221 research outputs found

    Causal Modeling of Soil Processes for Improved Generalization

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    Measuring and monitoring soil organic carbon is critical for agricultural productivity and for addressing critical environmental problems. Soil organic carbon not only enriches nutrition in soil, but also has a gamut of co-benefits such as improving water storage and limiting physical erosion. Despite a litany of work in soil organic carbon estimation, current approaches do not generalize well across soil conditions and management practices. We empirically show that explicit modeling of cause and-effect relationships among the soil processes improves the out-of-distribution generalizability of prediction models. We provide a comparative analysis of soil organic carbon estimation models where the skeleton is estimated using causal discovery methods. Our framework provide an average improvement of 81% in test mean squared error and 52% in test mean absolute error

    Identification of genes related to germination in aged maize seed by screening natural variability

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    Ageing reduces vigour and viability in maize inbred lines due to non-heritable degenerative changes. Besides non-heritable genetic changes due to chromosome aberrations and damage in the DNA sequence, heritable changes during maize conservation have been reported. Genetic variability among aged seeds of inbred lines could be used for association studies with seed germination. The objective of this study was to identify genes related to germination in aged seeds. The sweet corn inbred line P39 and the field corn inbred line EP44 were used as plant material. Bulks of living and dead seeds after 20 and 22 years of storage were compared by using simple sequence repeats (SSRs) and, when the bulks differed for a marker, the individual grains were genotyped. Differences between dead and living seeds could be explained by residual variability, spontaneous mutation, or ageing. Variability was larger for chromosome 7 than for other chromosomes, and for distal than for proximal markers, suggesting some relationships between position in the genome and viability in aged seed. Polymorphic SSRs between living and dead seeds were found in six known genes, including pathogenesis-related protein 2, superoxide dismutase 4, catalase 3, opaque endosperm 2, and metallothionein1 that were related to germination, along with golden plant 2. In addition, five novel candidate genes have been identified; three of them could be involved in resistance to diseases, one in detoxification of electrophillic compounds, and another in transcription regulation. Therefore, genetic variability among aged seeds of inbreds was useful for preliminary association analysis to identify candidate genes

    Association mapping for maize stover yield and saccharification efficiency using a multiparent advanced generation intercross (MAGIC) population

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    Cellulosic ethanol derived from fast growing C4 grasses could become an alternative to finite fossil fuels. With the potential to generate a major source of lignocellulosic biomass, maize has gained importance as an outstanding model plant for studying the complex cell wall network and also to optimize crop breeding strategies in bioenergy grasses. A genome-wide association study (GWAS) was conducted using a subset of 408 Recombinant Inbred Lines (RILs) from a Multi-Parent Advanced Generation Intercross (MAGIC) Population in order to identify single nucleotide polymorphisms (SNPs) associated with yield and saccharification efficiency of maize stover. We identified 13 SNPs significantly associated with increased stover yield that corresponded to 13 QTL, and 2 SNPs significantly associated with improved saccharification efficiency, that could be clustered into 2 QTL. We have pointed out the most interesting SNPs to be implemented in breeding programs based on results from analyses of averaged and yearly data. Association mapping in this MAGIC population highlight genomic regions directly linked to traits that influence the final use of maize. Markers linked to these QTL could be used in genomic or marker-assisted selection programs to improve biomass quality for ethanol production. This study opens a possible optimisation path for improving the viability of second-generation biofuelsPlan Estatal de Ciencia y Tecnología de España | Ref. RTI2018–096776-B-C21Plan Estatal de Ciencia y Tecnología de España | Ref. RTI2018–096776-B-C2

    Promotion of macrophage activation by Tie2 in the context of the inflamed synovia of rheumatoid arthritis and psoriatic arthritis patients

