Uncovering Gene Regulatory Networks from Time-Series Microarray Data with Variational Bayesian Structural Expectation Maximization

We investigate in this paper reverse engineering of gene regulatory networks from time-series microarray data. We apply dynamic Bayesian networks (DBNs) for modeling cell cycle regulations. In developing a network inference algorithm, we focus on soft solutions that can provide a posteriori probability (APP) of network topology. In particular, we propose a variational Bayesian structural expectation maximization algorithm that can learn the posterior distribution of the network model parameters and topology jointly. We also show how the obtained APPs of the network topology can be used in a Bayesian data integration strategy to integrate two different microarray data sets. The proposed VBSEM algorithm has been tested on yeast cell cycle data sets. To evaluate the confidence of the inferred networks, we apply a moving block bootstrap method. The inferred network is validated by comparing it to the KEGG pathway map

Complete fuzzy scheduling and fuzzy earned value management in construction projects

Complete fuzzy scheduling and fuzzy earned value management in construction projects Por: Luis Ponz-Tienda, Jose; Pellicer, Eugenio; Yepes, Victor JOURNAL OF ZHEJIANG UNIVERSITY-SCIENCE A Volumen: 13 Número: 1 Páginas: 56-68 Fecha de publicación: JAN 2012 Search For Full Text Cerrar abstractCerrar abstract This paper aims to present a comprehensive proposal for project scheduling and control by applying fuzzy earned value. It goes a step further than the existing literature: in the formulation of the fuzzy earned value we consider not only its duration, but also cost and production, and alternatives in the scheduling between the earliest and latest times. The mathematical model is implemented in a prototypical construction project with all the estimated values taken as fuzzy numbers. Our findings suggest that different possible schedules and the fuzzy arithmetic provide more objective results in uncertain environments than the traditional methodology. The proposed model allows for controlling the vagueness of the environment through the adjustment of the alpha-cut, adapting it to the specific circumstances of the project. © Zhejiang University and Springer-Verlag Berlin Heidelberg 2012.The authors want to thank Ms. Doria GIL-SENABRE, Universitat Politecnica de Valencia, Spain, for the support provided.Ponz Tienda, JL.; Pellicer Armiñana, E.; Yepes Piqueras, V. (2012). Complete fuzzy scheduling and fuzzy earned value management in construction projects. Journal of Zhejiang University Science A. 13(1):56-68. https://doi.org/10.1631/jzus.A1100160S566813

The Compound 2-Hexyl, 5-Propyl Resorcinol Has a Key Role in Biofilm Formation by the Biocontrol Rhizobacterium Pseudomonas chlororaphis PCL1606

The production of the compound 2-hexyl-5-propyl resorcinol (HPR) by the biocontrol rhizobacterium Pseudomonas chlororaphis PCL1606 (PcPCL1606) is crucial for fungal antagonism and biocontrol activity that protects plants against the phytopathogenic fungus Rosellinia necatrix. The production of HPR is also involved in avocado root colonization during the biocontrol process. This pleiotrophic response prompted us to study the potential role of HPR production in biofilm formation. The swimming motility of PcPLL1606 is enhanced by the disruption of HPR production. Mutants impaired in HPR production, revealed that adhesion, colony morphology, and typical air–liquid interphase pellicles were all dependent on HPR production. The role of HPR production in biofilm architecture was also analyzed in flow chamber experiments. These experiments revealed that the HPR mutant cells had less tight unions than those producing HPR, suggesting an involvement of HPR in the production of the biofilm matrix

Construcción de una comunidad sintética de tres Pseudomonas chlororaphis como modelo de estudio de interacciones bacteria-bacteria y planta-bacteria

