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

Untargeted MS-Based Metabolomics Analysis of the Responses to Drought Stress in Quercus ilex L. Leaf Seedlings and the Identification of Putative Compounds Related to Tolerance

The effect and responses to drought stress were analyzed in Quercus ilex L. seedlings using a nontargeted metabolomic approach, implementing the approaches of previous studies in which other -omics platforms, transcriptomics, and proteomics were employed. This work aimed to characterize the Q. ilex leaf metabolome, determining possible mechanisms and molecular markers of drought tolerance and identifying putative bioactive compounds. Six-month-old seedling leaves subjected to drought stress imposed by water withholding under high-temperature and irradiance conditions were collected when leaf fluorescence decreased by 20% (day 17) and 45% (day 24) relative to irrigated seedlings. A total of 3934 compounds were resolved, with 616 being variable and 342 identified, which belonged to five chemical families. Out of the identified compounds, 33 were variable, mostly corresponding to amino acids, carboxylic acids, benzenoids, flavonoids and isoprenoids. Epigallocatechin, ellagic acid, pulegone, indole-3-acrylic acid and dihydrozeatin-O-glucoside were up-accumulated under drought conditions at both sampling times. An integrated multi-omics analysis of phenolic compounds and related enzymes was performed, revealing that some enzymes involved in the flavonoid pathways (chalcone synthase, anthocyanidin synthase and anthocyanidin reductase) were up-accumulated at day 24 in non-irrigated seedlings. Some putative markers of tolerance to drought in Q. ilex are proposed for assisting breeding programs based on the selection of elite genotypes

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

A comprehensive dataset of annotated brain metastasis MR images with clinical and radiomic data.

Brain metastasis (BM) is one of the main complications of many cancers, and the most frequent malignancy of the central nervous system. Imaging studies of BMs are routinely used for diagnosis of disease, treatment planning and follow-up. Artificial Intelligence (AI) has great potential to provide automated tools to assist in the management of disease. However, AI methods require large datasets for training and validation, and to date there have been just one publicly available imaging dataset of 156 BMs. This paper publishes 637 high-resolution imaging studies of 75 patients harboring 260 BM lesions, and their respective clinical data. It also includes semi-automatic segmentations of 593 BMs, including pre- and post-treatment T1-weighted cases, and a set of morphological and radiomic features for the cases segmented. This data-sharing initiative is expected to enable research into and performance evaluation of automatic BM detection, lesion segmentation, disease status evaluation and treatment planning methods for BMs, as well as the development and validation of predictive and prognostic tools with clinical applicability