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    OBJECTIVE: To examine the role of Tie2 signalling in macrophage activation within the context of the inflammatory synovial microenvironment present in patients with RA and PsA. METHODS: Clinical responses and macrophage function were examined in wild-type and Tie2-overexpressing (Tie2-TG) mice in the K/BxN serum transfer model of arthritis. Macrophages derived from peripheral blood monocytes from healthy donors, RA and PsA patients, and RA and PsA synovial tissue explants were stimulated with TNF (10 ng/ml), angiopoietin (Ang)-1 or Ang-2 (200 ng/ml), or incubated with an anti-Ang2 neutralizing antibody. mRNA and protein expression of inflammatory mediators was analysed by quantitative PCR, ELISA and Luminex. RESULTS: Tie2-TG mice displayed more clinically severe arthritis than wild-type mice, accompanied by enhanced joint expression of IL6, IL12B, NOS2, CCL2 and CXCL10, and activation of bone marrow-derived macrophages in response to Ang-2 stimulation. Ang-1 and Ang-2 significantly enhanced TNF-induced expression of pro-inflammatory cytokines and chemokines in macrophages from healthy donors differentiated with RA and PsA SF and peripheral blood-derived macrophages from RA and PsA patients. Both Ang-1 and Ang-2 induced the production of IL-6, IL-12p40, IL-8 and CCL-3 in synovial tissue explants of RA and PsA patients, and Ang-2 neutralization suppressed the production of IL-6 and IL-8 in the synovial tissue of RA patients. CONCLUSION: Tie2 signalling enhances TNF-dependent activation of macrophages within the context of ongoing synovial inflammation in RA and PsA, and neutralization of Tie2 ligands might be a promising therapeutic target in the treatment of these diseases

    Angiopoietin-2 Promotes Inflammatory Activation in Monocytes of Systemic Sclerosis Patients

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    Angiopoietin-2 (Ang-2), a ligand of the tyrosine kinase receptor Tie2, is essential for vascular development and blood vessel stability and is also involved in monocyte activation. Here, we examined the role of Ang-2 on monocyte activation in patients with systemic sclerosis (SSc). Ang-2 levels were measured in serum and skin of healthy controls (HCs) and SSc patients by ELISA and array profiling, respectively. mRNA expression of ANG2 was analyzed in monocytes, dermal fibroblasts, and human pulmonary arterial endothelial cells (HPAECs) by quantitative PCR. Monocytes were stimulated with Ang-2, or with serum from SSc patients in the presence of a Tie2 inhibitor or an anti-Ang2 neutralizing antibody. Interleukin (IL)-6 and IL-8 production was analyzed by ELISA. Ang-2 levels were elevated in the serum and skin of SSc patients compared to HCs. Importantly, serum Ang-2 levels correlated with clinical disease parameters, such as skin involvement. Lipopolysaccharide (LPS) LPS, R848, and interferon alpha2a (IFN-alpha) stimulation up-regulated the mRNA expression of ANG2 in monocytes, dermal fibroblasts, and HPAECs. Finally, Ang-2 induced the production of IL-6 and IL-8 in monocytes of SSc patients, while the inhibition of Tie2 or the neutralization of Ang-2 reduced the production of both cytokines in HC monocytes stimulated with the serum of SSc patients. Therefore, Ang-2 induces inflammatory activation of SSc monocytes and neutralization of Ang-2 might be a promising therapeutic target in the treatment of SSc

    The study of soil, hydrological, erosion and vegetation processes following wildfire in the Colmeal study area, central Portugal

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    The EROSFIRE-II project (PTDC/AGR-CFL/70968/2006) has as overall aim to predict soil erosion risk in recently burnt forest areas, including following common post-fire forest management practices. Although the project’s main focus is on onsite erosion processes, also the export of sediments out of small catchments is addressed. To this end, a study area of about 60 ha located near to the village of Colmeal (municipality of Góis, central Portugal) was instrumented extensively following a wildfire during August 2008, and has been monitored intensively afterwards.(...

    An overview of digital speech watermarking

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    Digital speech watermarking is a robust way to hide and thus secure data like audio and video from any intentional or unintentional manipulation through transmission. In terms of some signal characteristics including bandwidth, voice/non-voice and production model, digital speech signal is different from audio, music and other signals. Although, various review articles on image, audio and video watermarking are available, there are still few review papers on digital speech watermarking. Therefore this article presents an overview of digital speech watermarking including issues of robustness, capacity and imperceptibility. Other issues discussed are types of digital speech watermarking, application, models and masking methods. This article further highlights the related challenges in the real world, research opportunities and future works in this area, yet to be explored fully
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