Comunicación oral a congresoLas comunidades microbianas presentes en la rizosfera de árboles de aguacate sanos presentan una elevada presencia de bacterias del filo Proteobacteria. Destacan aquellas especies pertenecientes al complejo Pseudomonas fluorescens que presentan actividades relacionadas con la promoción del crecimiento de plantas (Plant Growth Promotion: PGP), así como con el control biológico de diferentes fitopatógenos como hongos, bacterias e insectos. Para estudiar el comportamiento y las interacciones que tienen lugar entre distintas cepas de P. chlororaphis aisladas de la rizosfera de aguacate, se ha construido una comunidad sintética de tres cepas y se han analizado sus fenotipos. Los genomas de estas cepas están secuenciados y se realizó un estudio comparativo de sus genomas. Por un lado, se han realizado estudios de compatibilidad y competitividad in vitro e in vivo entre las distintas cepas, y se determinó el fenotipo dominante en las diferentes combinaciones de cepas para la morfología de colonias y formación de biofilm. Por otro lado, se observó mediante microscopía confocal la formación de biofilm in vitro, así como la distribución de las cepas en solitario y combinadas sobre la raíz de aguacate. Por último, se ha estudiado, el control biológico y la estabilidad del consorcio en la rizosfera de aguacate, determinando su capacidad de colonización y persistencia.Financiación: FPU18/05672, AGL2017-83368-C2-1-R, UMA18-FEDERJA-046, y Universidad de Málaga. Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How

The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, “dehesa.” It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors’ group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses

Eficacia del control biológico con bacterias antagonistas sobre enfermedades postcosecha causadas por hongos de la familia Botryosphaeriaceae

Comunicación a congreso presentada como pósterEl mango y el aguacate son los principales cultivos subtropicales del sur de España. Estos frutos se cultivas y se procesan en la misma área geográfica, y son transportados al resto de Europa. Sin embargo, las enfermedades postcosecha durante el almacenamiento y transporte podría perjudicar el mercado de exportación. En este trabajo se detectan algunos síntomas de podredumbre en frutos de mango que se analizan en busca del agente causal. Paralelamente, frutos de aguacate asintomáticos, también fueron analizados. Estos dos frutos comparten, en muchas ocasiones, fincas, procesado e incluso el transporte, y podría actuar como fuente de inoculación cruzada. Los principales géneros fúngicos encontrados, tanto en mango como en aguacate, fueron Alternaria sp. y Neofusicoccum sp. De estos dos géneros, solo Neofusicoccum sp. pudo reproducir los síntomas de podredumbre en mango y aguacate. Para estudiar el control de esta enfermedad mediante estrategias sostenibles, se probaron dos agentes microbianos de control biológico. Ambos son antagonistas aislados contra hongos fitopatógenos, y corresponde a la bacteria Pseudomonas chlororaphis PCL1606. y Bacillus velezensis UMAF6639. Las aplicaciones de ambos microorganismos sobre la fruta mostraron niveles de protección significativos, aunque solo UMAF6639 mostró mayor persistencia en la fruta durante las aplicaciones preventivas en campo.Financiación: Incentivos a los agentes del sistema andaluz del conocimiento. Ayudas a la I+D+i, en el ámbito del plan andaluz de investigación, desarrollo e innovación (PAIDI 2020). Ayudas a actividades de transferencia de conocimiento entre los agentes del sistema andaluz del conocimiento y el tejido productivo, proyecto AT17-5544-UMA, y la Universidad de Málaga. Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

La producción de gránulos de polihidroxialcanoatos por Pseudomonas chlororaphis PCL1606 tiene un papel durante la interacción con la rizosfera del aguacate.

Contribución a congreso presentado como pósterPseudomonas chlororaphis PCL1606 (PcPCL1606) es una bacteria antagonista y de control biológico frente a diferentes hongos fitopatógenos de suelo, incluido Rosellinia necatrix, agente causal de la podredumbre blanca radicular en cultivos de aguacate en el área mediterránea. El antagonismo esta mediado por la producción del compuesto antifúngico 2 hexil, 5 propil resorcinol (HPR). Además, se ha comprobado que la producción de HPR también influye en otros procesos, como la colonización de la raíz de aguacate y la formación de biopelícula. Para ello se realizó un estudio transcriptómico para dilucidar el papel de la producción de HPR en la expresión génica de PcPCL1606 en interacción con la rizosfera del aguacate. A partir de los resultados transcriptómicos, se observó la expresión diferencial de genes relacionados con la síntesis de gránulos de polihidroxialcanoatos (PHA). La construcción de un mutante dirigido en el gen phaG, reveló que la producción de gránulos PHA estaba implicada en el control biológico contra R. necatrix y en la tolerancia a distintos estreses que tienen lugar durante la interacción con la rizosfera de aguacate.AGL2017-83368-C2-1-R, y la Universidad de Málag

Access to primary care is associated with better autoimmune hepatitis outcomes in an urban county hospital

