Convergence of adaptive mixtures of importance sampling schemes

In the design of efficient simulation algorithms, one is often beset with a poor choice of proposal distributions. Although the performance of a given simulation kernel can clarify a posteriori how adequate this kernel is for the problem at hand, a permanent on-line modification of kernels causes concerns about the validity of the resulting algorithm. While the issue is most often intractable for MCMC algorithms, the equivalent version for importance sampling algorithms can be validated quite precisely. We derive sufficient convergence conditions for adaptive mixtures of population Monte Carlo algorithms and show that Rao--Blackwellized versions asymptotically achieve an optimum in terms of a Kullback divergence criterion, while more rudimentary versions do not benefit from repeated updating.Comment: Published at http://dx.doi.org/10.1214/009053606000001154 in the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Phytophthora nicotianae causando podridão de raiz e caule em Dieffenbachia picta em Buenos Aires, Argentina

327-331Dieffenbachia picta is a worldwide appreciated crop due to its ornamental value. In Argentina it is cultivated in warm provinces and in the outskirts of Buenos Aires city, where in spring 2007 a great amount of plants were lost in commercial greenhouses. Symptoms such as wilting and soaked lesions in the basal leaves began in four- to six-month-old plants causing plants to wilt due to basal stem and root rot processes. A Peronosporomycete was consistently isolated from diseased tissues. The pathogen was identified as Phytophthora nicotianae based on cultural characteristics, morphology of vegetative and reproductive structures, and on the analysis of the sequence of the nuclear ribosomal internal transcribed spacer (ITS) region. Pathogenicity tests were carried out and Koch's postulates were fulfilled. In complementary studies, the dieffenbachia varieties Alex, Compact, Camilla and Marianne were susceptible to the infection caused by P. nicotianae, whereas Tropic snow (D. amonea) was resistant. This is the first report of P. nicotianae causing stem and root rot of D. picta in Argentina and in the Americas

Adaptive Importance Sampling in General Mixture Classes

In this paper, we propose an adaptive algorithm that iteratively updates both the weights and component parameters of a mixture importance sampling density so as to optimise the importance sampling performances, as measured by an entropy criterion. The method is shown to be applicable to a wide class of importance sampling densities, which includes in particular mixtures of multivariate Student t distributions. The performances of the proposed scheme are studied on both artificial and real examples, highlighting in particular the benefit of a novel Rao-Blackwellisation device which can be easily incorporated in the updating scheme.Comment: Removed misleading comment in Section

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.Gerencia de Comunicación e Imagen InstitucionalFil: Iribarren, Maria Josefina. Universidad Nacional de Luján; ArgentinaFil: Borassi, C. Universidad Nacional de Luján; ArgentinaFil: Ferri, Andrea Matilde. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaFil: González, B. Universidad Nacional de Luján; ArgentinaFil: Steciow, M. Universidad Nacional de La Plata; ArgentinaFil: Guillin, Eduardo Alejandro. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentin

More cercospora species infect soybeans across the Americas than meets the eye

1-20Diseases of soybean caused by Cercospora spp. are endemic throughout the world`s soybean production regions. Species diversity in the genus Cercospora has been underestimated due to overdependence on morphological characteristics, symptoms, and host associations. Currently, only two species (Cercospora kikuchii and C. sojina) are recognized to infect soybean; C. kikuchii causes Cercospora leaf blight (CLB) and purple seed stain (PSS), whereas C. sojina causes frogeye leaf spot. To assess cryptic speciation among pathogens causing CLB and PSS, phylogenetic and phylogeographic analyses were performed with isolates from the top three soybean producing countries (USA, Brazil, and Argentina; collectively accounting for ~ 80 per cent of global production). Eight nuclear genes and one mitochondrial gene were partially sequenced and analyzed. Additionally, amino acid substitutions conferring fungicide resistance were surveyed, and the production of cercosporin (a polyketide toxin produced bymany Cercospora spp.) was assessed. From these analyses, the longheld assumption of C. kikuchii as the single causal agent of CLB and PSS was rejected experimentally. Four cercosporin-producing lineages were uncovered with origins (about 1 Mya) predicted to predate agriculture. Some of the Cercospora spp. newly associated with CLB and PSS appear to represent undescribed species; others were not previously reported to infect soybeans. Lineage 1, which contained the ex-type strain of C. kikuchii, was monophyletic and occurred in Argentina and Brazil. In contrast, lineages 2 and 3 were polyphyletic and contained wide-host range species complexes. Lineage 4 was monophyletic, thrived in Argentina and the USA, and included the generalist Cercospora cf. flagellaris. Interlineage recombination was detected, along with a high frequency of mutations linked to fungicide resistance in lineages 2 and 3. These findings point to cryptic Cercospora species as underappreciated global considerations for soybean production and phytosanitary vigilance, and urge a reassessment of host-specificity as a diagnostic tool for Cercospora

More Cercospora species infect soybeans across the Americas than meets the eye.

Diseases of soybean caused by Cercospora spp. are endemic throughout the world's soybean production regions. Species diversity in the genus Cercospora has been underestimated due to overdependence on morphological characteristics, symptoms, and host associations. Currently, only two species (Cercospora kikuchii and C. sojina) are recognized to infect soybean; C. kikuchii causes Cercospora leaf blight (CLB) and purple seed stain (PSS), whereas C. sojina causes frogeye leaf spot. To assess cryptic speciation among pathogens causing CLB and PSS, phylogenetic and phylogeographic analyses were performed with isolates from the top three soybean producing countries (USA, Brazil, and Argentina; collectively accounting for ~80% of global production). Eight nuclear genes and one mitochondrial gene were partially sequenced and analyzed. Additionally, amino acid substitutions conferring fungicide resistance were surveyed, and the production of cercosporin (a polyketide toxin produced bymany Cercospora spp.) was assessed. From these analyses, the longheld assumption of C. kikuchii as the single causal agent of CLB and PSS was rejected experimentally. Four cercosporin-producing lineages were uncovered with origins (about 1 Mya) predicted to predate agriculture. Some of the Cercospora spp. newly associated with CLB and PSS appear to represent undescribed species; others were not previously reported to infect soybeans. Lineage 1, which contained the ex-type strain of C. kikuchii, was monophyletic and occurred in Argentina and Brazil. In contrast, lineages 2 and 3 were polyphyletic and contained wide-host range species complexes. Lineage 4 was monophyletic, thrived in Argentina and the USA, and included the generalist Cercospora cf. flagellaris. Interlineage recombination was detected, along with a high frequency of mutations linked to fungicide resistance in lineages 2 and 3. These findings point to cryptic Cercospora species as underappreciated global considerations for soybean production and phytosanitary vigilance, and urge a reassessment of host-specificity as a diagnostic tool for Cercospora

Cooperative Regulation of the Activity of Factor Xa within Prothrombinase by Discrete Amino Acid Regions from Factor Va Heavy Chain†

ABSTRACT: The prothrombinase complex catalyzes the activation of prothrombin to R-thrombin. We have repetitively shown that amino acid region 695DYDY698 from the COOH terminus of the heavy chain of factor Va regulates the rate of cleavage of prothrombin at Arg271 by prothrombinase. We have also recently demonstrated that amino acid region 334DY335 is required for the optimal activity of prothrombinase. To assess the effect of these six amino acid residues on cofactor activity, we created recombinant factor Va molecules combining mutations at amino acid regions 334–335 an