Exploring Replica-Exchange Wang-Landau sampling in higher-dimensional parameter space

We considered a higher-dimensional extension for the replica-exchange Wang-Landau algorithm to perform a random walk in the energy and magnetization space of the two-dimensional Ising model. This hybrid scheme combines the advantages of Wang-Landau and Replica-Exchange algorithms, and the one-dimensional version of this approach has been shown to be very efficient and to scale well, up to several thousands of computing cores. This approach allows us to split the parameter space of the system to be simulated into several pieces and still perform a random walk over the entire parameter range, ensuring the ergodicity of the simulation. Previous work, in which a similar scheme of parallel simulation was implemented without using replica exchange and with a different way to combine the result from the pieces, led to discontinuities in the final density of states over the entire range of parameters. From our simulations, it appears that the replica-exchange Wang-Landau algorithm is able to overcome this difficulty, allowing exploration of higher parameter phase space by keeping track of the joint density of states.Comment: Proceedings of CCP2014 will appear in Journal of Physics: Conference Series (JPCS), published by the IO

Quantitative analysis of interferon alpha receptor subunit 1 and suppressor of cytokine signaling 1 gene transcription in blood cells of patients with chronic hepatitis C

<p>Abstract</p> <p>Background</p> <p>Interferon (IFN)-α receptor 1 (<it>ifnar1</it>) and suppressor of cytokine signaling 1 (<it>socs1</it>) transcription levels were quantified in peripheral blood mononuclear cells (PBMC) of 59 patients infected with hepatitis C virus (HCV) and 17 non-infected individuals. Samples were obtained from patients infected with HCV that were either untreated or treated with IFN-α2 plus ribavirin for 1 year and divided into responders and non-responders based on viral load reduction 6 months after treatment. <it>Ifnar1 </it>and <it>socs1 </it>transcription was quantified by real-time RT-PCR, and the fold difference (2^-ΔΔCT) with respect to <it>hprt </it>housekeeping gene was calculated.</p> <p>Results</p> <p><it>Ifnar1 </it>transcription increased significantly in HCV-infected patients either untreated (3.26 ± 0.31), responders (3.1 ± 0.23) and non-responders (2.18 ± 0.23) with respect to non-infected individuals (1 ± 0.34; <it>P </it>= 0.005). <it>Ifnar1 </it>transcription increased significantly (<it>P </it>= 0.003) in patients infected with HCV genotypes 1a (4.74 ± 0.25) and 1b (2.81 ± 0.25) but not in 1a1b (1.58 ± 0.21). No association was found of <it>Ifnar1 </it>transcription with disease progress, initial viral load or other clinical factors. With respect to <it>socs1 </it>transcription, values were similar for non-infected individuals (1 ± 0.28) and untreated patients (0.99 ± 0.41) but increased in responders (2.81 ± 0.17) and non-responder patients (1.67 ± 0.41). Difference between responder and non-responder patients was not statistically significant. <it>Socs1 </it>transcription increased in patients infected with HCV genotypes 1a and 1b (2.87 ± 0.45 and 2.22 ± 0.17, respectively) but not in 1a1b (1.28 ± 0.40). <it>Socs1 </it>transcript was absent in three patients infected with HCV genotype 1b. A weak correlation between <it>ifnar1 </it>and <it>socs1 </it>transcription was found, when Spearman's correlation coefficient was calculated.</p> <p>Conclusion</p> <p>Our results suggest that HCV infection may up-regulate <it>ifnar1 </it>transcription. HCV genotypes differ in their capacity to affect <it>ifnar1 </it>and <it>socs1 </it>transcription, as well as in the ability to evade the antiviral response.</p

Resposta imune a doenças infecciosas

The interaction between pathogens and immune system occurs in a dynamic way with sophisticate mechanisms of evasion and immune control of infection, respectively. Therefore, it is a sine qua non condition to understand the complexity of this relationship in order to developed new strategies for infection control. Although the immune system has specialized mechanisms to control infection, different conditions involved in the interaction between immune system and pathogens can or cannot determine the development of disease. Interestingly, a protective immune response against one kind of parasite may not be protective against another. So, each pathogen presents a specific way of interaction with the immune system. The development of research in this area has contributed with a better comprehension of the immune system and pathogen relationship and opened perspective in improving the treatment with the development of new drugs and/or vaccines.A interação do sistema imune com os agentes infecciosos ocorre de uma maneira dinâmica, com mecanismos de controle da infecção e de escape sofisticados. A compreensão dessa complexidade é condição sine qua non para que se estabeleça uma ação total no controle dessas infecções. Embora a resposta imune desenvolvida para controle das diferentes infecções apresente certas particularidades, em geral, apresentam também mecanismos comuns. A priori os mecanismos podem ser redundantes, no entanto existe uma gama de sutilezas entre a interação hospedeiro-parasita que define o estabelecimento ou não de doença. Por outro lado, não se pode deixar de alertar que melhores condições de saneamento básico diminuiriam a incidência de inúmeras doenças. A classificação de uma resposta imune protetora tem que ser avaliada sempre em relação ao tipo de agente agressor, pois um mecanismo protetor conta um vírus pode não ser essencial contra uma bactéria extracelular. De qualquer forma, o avanço na pesquisa com diferentes patógenos tem contribuído para uma melhor compreensão da resposta imune decorrente da interação entre o hospedeiro e parasita o que pode resultar no desenvolvimento de novas drogas e vacinas