BACKGROUND: Autoimmune hepatitis causes chronic hepatitis and often leads to cirrhosis and death without treatment. We wanted to see if having access to primary care or insurance prior to diagnosis is associated with better outcomes for patients in an urban, public hospital with mostly socioeconomically disadvantaged Hispanic patients. METHODS: We did a retrospective study at our institution. Kaplan Meier survival analysis was done looking at transplant-free overall survival for patients diagnosed at our institution. The log-rank test was done to compare survival between patients with and without prior access to primary care, and between patients with and without insurance at diagnosis. RESULTS: Overall 5- and 10-year transplant-free overall survival was 91 % (95 % CI, 83-100 %) and 75 % (95 % CI, 50-99 %), respectively. Patients with primary care prior to diagnosis had significantly better transplant-free overall survival than those without (log rank test p = 0.019). Patients with primary care also had better clinical markers at diagnosis. Having insurance at diagnosis was not associated with better outcomes. CONCLUSIONS: Outcomes of autoimmune hepatitis are poor in our setting but access to primary care prior to diagnosis was associated with better outcomes. This is likely due to the important role that primary care plays in detecting disease and initiating treatment earlier. With the expansion of access to healthcare that the Affordable Care Act provides, future patients are likely to do better with even rare diseases like autoimmune hepatitis

Modelling the duration of residence and plans for future residential relocation: A multilevel analysis

Amongst the multitude of studies of factors that determine residential (im)mobility, relatively little attention has been paid to the length of time that people spend in a particular location and the importance of duration of stay for future relocation propensities. This study uses a large and detailed commercial survey sample of individuals in England and Wales and an appropriately tailored statistical approach to uncover new insights into the multilevel and spatially heterogeneous interactions that exist between residential duration, place attachment and plans for future residential relocation. We demonstrate how an individual’s residential duration, as an essential ingredient for the accumulation of social capital and place-based attachment, is critical for informing plans for future (im)mobility. After controlling for a range of individual and contextual covariates, the predicted probability of planning a residential relocation is found to increase initially with duration of stay, to a peak after 4-5 years, and then to decline as the length of duration increases. However, there is evidence of strong geographical variation in this relationship, with some neighbourhoods being characterised by stable or even increasing propensities for movement with duration. The paper pays particular attention to the importance of wider neighbourhood dynamics (composition, selective sorting and population (in)stability), suggesting that they too play an important role in mediating duration-of-stay effects for individuals. The paper concludes by highlighting the need for researchers and policy practitioners interested in community dynamics, the development/accumulation of social capital and place attachment/rootedness, to give due consideration to multilevel durations of residence and, more broadly, the inherently spatial and temporal ties that bind individuals to place

A multilevel analysis of neighborhood and individual effects on individual smoking and drinking in Taiwan

<p>Abstract</p> <p>Background</p> <p>We assessed direct effects of neighborhood-level characteristics and interactive effects of neighborhood-level characteristics and individual socioeconomic position on adult smoking and drinking, after consideration of individual-level characteristics in Taiwan.</p> <p>Methods</p> <p>Data on individual sociodemographic characteristics, smoking, and drinking were obtained from Taiwan Social Change Survey conducted in 1990, 1995, and 2000. The overall response rate was 67%. A total of 5883 women and men aged over 20 living in 434 neighborhoods were interviewed. Participants' addresses were geocoded and linked with Taiwan census data for measuring neighborhood-level characteristics including neighborhood education, neighborhood concentration of elderly people, and neighborhood social disorganization. The data were analyzed with multilevel binomial regression models.</p> <p>Results</p> <p>Several interaction effects between neighborhood characteristics and individual socioeconomic status (SES) were found in multilevel analyses. Our results indicated that different neighborhood characteristics led to different interaction patterns. For example, neighborhood education had a positive effect on smoking for low SES women, in contrast to a negative effect on smoking for high SES women. This result supports the hypothesis of "relative deprivation," suggesting that poor people living in affluent neighborhoods suffer from relative deprivation and relative standing. On the other hand, neighborhood social disorganization has positive effects on drinking for low SES individuals, but not for high SES individuals. These interactive effects support the hypothesis of the double jeopardy theory, suggesting that living in neighborhoods with high social disorganization will intensify the effects of individual low SES.</p> <p>Conclusion</p> <p>The findings of this study show new evidence for the effects of neighborhood characteristics on individual smoking and drinking in Taiwan, suggesting that more studies are needed to understand neighborhood effects in Asian societies.</p