KADABRA is an ADaptive Algorithm for Betweenness via Random Approximation

We present KADABRA, a new algorithm to approximate betweenness centrality in directed and undirected graphs, which significantly outperforms all previous approaches on real-world complex networks. The efficiency of the new algorithm relies on two new theoretical contributions, of independent interest. The first contribution focuses on sampling shortest paths, a subroutine used by most algorithms that approximate betweenness centrality. We show that, on realistic random graph models, we can perform this task in time $|E|^{\frac{1}{2}+o(1)}$ with high probability, obtaining a significant speedup with respect to the $\Theta(|E|)$ worst-case performance. We experimentally show that this new technique achieves similar speedups on real-world complex networks, as well. The second contribution is a new rigorous application of the adaptive sampling technique. This approach decreases the total number of shortest paths that need to be sampled to compute all betweenness centralities with a given absolute error, and it also handles more general problems, such as computing the $k$ most central nodes. Furthermore, our analysis is general, and it might be extended to other settings.Comment: Some typos correcte

Development of a method for biomarkers characterization by mass spectrometry techniques

The purpose of this study is to define an extractive approach for the detection of the low-molecule peptide fraction from human plasma or serum and the subsequent analysis and interpretation of the obtained data, with the ultimate aim of developing a standardised protocol for the identification of potential biomarkers. The extraction of the low molecular protein fraction was developed thanks to a series of standard peptides solutions and using silica magnetic beads techniques differently functionalised with the purpose to bind target molecules with a different type of intermolecular force. The treatment of the samples, plasma or serum, took place without the use of proteases, as trypsin, to generate digested lysates, or electrophoresis and gel separation techniques, to avoid creating additional complexity in subsequent steps of data interpretation and to use the lower quantity of sample as possible. Both the peptides contained in the standard solution and those in the low molecular weight fraction of the pre-treated biological sample were separated and characterized through high performance liquid chromatography (HPLC) coupled to full scan and tandem mass spectrometry equipped with an electrospray ion source (ESI-MS/MS). Samples from biological sources were subsequently analysed using the mass spectrometry MALDI-TOF technique. In this project the development of the extraction method was followed by its application to real samples. The presence of low-molecular-weight peptides in plasma samples, from dialysis nephrotic patients at various stages of Sars-COV2 infection, and in plasma from healthy donors was evaluated with the aim to find significant differences between groups, especially in terms of qualitative/quantitative differences in the m/z ratios present in MS spectra. A bioinformatics approach to data processing has also been implemented, either by using statistical tools such as the Venn diagram or the Meaning Analysis of Microarrays (SAM) or by developing a series of codes in Python, for processing spectral data combined with algorithms with silico fragmentation rules. Outputs were compared with information from peptide databases to obtain significant correspondences between the theoretical and experimental spectrum

Into the Square: On the Complexity of Some Quadratic-time Solvable Problems

International audienceWe analyze several quadratic-time solvable problems, and we show that these problems are not solvable in truly subquadratic time (that is, in time O(n2−ϵ) for some ϵ>0), unless the well known Strong Exponential Time Hypothesis (in short, SETH) is false. In particular, we start from an artificial quadratic-time solvable variation of the k-Sat problem (already introduced and used in the literature) and we will construct a web of Karp reductions, proving that a truly subquadratic-time algorithm for any of the problems in the web falsifies SETH. Some of these results were already known, while others are, as far as we know, new. The new problems considered are: computing the betweenness centrality of a vertex (the same result was proved independently by Abboud et al.), computing the minimum closeness centrality in a graph, computing the hyperbolicity of a graph, and computing the subset graph of a collection of sets. On the other hand, we will show that testing if a directed graph is transitive and testing if a graph is a comparability graph are subquadratic-time solvable (our algorithm is practical, since it is not based on intricate matrix multiplication algorithms)

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

Filling the Gaps to Solve the Extensin Puzzle

Extensins (EXTs) are highly repetitive plant O-glycoproteins that require several post-translational modifications (PTMs) to become functional in plant cell walls. First, they are hydroxylated on contiguous proline residues; then they are O-glycosylated on hydroxyproline and serine. After secretion into the apoplast, O-glycosylated EXTs form a tridimensional network organized by inter- and intra-Tyr linkages. Recent studies have made significant progress in the identification of the enzymatic machinery required to process EXTs, which includes prolyl 4-hydroxylases, glycosyltransferases, papain-type cysteine endopeptidases, and peroxidases. EXTs are abundant in plant tissues and are particularly important in rapidly expanding root hairs and pollen tubes, which grow in a polar manner. Small changes in EXT PTMs affect fast-growing cells, although the molecular mechanisms underlying this regulation are unknown. In this review, we highlight recent advances in our understanding of EXT modifications throughout the secretory pathway, EXT assembly in cell walls, and possible sensing mechanisms involving the Catharanthus roseus cell surface sensor receptor-like kinases located at the interface between the apoplast and the cytoplasmic side of the plasma membrane. This review describes recent progress in our understanding of extensin post-translational modifications throughout the secretory pathway, extensin secretion and assembly in the cell walls, and possible sensing mechanisms at the interface between the apoplast and the cytoplasmic side of the cell surface.Fil: Marzol, Eliana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Borassi, Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Bringas, Mauro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; ArgentinaFil: Sede, Ana Rocío. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Rodríguez Garcia, Diana Rosa. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Capece, Luciana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; ArgentinaFil: Estevez, Jose Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentin

KADABRA is an ADaptive Algorithm for Betweenness via Random Approximation

International audienceWe present KADABRA, a new algorithm to approximate betweenness centrality in directed and undirected graphs, which significantly outperforms all previous approaches on real-world complex networks. The efficiency of the new algorithm relies on two new theoretical contributions, of independent interest. The first contribution focuses on sampling shortest paths, a subroutine used by most algorithms that approximate betweenness centrality. We show that, on realistic random graph models, we can perform this task in time |E| 1 2 +o (1) with high probability, obtaining a significant speedup with respect to the Θ(|E|) worst-case performance. We experimentally show that this new technique achieves similar speedups on real-world complex networks, as well. The second contribution is a new rigorous application of the adaptive sampling technique. This approach decreases the total number of shortest paths that need to be sampled to compute all betweenness centralities with a given absolute error, and it also handles more general problems, such as computing the k most central nodes. Furthermore, our analysis is general, and it might be extended to other settings

Estructura genética de poblaciones de Phytophthora capsici en el noreste de la provincia de Buenos Aires, Argentina

Phytophthora capsici causa enfermedades destructivas en todo el mundo. El patógeno es heterotálico y los dos tipos de apareamiento (TAs) son requeridos para la reproducción sexual. La razón de TAs varía entre regiones geográficas y por lo tanto también la chance para reproducirse sexualmente. Si se toma en cuenta que la durabilidad de las medidas de control depende de la variación genética, es aconsejable considerar la cantidad y la distribución de variación genética dentro y entre poblaciones de especies, es decir, la estructura genética. Esta está determinada por factores que influencian la evolución poblacional como la mutación, la deriva genética, el flujo genético, el sistema de reproducción y de selección. En este sentido, poco se conoce sobre las poblaciones de P. capsici en Argentina. El objetivo fue evaluar la variabilidad genética de aislamientos de P. capsici de tres sitios de producción hortícola del NE de Buenos Aires. Sesenta y un aislamientos de P. capsici colectados de cultivos de Capsicum annuum, Solanum melongena, Solanum lycopersicum y Cucurbita spp. fueron identificados morfológicamente y analizados por tipo de reproducción. Los aislamientos fueron identificados por técnicas moleculares basadas en las secuencias de las regiones ITS1-5.8S e ITS2 del ADNr. Se definieron los haplotipos para cada aislamiento y los parámetros poblacionales fueron estimados por zona geográfica y por especie hospedante junto con el número mínimo de eventos de recombinación. Las desviaciones de la coalescencia básica fueron estimadas a través de Tajima´s D.; la estructura genética fue evaluada subsecuentemente a través de pruebas de AMOVA y de estimadores de Fst. La reconstrucción de redes filogenéticas fue analizada con la intención de evaluar las relaciones genealógicas entre haplotipos. Todos los aislamientos mostraron características morfológicas y genéticas típicas de P. capsici y pertenecieron al TA A1. No se evidenció una estructura genética cuando fueron incluidas como criterio de partición las especies hospedantes. Sin embargo, la partición geográfica permitió evidenciar alguna estructuración entre poblaciones, con la excepción de Exaltación de La Cruz que resultó el sitio más contrastante con respecto a ambos estimadores de índices de fijación. Al mismo tiempo, esta ubicación redituó los estimadores más bajos de diversidad, lo que probablemente refleja su origen reciente como zona hortícola. Dos a tres eventos de recombinación fueron detectados, lo que sugiere que la reproducción sexual podría haber influido sobre el proceso de diversificación en esta área. La estructura genética y los niveles de variación en esta región son opuestos a los resultados obtenidos por otros investigadores en la región centro oeste de Argentina y podría significar una amenaza para esta área de cultivo, al presente.Phytophthora capsici causes destructive diseases worldwide. The pathogen is heterothallic and the two mating types (MTs) are required for sexual reproduction. MTs rates vary amongst geographical regions and so does the chance for sexual reproduction. Taking into account that the durability of control measures depends upon genetic variation, it is advisable to consider its structure within and between populations. The objective of the present paper was to evaluate the genetic variability of P. capsici isolates from three horticultural production areas of the Northeast of Buenos Aires. Sixty one isolates of P. capsici collected from Capsicum annuum, Solanum melongena, Solanum lycopersicum and Cucurbita spp. crops were morphologically identified and analyzed for MTs. The isolates were further identified via molecular techniques based on the sequences of the ITS1 - 5.8S - ITS2 region of the ADNr. Haplotypes were defined for every isolate, and population parameterts were estimated both for geographic and hostspecies partitions, along with the minimum number of recombination events. Departures from the basic coalescent were estimated through Tajima´s D; the genetic structure was subsequently evaluated through AMOVA tests and Fst estimations. Phylogenetic network reconstruction was analysed in an attempt to assess genealogical relationships amongst haplotypes. All isolates showed morphological and genetic characteristics of P. capsici and belonged to the A1 MT. No genetic structure was detected when host-species was taken as a criterion for partition; on the other hand, geographic partition detected some structure among populations, with Exaltación de La Cruz resulting in the most contrasting site with regards to both fixation index estimates. At the same time, this location yielded the lowest estimates of diversity, probably reflecting its recent horticultural origin. Two to three recombination events were detected, suggesting that sexual reproduction could have been part of the diversification process in this area. The genetic structure and levels of variation in the region is opposite to what other researchers have found in Northwestern Argentina and could mean a threat to that breeding area now.Fil: Iribarren, María Josefina. Universidad Nacional de Luján; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Borassi, Cecilia. Universidad Nacional de Luján; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Ferri, A.. Instituto Nacional de Tecnología Agropecuaria; ArgentinaFil: González, Beatriz Ángela. Universidad Nacional de Luján; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Steciow, Mónica Mirta. Universidad Nacional de La Plata; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Guillín, Eduardo. Instituto Nacional de Tecnología Agropecuaria; Argentin