Alternativas de control sobre Bemisia spp. en el cultivo de Capsicum annum L. (criollo) en el municipio de Tepetzintla, Veracruz

Para  el  manejo  de  Bemisia  spp.  en  cultivo  de  chile  criollo  (Capsicum  annum  L.),  se  evaluaron diferentes alternativas, entre ellas, los insecticidas químicos: endosulfan, malathion; los bioplaguicidas: Paecilomyces fumosoroseus, Beauveria bassiana; el extracto vegetales: Allium sp.; aceite mineral: Saf- t-side, los jabones: foca y vel rosita, en ciclo 2008. Se utilizó un diseño de bloques completos al azar con 4 repeticiones, evaluando las poblaciones de adultos, ninfas, y huevos a través de análisis de varianza y una prueba de comparación de medias. Los productos se aplicaron una vez por semana y se hicieron 6 aplicaciones semanales y se tomaron los datos de campo y laboratorio dos días después de cada aplicación. Se observa que los diferentes tratamientos con extractos, aceites, jabones, hongos y químicos los fueron capaces de mantener las poblaciones de adultos de Bemisia spp. en niveles mucho más  bajos  que  el  testigo,  durante  el  tiempo  que  duró  el  experimento.  Las  alternativas  donde  se utilizaron insecticidas químicos, hongos entomopatógenos y los extractos vegetales y aceites minerales fueron similares estadísticamente, y lograron niveles poblacionales de huevos relativamente bajos. En huevos la variante donde se utilizaron los jabones difirió significativamente de todas las demás, que no difirieron entre sí. Ninfas Todas las variantes evaluadas difirieron estadísticamente del testigo, y se observó el menor efecto de regulación de la población de ninfas en la variante con jabones, con diferencia significativa con relación a los demás tratamientos, después, se ubicó la variantes de hongos entomopatógenos, con extractos y aceites, y por último, la de insecticidas químicos que fue el que mayor efecto presento para el control de mosca blanca. Los resultados de este ensayo demuestran que todos los tratamientos difirieron estadísticamente del testigo y que reducen las poblaciones de mosca blanca, por lo que pueden utilizarse exitosamente como alternativa en el manejo integrado de esta plaga

Alternativas para el control de Diaphorina citri (Kuwayama) con insecticidas botánicos, en Citrus latifolia tanaca, Tlapacoyan, Veracruz.

Para el manejo Diaphorina citri(Kuwayama), se evaluaron, en lima persa (Citrus Latifolia Tan.), en la región   de   Tlapacoyan,   Ver.,   México.   Otoño-Invierno,   2008-2009,   diferentes,   productos   con insecticidas botánicos. BIO-Die PROGRANIC® PROGRANIC ® Omega, PROGRANIC® Gama, PROGRANIC®  UltraluxS. PROGRANIC®  Oil Aceite y Testigo. Se utilizó un diseño de bloques completos al azar con 4 repeticiones, evaluando las poblaciones de adultos, ninfas, a través de análisis de varianza mediante la prueba de comparación de medias. Se realizó un conteo previo para establecer el umbral de aplicación con la sola presencia de adultos o ninfas por cada brote recién emergido, para determinar la persistencia de los productos durante periodos de 7, 17, 27 y 37 días, en cada unidad experimental se realizo aplicaciones y evaluaciones. Los efectos más marcados sobre la población de ninfas se manifestaron en las variantes con Oíl, Omega, Biodie, Gama, NeemAcar, Ultralux-s que no difirieron estadísticamente entre ellos y por último difiriendo de todos los demás el testigo. En adultos Diaphorina citri, todos los tratamientos con extractos y aceites difirieron estadísticamente del testigo, después del testigo, a nivel poblacional, se ubicó el extracto Gama, que no marco diferencia del aceite OIL y este a la vez de el extracto vegetal Ultralux-s, NeemAcar y Biodie y por último el Omega que difirió de todas las demás variantes. Estos productos pueden utilizarse exitosamente como alternativa en el manejo integrado de esta plaga

B cells Can Modulate the CD8 Memory T Cell after DNA Vaccination Against Experimental Tuberculosis

Abstract\ud \ud \ud \ud Background\ud \ud Although B cells are important as antigen presenting cells (APC) during the immune response, their role in DNA vaccination models is unknown.\ud \ud \ud \ud Methods\ud \ud In this study in vitro and in vivo experiments were performed to evaluate the ability of B cells to protect mice against Mycobacterium tuberculosis challenge.\ud \ud \ud \ud Results\ud \ud \ud In vitro and in vivo studies showed that B cells efficiently present antigens after naked plasmid pcDNA3 encoding M. leprae 65-kDa heat shock protein (pcDNA3-Hsp65) internalization and protect B knock-out (BKO) mice against Mycobacterium tuberculosis infection. pcDNA3-Hsp65-transfected B cells adoptively transferred into BKO mice rescued the memory phenotypes and reduced the number of CFU compared to wild-type mice.\ud \ud \ud \ud Conclusions\ud \ud These data not only suggest that B cells play an important role in the induction of CD8 T cells but also that they improve bacterial clearance in DNA vaccine model.We are thankful to Ana Paula Masson and Izaíra T Brandão for providing the DNA vaccine and recombinant protein. This study was supported by a FAPESP fellowship (05/030873) to LPA.We are thankful to Ana Paula Masson and Izaíra T Brandão for providing the DNA vaccine and recombinant protein. This study was supported by a FAPESP fellowship (05/03087-3) to LPA