Bayesian additive regression trees for probabilistic programming

Bayesian additive regression trees (BART) is a non-parametric method to approximate functions. It is a black-box method based on the sum of many trees where priors are used to regularize inference, mainly by restricting trees' learning capacity so that no individual tree is able to explain the data, but rather the sum of trees. We discuss BART in the context of probabilistic programming languages (PPL), i.e., we present BART as a primitive that can be used as a component of a probabilistic model rather than as a standalone model. Specifically, we introduce the Python library PyMC-BART, which works by extending PyMC, a library for probabilistic programming. We showcase a few examples of models that can be built using PyMC-BART, discuss recommendations for the selection of hyperparameters, and finally, we close with limitations of our implementation and future directions for improvement.Comment: 22 pages, 17 figure

Information Theory Perspective on Network Robustness

A crucial challenge in network theory is the study of the robustness of a network after facing a sequence of failures. In this work, we propose a dynamical definition of network's robustness based on Information Theory, that considers measurements of the structural changes caused by failures of the network's components. Failures are defined here, as a temporal process defined in a sequence. The robustness of the network is then evaluated by measuring dissimilarities between topologies after each time step of the sequence, providing a dynamical information about the topological damage. We thoroughly analyze the efficiency of the method in capturing small perturbations by considering both, the degree and distance distributions. We found the network's distance distribution more consistent in capturing network structural deviations, as better reflects the consequences of the failures. Theoretical examples and real networks are used to study the performance of this methodology.Comment: 5 pages, 2 figures, submitte

Endogenously-expressed NH2-terminus of circumsporozoite protein interferes with sporozoite invasion of mosquito salivary glands

Abstract\ud \ud Background\ud The circumsporozoite protein is the most abundant polypeptide expressed by sporozoites, the malaria parasite stage capable of infecting humans. Sporozoite invasion of mosquito salivary glands prior to transmission is likely mediated by a receptor/ligand-like interaction of the parasites with the target tissues, and the amino (NH2)-terminal portion of CSP is involved in this interaction but not the TSR region on the carboxyl (C)-terminus. Peptides based on the NH2-terminal domain could compete with the parasites for the salivary gland receptors and thus inhibit penetration.\ud \ud \ud Methods\ud Peptides based on the NH2-terminus and TSR domains of the CSP from avian or human malaria parasites, Plasmodium gallinaceum and Plasmodium falciparum, respectively, were expressed endogenously in mosquito haemolymph using a transient (Sindbis virus-mediated) or stable (piggyBac-mediated transgenesis) system.\ud \ud \ud Results\ud Transient endogenous expression of partial NH2-terminus peptide from P. falciparum CSP in P. gallinaceum-infected Aedes aegypti resulted in a reduced number of sporozoites in the salivary glands. When a transgenic approach was used to express a partial CSP NH2-terminal domain from P. gallinaceum the number of sporozoites in the salivary glands did not show a difference when compared to controls. However, a significant difference could be observed when mosquitoes with a lower infection were analysed. The same result could not be observed with mosquitoes endogenously expressing peptides based on the TSR domain from either P. gallinaceum or P. falciparum.\ud \ud \ud \ud Conclusion\ud These results support the conclusion that CSP partial NH2-terminal domain can be endogenously expressed to promote a competition for the receptor used by sporozoites to invade salivary glands, and they could be used to block this interaction and reduce parasite transmission. The same effect cannot be obtained with peptides based on the TSR domain.We thank Neuza Saraiva Fernandes and Ediane Saraiva Fernandes for technical\ud assistance and Alexandre Santos de Moura for sample sequencing. This work\ud was supported by FAPESP (Process#04/00889-9 and#00/12138-7). AAJ was\ud supported in part by an award from the National Institute of Allergy and Infec‑\ud tious Diseases (USA) (R37AI029746)

Environmental heterogeneity modulates the effect of plant diversity on the spatial variability of grassland biomass

