performed in the slow driving limit, the unique time scale present in our system allows us to measure unambiguously response and correlation functions. We discuss the dynamic scaling of the model and show that fluctuation-dissipation relations are not obeyed in this system.Comment: 5 pages, latex, 4 postscript figure

Genome sequencing of Prototheca zopfii genotypes 1 and 2 provides evidence of a severe reduction in organellar genomes

Abstract Prototheca zopfii (P. zopfii, class Trebouxiophyceae, order Chlorellales, family Chlorellaceae), a non-photosynthetic predominantly free-living unicellular alga, is one of the few pathogens belonging to the plant kingdom. This alga can affect many vertebrate hosts, sustaining systemic infections and diseases such as mastitis in cows. The aim of our work was to sequence and assemble the P. zopfii genotype 1 and genotype 2 mitochondrial and plastid genomes. Remarkably, the P. zopfii mitochondrial (38 Kb) and plastid (28 Kb) genomes are models of compaction and the smallest known in the Trebouxiophyceae. As expected, the P. zopfii genotype 1 and 2 plastid genomes lack all the genes involved in photosynthesis, but, surprisingly, they also lack those coding for RNA polymerases. Our results showed that plastid genes are actively transcribed in P. zopfii, which suggests that the missing RNA polymerases are substituted by nuclear-encoded paralogs. The simplified architecture and highly-reduced gene complement of the P. zopfii mitochondrial and plastid genomes are closer to those of P. stagnora and the achlorophyllous obligate parasite Helicosporidium than to those of P. wickerhamii or P. cutis. This similarity is also supported by maximum likelihood phylogenetic analyses inferences. Overall, the P. zopfii sequences reported here, which include nuclear genome drafts for both genotypes, will help provide both a deeper understanding of the evolution of Prototheca spp. and insights into the corresponding host/pathogen interactions

Crossover phenomenon in self-organized critical sandpile models

We consider a stochastic sandpile where the sand-grains of unstable sites are randomly distributed to the nearest neighbors. Increasing the value of the threshold condition the stochastic character of the distribution is lost and a crossover to the scaling behavior of a different sandpile model takes place where the sand-grains are equally transferred to the nearest neighbors. The crossover behavior is numerically analyzed in detail, especially we consider the exponents which determine the scaling behavior.Comment: 6 pages, 9 figures, accepted for publication in Physical Review