Plant productivity varies due to environmental heterogeneity, and theory suggests that plant diversity can reduce this variation. While there is strong evidence of diversity effects on temporal variability of productivity, whether this mechanism extends to variability across space remains elusive. Here we determine the relationship between plant diversity and spatial variability of productivity in 83 grasslands, and quantify the effect of experimentally increased spatial heterogeneity in environmental conditions on this relationship. We found that communities with higher plant species richness (alpha and gamma diversity) have lower spatial variability of productivity as reduced abundance of some species can be compensated for by increased abundance of other species. In contrast, high species dissimilarity among local communities (beta diversity) is positively associated with spatial variability of productivity, suggesting that changes in species composition can scale up to affect productivity. Experimentally increased spatial environmental heterogeneity weakens the effect of plant alpha and gamma diversity, and reveals that beta diversity can simultaneously decrease and increase spatial variability of productivity. Our findings unveil the generality of the diversity-stability theory across space, and suggest that reduced local diversity and biotic homogenization can affect the spatial reliability of key ecosystem functions.Fil: Daleo, Pedro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Alberti, Juan. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Chaneton, Enrique Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; ArgentinaFil: Iribarne, Oscar Osvaldo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Tognetti, Pedro Maximiliano. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; ArgentinaFil: Bakker, Jonathan. University of Washington; Estados UnidosFil: Borer, Elizabeth. University of Minnesota; Estados UnidosFil: Bruschetti, Carlos Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: MacDougall, Andrew S.. University Of Guelph. Department Of Integrative Biology.; CanadáFil: Pascual, Jesus Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Sankaran, Mahesh. University of Leeds; Reino Unido. Tata Institute of Fundamental Research; IndiaFil: Seabloom, Eric. University of Minnesota; Estados UnidosFil: Wang, Shaopeng. Peking University; ChinaFil: Bagchi, Sumanta. Indian Institute of Science; IndiaFil: Brudvig, Lars A.. Michigan State University; Estados UnidosFil: Catford, Jane A.. University of Melbourne; Australia. Kings College London (kcl);Fil: Dickman, Chris R.. The University Of Sydney; AustraliaFil: Dickson, Tymothy L.. University of Nebraska; Estados UnidosFil: Donohue, Ian. Trinity College Dublin; Reino UnidoFil: Eisenhauer, Nico. Universitat Leipzig; Alemania. German Centre for Integrative Biodiversity Research; AlemaniaFil: Gruner, Daniel S.. University of Maryland; Estados UnidosFil: Haider, Sylvia. German Centre for Integrative Biodiversity Research; Alemania. Martin Luther University Halle-Wittenberg; Alemania. Leuphana University of Lüneburg; AlemaniaFil: Jentsch, Anke. University of Bayreuth; AlemaniaFil: Knops, Johannes M. H.. Xi’an Jiaotong-Liverpool University; ChinaFil: Lekberg, Ylva. University of Montana; Estados UnidosFil: McCulley, Rebecca L.. University of Kentucky; Estados UnidosFil: Moore, Joslin L.. University of Melbourne; Australia. Monash University; Australia. Arthur Rylah Institute for Environmental Research; AustraliaFil: Mortensen, Brent. Benedictine College; Estados UnidosFil: Peri, Pablo Luis. Instituto Nacional de Tecnología Agropecuaria; Argentina. Universidad Nacional de la Patagonia Austral; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Rocca, Camila. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; Argentin

Plan piloto "Horticultura responsable". Trabajo conjunto entre INTA y SENASA

Con el objetivo de incentivar a productores de hortalizas en la implementación de buenas prácticas agrícolas, se está llevando adelante un plan piloto en Baradero. La intención fue ayudarlos a posicionar sus productos de una manera más conveniente en los distintos puntos de venta utilizados (ferias, mercados, verdulerías), a través de un logo que identifica las hortalizas provenientes de las quintas donde se está ejecutando el plan. El proyecto se inició en agosto de 2015, y es fruto del trabajo conjunto entre el INTA y el SENASA. Se realizaron capacitaciones a los productores sobre manejo integrado de plagas y enfermedades, manejo del suelo, buenas prácticas agrícolas, normativa vigente en lo referente al uso de agroquímicos, plaguicidas permitidos, desinfección del suelo, seguridad e higiene, etc. Se evaluó el desempeño ambiental de los predios a través del sistema SEPIA (Sistema de Evaluación de Impacto Ambiental Ponderado), el cual permitió elaborar diagnósticos participativos y planificar procesos de mejora. Los productores realizan un registro de las labores y agroquímicos utilizados. Se realizaron monitoreos y análisis de laboratorio para residuos de plaguicidas y contaminación microbiológica por parte del SENASA. Se diseñaron piezas comunicacionales como afiches, volantes y etiquetas para cada productor, siguiendo los requisitos de la normativa. Los productores se inscribieron en el Renspa. La iniciativa contó con el apoyo del Municipio de Baradero, quién realizó difusión en los medios de comunicación y en una Jornada Municipal de Medio Ambiente realizada en mayo del 2017. Además se cuenta con el apoyo del Programa Cambio Rural ya que los productores conformaron el grupo Altiplano en Baradero y de Pro Huerta, a través de un Proyecto Especial aprobado recientemente, y gracias al cual se podrán adquirir bienes necesarios para implementar las mejoras propuestas. Los logros obtenidos son fruto del esfuerzo conjunto de proyectos de investigación y proyectos regionales, así como de distintos organismos del Estado y programas de intervención.EEA San PedroFil: Mitidieri, Mariel Silvina . Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaFil: Delprino, María Rosa. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaFil: Fortunato, Nicolás. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaFil: Fernández, A. Senasa. Servicio Nacional de Sanidad y Calidad Agroalimentaria; ArgentinaFil: Sampietro, Esteban. Senasa. Servicio Nacional de Sanidad y Calidad Agroalimentaria; ArgentinaFil: D´Angelcola, María Elena. Instituto Nacional de Tecnología Agropecuaria (INTA). Gerencia de Control de Gestión; ArgentinaFil: Cuellas, Marisol Virginia. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Área Metropolitana de Buenos Aires; ArgentinaFil: Valenzuela, Osvaldo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaFil: Bernardez, Alejandra. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaFil: Piris, Estela Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaFil: Barbieri, Martín Osvaldo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaFil: Brambilla, María Virginia. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaFil: Del Pardo, Cecilia Karina. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaFil: Ciaponi, Mirta Mabel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaFil: Taquichiri, E. Actividad privada. Productor hortícola. Baradero; ArgentinaFil: Aricoma, Alfredo. Actividad privada. Productor hortícola. Baradero; ArgentinaFil: Yucra, M. Actividad privada. Productor hortícola. Baradero; ArgentinaFil: Calva, L. Actividad privada. Productor hortícola. Baradero; ArgentinaFil: Sánchez, Florencia. Ministerio de Agroindustria. Unidad de Cambio Rural II; ArgentinaFil: Heguiabeheri, Adolfo Ricardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaFil: Piola, Mariana. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaFil: Peña, Lorena Claudina. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentin

Tumor Associated Stromal Cells Play a Critical Role on the Outcome of the Oncolytic Efficacy of Conditionally Replicative Adenoviruses

The clinical efficacy of conditionally replicative oncolytic adenoviruses (CRAd) is still limited by the inefficient infection of the tumor mass. Since tumor growth is essentially the result of a continuous cross-talk between malignant and tumor-associated stromal cells, targeting both cell compartments may profoundly influence viral efficacy. Therefore, we developed SPARC promoter-based CRAds since the SPARC gene is expressed both in malignant cells and in tumor-associated stromal cells. These CRAds, expressing or not the Herpes Simplex thymidine kinase gene (Ad-F512 and Ad(I)-F512-TK, respectively) exerted a lytic effect on a panel of human melanoma cells expressing SPARC; but they were completely attenuated in normal cells of different origins, including fresh melanocytes, regardless of whether cells expressed or not SPARC. Interestingly, both CRAds displayed cytotoxic activity on SPARC positive-transformed human microendothelial HMEC-1 cells and WI-38 fetal fibroblasts. Both CRAds were therapeutically effective on SPARC positive-human melanoma tumors growing in nude mice but exhibited restricted efficacy in the presence of co-administered HMEC-1 or WI-38 cells. Conversely, co-administration of HMEC-1 cells enhanced the oncolytic efficacy of Ad(I)-F512-TK on SPARC-negative MIA PaCa-2 pancreatic cancer cells in vivo. Moreover, conditioned media produced by stromal cells pre-infected with the CRAds enhanced the in vitro viral oncolytic activity on pancreatic cancer cells, but not on melanoma cells. The whole data indicate that stromal cells might play an important role on the outcome of the oncolytic efficacy of conditionally replicative adenoviruses

Genome-Wide Patterns of Gene Expression during Aging in the African Malaria Vector Anopheles gambiae

The primary means of reducing malaria transmission is through reduction in longevity in days of the adult female stage of the Anopheles vector. However, assessing chronological age is limited to crude physiologic methods which categorize the females binomially as either very young (nulliparous) or not very young (parous). Yet the epidemiologically relevant reduction in life span falls within the latter category. Age-grading methods that delineate chronological age, using accurate molecular surrogates based upon gene expression profiles, will allow quantification of the longevity-reducing effects of vector control tools aimed at the adult, female mosquito. In this study, microarray analyses of gene expression profiles in the African malaria vector Anopheles gambiae were conducted during natural senescence of females in laboratory conditions. Results showed that detoxification-related and stress-responsive genes were up-regulated as mosquitoes aged. A total of 276 transcripts had age-dependent expression, independently of blood feeding and egg laying events. Expression of 112 (40.6%) of these transcripts increased or decreased monotonically with increasing chronologic age. Seven candidate genes for practical age assessment were tested by quantitative gene amplification in the An. gambiae G3 strain in a laboratory experiment and the Mbita strain in field enclosures set up in western Kenya under conditions closely resembling natural ones. Results were similar between experiments, indicating that senescence is marked by changes in gene expression and that chronological age can be gauged accurately and repeatedly with this method. These results indicate that the method may be suitable for accurate gauging of the age in days of field-caught, female An. gambiae